Pubmed Chromosome Start_position End_position Enhancer_related_genes Description Species Tissue_class Experiment_class Title SNP_related SNP_id Disease Cell_class Enhancer_id Enhancer_experiment Enhancer_tar_ex_De Enhancer_type Target_gene target_gene_strong_experiment target_gene_weak_experiment target_gene_experiment_description target_gene_other_name Enhancer_function Enhancer_function_experiment En_function_ex_de TF_name TF_other_name Experiment TF_experiment_de SNP_position SNP_experiment 29364907 chr2 28389994 28391994 FOSL2 FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes. human Cervix High+Lowthroughput HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression 否 HPV positive tumors cervical-derived cell line 20861 E_01_0001 Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes. Immunohistochemical staining FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes. FOSL2 Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes. 29364907 chr17 32412637 32414637 Brd4 ChIP-seq analysis showed two strong peaks of enrichment of the super-enhancer markers Brd4 and H3K27ac at both the viral URR and adjacent cellular sequence at the integration locus, the latter of which was not observed in the same region of cellular DNA in the W12 20863 sub-clone that harbors extrachromosomal viral DNA mouse Cervix High+Lowthroughput HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression 否 HPV positive tumors cervical-derived cell line 20861 E_01_0001 Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH ChIP-seq analysis showed two strong peaks of enrichment of the super-enhancer markers Brd4 and H3K27ac at both the viral URR and adjacent cellular sequence at the integration locus, the latter of which was not observed in the same region of cellular DNA in the W12 20863 sub-clone that harbors extrachromosomal viral DNA Enhancer Brd4 qRT-PCR,qPCR,ChIP,3C RNA-Seq ChIP-seq analysis showed two strong peaks of enrichment of the super-enhancer markers Brd4 and H3K27ac at both the viral URR and adjacent cellular sequence at the integration locus, the latter of which was not observed in the same region of cellular DNA in the W12 20863 sub-clone that harbors extrachromosomal viral DNA ChIP-seq analysis showed two strong peaks of enrichment of the super-enhancer markers Brd4 and H3K27ac at both the viral URR and adjacent cellular sequence at the integration locus, the latter of which was not observed in the same region of cellular DNA in the W12 20863 sub-clone that harbors extrachromosomal viral DNA Immunohistochemical staining ChIP-seq analysis showed two strong peaks of enrichment of the super-enhancer markers Brd4 and H3K27ac at both the viral URR and adjacent cellular sequence at the integration locus, the latter of which was not observed in the same region of cellular DNA in the W12 20863 sub-clone that harbors extrachromosomal viral DNA Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH 29363938 chr2 207527779 207529779 CREB1 The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively. human Cervix High+Lowthroughput Universal mRNA Translation Enhancement with Gold Nanoparticles Conjugated to Oligonucleotides with a Poly(T) Sequence 否 cervical cancer HeLa cell E_01_0002 Western blot,RT-PCR,PCR The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively. Immunohistochemical staining The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively. CREB1 Western blot,RT-PCR,PCR The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively. 29363553 chr6 47503992 47505992 Ezh2 Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. mouse Bone marrow High+Lowthroughput Hematopoietic stem/progenitor cell senescence is associated with altered expression profiles of cellular memory-involved gene 否 Enhancer_experiment senescence associated disease progenitor cell E_02_0001 qRT-PCR Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Enhancer Ezh2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Immunohistochemical staining Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. qRT-PCR 29358714 chr15 58585627 58587627 ADAM10 ADAM10 is a metalloproteinase acting on the amyloid precursor protein (APP) as an alpha-secretase in neurons. human,mouse Nerve High+Lowthroughput Identification of disulfiram as a secretase-modulating compound with beneficial effects on Alzheimer's disease hallmarks 否 Alzheimer’s disease SH-SY5Y human neuronal cell E_02_0002 Western blot,RT-PCR ADAM10 is a metalloproteinase acting on the amyloid precursor protein (APP) as an alpha-secretase in neurons. Enhancer ADAM10 qRT-PCR,qPCR,ChIP,3C RNA-Seq ADAM10 is a metalloproteinase acting on the amyloid precursor protein (APP) as an alpha-secretase in neurons. ADAM10 is a metalloproteinase acting on the amyloid precursor protein (APP) as an alpha-secretase in neurons. Immunohistochemical staining ADAM10 is a metalloproteinase acting on the amyloid precursor protein (APP) as an alpha-secretase in neurons. Western blot,RT-PCR 29358650 chr4 139461205 139463205 Pax7 Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. mouse Hypophysoma High+Lowthroughput Pioneer factor Pax7 deploys a stable enhancer repertoire for specification of cell fate 否 Hypophysoma AtT-20 cell E_02_0003 ChIP–seq,ATAC–seq,RNA-seq Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. Enhancer Pax7 qRT-PCR,qPCR,ChIP,3C RNA-Seq Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. Immunohistochemical staining Pax7 binds its targeted enhancers rapidly, but chromatin remodeling and gene activation are slower. ChIP–seq,ATAC–seq,RNA-seq 29357419 chr7 148804764 148806764 EZH2 Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2 human Kidney High+Lowthroughput Modulation of apolipoprotein L1-microRNA-193a axis prevents podocyte dedifferentiation in high-glucose milieu 否 kidney disease epithelial cell E_01_0003 Western blot,Immunofluorescence,Transfection Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2 Immunohistochemical staining Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2 EZH2 Western blot,Immunofluorescence,Transfection Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2 29344674 chr7 148805135 148807135 EZH2 In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells. human Oral cavity High+Lowthroughput Long non-coding RNA H1 promotes cell proliferation and invasion by acting as a ceRNA of miR?138 and releasing EZH2 in oral squamous cell carcinoma 否 oral squamous cell carcinoma oral squamous cell carcinoma cell E_01_0004 RT-qPCR,transfection,Western blot In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells. Immunohistochemical staining In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells. EZH2 RT-qPCR,transfection,Western blot In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells. 29344090 chr12 102954386 102956386 ASCL1 As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. human Bone marrow and lymphatic tissue High+Lowthroughput Overexpression of the proneural transcription factor ASCL1 in chronic lymphocytic leukemia with a t(12;14)(q23.2;q32.3) 否 chronic lymphocytic leukemia chronic lymphocytic leukemia cell E_01_0005 qPCR,FISH As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. Immunohistochemical staining As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. ASCL1 qPCR,FISH As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry. 29344006 chr6 113930322 113932322 HDAC2 HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages. human Connective tissue High+Lowthroughput Histone deacetylase 2 (HDAC2) attenuates lipopolysaccharide (LPS)-induced inflammation by regulating PAI-1 expression 否 Sepsis macrophage E_01_0006 ChIP,qRT-PCR,Western blot HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages. Enhancer HDAC2 qRT-PCR,qPCR,ChIP,3C RNA-Seq HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages. HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages. Immunohistochemical staining HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages. ChIP,qRT-PCR,Western blot 29344006 chr6 31572978 31574978 TNF Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation. human Connective tissue High+Lowthroughput Histone deacetylase 2 (HDAC2) attenuates lipopolysaccharide (LPS)-induced inflammation by regulating PAI-1 expression 否 Sepsis macrophage E_01_0006 ChIP,qRT-PCR,Western blot Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation. Immunohistochemical staining Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation. TNF ChIP,qRT-PCR,Western blot Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation. 29343853 chr7 78700257 78702257 Acan Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood mouse Cartilage tissue High+Lowthroughput Differential tissue specific, temporal and spatial expression patterns of the Aggrecan gene is modulated by independent enhancer elements 否 In debilitating diseases such as osteoarthritis, where increased mechanical stress on chondrocytes. chondroblast E_02_0004 Western blot Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood Enhancer Acan qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood Immunohistochemical staining Thus, the Acan enhancers orchestrate the precise spatiotemporal expression of this gene in cartilage types at different stages of development and adulthood Western blot 29343853 chr17 72118279 72120279 SOX9 The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (−30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. human Cartilage tissue High+Lowthroughput Differential tissue specific, temporal and spatial expression patterns of the Aggrecan gene is modulated by independent enhancer elements 否 In debilitating diseases such as osteoarthritis, where increased mechanical stress on chondrocytes. chondroblast E_02_0004 Western blot The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (−30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (−30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. Immunohistochemical staining The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (−30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. SOX9 Western blot The transcription factor SOX9 interacted with all the enhancers in vitro and mutation of SOX9 binding sites in one of the enhancers (−30) resulted in a loss of its chondrocyte specificity and ectopic enhancer reporter activity. 29343500 chr9 123505056 123507056 Ccr9 Furthermore, cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, ccr9. mouse Thymus High+Lowthroughput Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors 否 thymus homing thymocyte E_02_0005 Western blot,ChIP-seq,RNA-seq Furthermore, cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, ccr9. Enhancer Ccr9 qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, ccr9. Furthermore, cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, ccr9. Immunohistochemical staining Furthermore, cbfβ2 endows extrathymic progenitors with thymus-homing capacity by inducing expression of the principal thymus-homing receptor, ccr9. Western blot,ChIP-seq,RNA-seq 29343500 chr8 105894833 105896833 Cbfb Cbfβ forms transcription factor complexes with runx proteins, and here we show that cbfβ2, encoded by an rnA splice variant of the cbfb gene, is essential for extrathymic differentiation of t cell progenitors. mouse Thymus High+Lowthroughput Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors 否 thymus homing thymocyte E_02_0005 Western blot,ChIP-seq,RNA-seq Cbfβ forms transcription factor complexes with runx proteins, and here we show that cbfβ2, encoded by an rnA splice variant of the cbfb gene, is essential for extrathymic differentiation of t cell progenitors. Enhancer Cbfb qRT-PCR,qPCR,ChIP,3C RNA-Seq Cbfβ forms transcription factor complexes with runx proteins, and here we show that cbfβ2, encoded by an rnA splice variant of the cbfb gene, is essential for extrathymic differentiation of t cell progenitors. Cbfβ forms transcription factor complexes with runx proteins, and here we show that cbfβ2, encoded by an rnA splice variant of the cbfb gene, is essential for extrathymic differentiation of t cell progenitors. Immunohistochemical staining Cbfβ forms transcription factor complexes with runx proteins, and here we show that cbfβ2, encoded by an rnA splice variant of the cbfb gene, is essential for extrathymic differentiation of t cell progenitors. Western blot,ChIP-seq,RNA-seq 29343483 chr7 34815932 34817932 Cebpa Mechanistically, we demonstrate that NR4A1/3 restrict HSC proliferation in part through activation of a C/EBPα-driven anti-proliferative network by directly binding to a hematopoietic-specific Cebpa enhancer and activating Cebpa transcription. mouse Bone marrow High+Lowthroughput NR4A1 and NR4A3 restrict HSC proliferation via reciprocal regulation of C/EBPα and inflammatory signaling 否 myelodysplastic disease hematopoietic stem cell E_02_0006 RT-qPCR Mechanistically, we demonstrate that NR4A1/3 restrict HSC proliferation in part through activation of a C/EBPα-driven anti-proliferative network by directly binding to a hematopoietic-specific Cebpa enhancer and activating Cebpa transcription. Enhancer Cebpa qRT-PCR,qPCR,ChIP,3C RNA-Seq Mechanistically, we demonstrate that NR4A1/3 restrict HSC proliferation in part through activation of a C/EBPα-driven anti-proliferative network by directly binding to a hematopoietic-specific Cebpa enhancer and activating Cebpa transcription. Mechanistically, we demonstrate that NR4A1/3 restrict HSC proliferation in part through activation of a C/EBPα-driven anti-proliferative network by directly binding to a hematopoietic-specific Cebpa enhancer and activating Cebpa transcription. Immunohistochemical staining Mechanistically, we demonstrate that NR4A1/3 restrict HSC proliferation in part through activation of a C/EBPα-driven anti-proliferative network by directly binding to a hematopoietic-specific Cebpa enhancer and activating Cebpa transcription. RT-qPCR 29343483 chr12 52019947 52021947 NR4A1 Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses human,mouse Bone marrow High+Lowthroughput NR4A1 and NR4A3 restrict HSC proliferation via reciprocal regulation of C/EBPα and inflammatory signaling 否 myelodysplastic disease hematopoietic stem cell E_02_0006 RT-qPCR Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Enhancer NR4A1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Immunohistochemical staining Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses RT-qPCR 29343483 chr9 99818517 99820517 NR4A3 Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses human,mouse Bone marrow High+Lowthroughput NR4A1 and NR4A3 restrict HSC proliferation via reciprocal regulation of C/EBPα and inflammatory signaling 否 myelodysplastic disease hematopoietic stem cell E_02_0006 RT-qPCR Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Enhancer NR4A3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses Immunohistochemical staining Taken together, our results reveal a novel coordinate control of HSC quiescence by NR4A1/3 through direct activation of C/EBPα and suppression of activation of NF-κB-driven proliferative inflammatory responses RT-qPCR 29343442 chr12 57092345 57094345 STAT6 Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. human,mouse Bone marrow High+Lowthroughput The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages 否 inflammatory diseases macrophage E_02_0007 ATAC-seq, ChIP-seq,GRO-seq,RNA-seq,Western Blot,qPCR,ChIP-qPCR Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. Enhancer STAT6 qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. Immunohistochemical staining Thus, the IL-4-STAT6 signaling pathway establishes an alternative polarization-specific epigenenomic signature resulting in dampened macrophage responsiveness to inflammatory stimuli. ATAC-seq, ChIP-seq,GRO-seq,RNA-seq,Western Blot,qPCR,ChIP-qPCR 29343442 chr5 141618696 141620696 HDAC3 The Presence of HDAC3 Is Required for IL-4-STAT6-Mediated Repression on a Subset of Genes human,mouse Bone marrow High+Lowthroughput The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages 否 ainflammatory diseases macrophage E_02_0007 ATAC-seq, ChIP-seq,GRO-seq,RNA-seq,Western Blot,qPCR,ChIP-qPCR The Presence of HDAC3 Is Required for IL-4-STAT6-Mediated Repression on a Subset of Genes Enhancer HDAC3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The Presence of HDAC3 Is Required for IL-4-STAT6-Mediated Repression on a Subset of Genes The Presence of HDAC3 Is Required for IL-4-STAT6-Mediated Repression on a Subset of Genes Immunohistochemical staining The Presence of HDAC3 Is Required for IL-4-STAT6-Mediated Repression on a Subset of Genes ATAC-seq, ChIP-seq,GRO-seq,RNA-seq,Western Blot,qPCR,ChIP-qPCR 29342503 chr5 173229371 173231371 NKX2-5 NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. human Vascular tissue High+Lowthroughput Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis 是 rs3095870 scleroderma associated pulmonary hypertensio smooth muscle cell of the pulmonary artery E_01_0007 Western blot,qPCR NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. Immunohistochemical staining NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. NKX2-5 Western blot,qPCR NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. 29342503 chr11 12671461 12673461 TEAD1 TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease human Vascular tissue High+Lowthroughput Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis 是 rs3095870 scleroderma associated pulmonary hypertensio smooth muscle cell of the pulmonary artery E_01_0007 Western blot,qPCR TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease Immunohistochemical staining TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease TEAD1 Western blot,qPCR TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease 29342133 chr15 63714919 63952099 Myc The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies mouse Haematopoietic tissue Low+High throughput A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies 否 -- Leukaemia hematopoietic stem cell E_02_0008 ChIP-seq Here we show that an evolutionarily conserved region located 1.7 megabases downstream of the Myc gene that has previously been labelled as a ‘super_x0002_enhancer’2 is essential for the regulation of Myc expression levels in both normal haematopoietic and leukaemic stem cell hierarchies in mice and humans. Deletion of this region in mice leads to a complete loss of Myc expression in haematopoietic stem cells and progenitors. Super-Enhancer Myc -- ChIP-seq,ATAC-seq,RT-qPCR In line with this hypothesis, chromatin conformation capture performedon mouse leukaemic cells2 as well as DNA proximity analysis using fluorescence in situ hybridization (DNA FISH) in LSK cells showed that the Myc promoter and BENC are in close physical proximity to each other, suggesting that cis-regulation is mediated by chromosomal looping in haematopoietic stem and progenitor cells. AU0167572,Niard,Nird,bHLHe39,?Myc Clusters of enhancers, such as BENC, form highly combinatorial systems that allow precise control of gene expression across normal cellular hierarchies and which also can be hijacked in malignancies. ATAC-seq,RT-qPCR Analysis of mice carrying deletions of individual Enhancer modules suggests that specific Myc expression levels throughout most of the haematopoietic hierarchy are controlled by the combinatorial and additive activity of individual Enhancer modules, which collectively function as a ‘blood Enhancer cluster’(BENC). -- -- -- -- -- -- 29339538 chr7 55016139 55018139 EGFR Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET. human Cervix High+Lowthroughput E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C 否 human papillomaviruses CaSki cell(human cervical cancer cell line) E_01_0008 ChIP-seq,RNA-seq Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET. Immunohistochemical staining Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET. EGFR ChIP-seq,RNA-seq Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET. 29339538 chrX 53173366 53175366 KDM5C Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. human Cervix High+Lowthroughput E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C 否 human papillomaviruses CaSki cell(human cervical cancer cell line) E_01_0008 ChIP-seq,RNA-seq Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. Immunohistochemical staining Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. KDM5C ChIP-seq,RNA-seq Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line. 29339121 chr8 144288666 144290666 HSF1 HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells. human Gastric cancer tissues High+Lowthroughput HSF1, in association with MORC2, downregulates ArgBP2 via the PRC2 family in gastric cancer cells 否 gastric cancer gastric cancer cell E_01_0009 ChIP,Real-time PCR,Western blot HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells. Immunohistochemical staining HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells. HSF1 ChIP,Real-time PCR,Western blot HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells. 29339121 chr7 148804519 148806519 EZH2 EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED human Gastric cancer tissues High+Lowthroughput HSF1, in association with MORC2, downregulates ArgBP2 via the PRC2 family in gastric cancer cells 否 gastric cancer gastric cancer cell E_01_0009 ChIP,Real-time PCR,Western blot EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED Immunohistochemical staining EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED EZH2 ChIP,Real-time PCR,Western blot EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED 29339121 chr22 30922434 30924434 MORC2 In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2 human Gastric cancer tissues High+Lowthroughput HSF1, in association with MORC2, downregulates ArgBP2 via the PRC2 family in gastric cancer cells 否 gastric cancer gastric cancer cell E_01_0009 ChIP,Real-time PCR,Western blot In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2 Enhancer MORC2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2 In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2 Immunohistochemical staining In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2 ChIP,Real-time PCR,Western blot 29337370 chr16 28929378 28931378 CD19 GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). human Lymphoid tissue bone marrow High+Lowthroughput Modulating Gene Expression in Epstein-Barr Virus (EBV)-Positive B Cell Lines with CRISPRa and CRISPRi 否 Epstein-Barr virus B cell E_01_0010 ChIP-seq,ChIA-PET,RT-PCR GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). Enhancer CD19 qRT-PCR,qPCR,ChIP,3C RNA-Seq GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). Immunohistochemical staining GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). ChIP-seq,ChIA-PET,RT-PCR 29337370 chr3 122052540 122054540 CD86 GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). human Lymphoid tissue bone marrow High+Lowthroughput Modulating Gene Expression in Epstein-Barr Virus (EBV)-Positive B Cell Lines with CRISPRa and CRISPRi 否 Epstein-Barr virus B cell E_01_0010 ChIP-seq,ChIA-PET,RT-PCR GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). Immunohistochemical staining GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). CD86 ChIP-seq,ChIA-PET,RT-PCR GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86). 29334376 chr1 94526560 94528560 F3 We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. human Osteosarcoma High+Lowthroughput Positively selected enhancer elements endow osteosarcoma cells with metastatic competence 否 Osteosarcoma osteosarcoma cell E_01_0011 RNA-seq,ChIP–seq We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. Enhancer F3 qRT-PCR,qPCR,ChIP,3C RNA-Seq We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. Immunohistochemical staining We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung. RNA-seq,ChIP–seq 29331299 chr16 29880720 29882720 Hes1 During the transition from osteoblasts to osteocytes, Hes1 is upregulated rather than Hes3 and Hes5, and Hes3 and Hes5 null mice display no skeletal phenotype, indicating that Hes1 is a major target of Notch signaling conduction in the skeleton human,mouse Bone High+Lowthroughput The regulatory roles of Notch in osteocyte differentiation via the crosstalk with canonical Wnt pathways during the transition of osteoblasts to osteocytes 否 osteocyte E_02_0009 RT-qPCR,Western blot, transfection, Immunofluorescence During the transition from osteoblasts to osteocytes, Hes1 is upregulated rather than Hes3 and Hes5, and Hes3 and Hes5 null mice display no skeletal phenotype, indicating that Hes1 is a major target of Notch signaling conduction in the skeleton Enhancer Hes1 qRT-PCR,qPCR,ChIP,3C RNA-Seq During the transition from osteoblasts to osteocytes, Hes1 is upregulated rather than Hes3 and Hes5, and Hes3 and Hes5 null mice display no skeletal phenotype, indicating that Hes1 is a major target of Notch signaling conduction in the skeleton During the transition from osteoblasts to osteocytes, Hes1 is upregulated rather than Hes3 and Hes5, and Hes3 and Hes5 null mice display no skeletal phenotype, indicating that Hes1 is a major target of Notch signaling conduction in the skeleton Immunohistochemical staining During the transition from osteoblasts to osteocytes, Hes1 is upregulated rather than Hes3 and Hes5, and Hes3 and Hes5 null mice display no skeletal phenotype, indicating that Hes1 is a major target of Notch signaling conduction in the skeleton RT-qPCR,Western blot, transfection, Immunofluorescence 29331016 chr10 112947442 112949442 TCF7L2 The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. human Liver High+Lowthroughput A candidate functional SNP rs7074440 in TCF7L2 alters gene expression through C-FOS in hepatocytes 是 rs7903146 type 2 diabetes hepatocyte E_01_0012 qRT-PCR,ChIP,Transfection The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. Immunohistochemical staining The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. TCF7L2 qRT-PCR,ChIP,Transfection The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies. 29327713 chr7 148804434 148806434 EZH2 EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms. human Lymphoid tissue High+Lowthroughput Expression of enhancer of zeste homolog 2 (EZH2) protein in histiocytic and dendritic cell neoplasms with evidence for p-ERK1/2-related, but not MYC- or p-STAT3-related cell signaling 否 histiocytic and dendritic cell neoplasms histiocytic and dendritic cell neoplasm cell E_01_0013 Immunohistochemical staining EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms. Immunohistochemical staining EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms. EZH2 Immunohistochemical staining EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms. 29325110 chr5 56096484 56098484 ANKRD55 As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. human Lymphoid tissue High+Lowthroughput Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients 是 rs71624119 multiple sclerosis peripheral blood mononuclear cell E_01_0014 RNA-Seq As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. Enhancer ANKRD55 qRT-PCR,qPCR,ChIP,3C RNA-Seq As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. Immunohistochemical staining As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression. RNA-Seq 29323272 chr19 10958350 10960350 SMARCA4 Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. human Tumor High+Lowthroughput Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers 否 Tumor embryonic stem cell E_01_0015 Western blot,ATAC-seq,ChIP-seq,RNA-seq Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. Immunohistochemical staining Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 Western blot,ATAC-seq,ChIP-seq,RNA-seq Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. 29321660 chr3 186043535 186045535 ETV5 Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. human,mouse Neuroblastoma High+Lowthroughput Activated ALK signals through the ERK-ETV5-RET pathway to drive neuroblastoma oncogenesis 否 neuroblastoma neuroblastoma cell lines E_02_0010 ChIP-seq,RT-qPCR Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Enhancer ETV5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Immunohistochemical staining Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. ChIP-seq,RT-qPCR 29321660 chr10 43074431 43076431 RET Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. human,mouse Neuroblastoma High+Lowthroughput Activated ALK signals through the ERK-ETV5-RET pathway to drive neuroblastoma oncogenesis 否 neuroblastoma neuroblastoma cell lines E_02_0010 ChIP-seq,RT-qPCR Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Enhancer RET qRT-PCR,qPCR,ChIP,3C RNA-Seq Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. Immunohistochemical staining Altogether, these results define the ERK–ETV5–RET pathway as a critical axis driving neuroblastoma oncogenesis downstream of activated ALK. ChIP-seq,RT-qPCR 29321583 chr3 34155732 34157732 Sox2ot Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development. mouse Embryo High+Lowthroughput Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot 否 embryonic stem cell E_02_0011 qRT-PCR,qPCR,ChIP,3C Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development. Enhancer Sox2ot qRT-PCR,qPCR,ChIP,3C RNA-Seq Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development. Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development. Immunohistochemical staining Our study indicates that, in addition to previously reported in trans mechanisms, Sox2ot can regulate Sox2 by an allele-specific mechanism, in particular during development. qRT-PCR,qPCR,ChIP,3C 29321583 chr3 34702062 34704062 Sox2 The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. mouse Embryo High+Lowthroughput Allele-specific repression of Sox2 through the long non-coding RNA Sox2ot 否 embryonic stem cell E_02_0011 qRT-PCR,qPCR,ChIP,3C The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. Enhancer Sox2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. Immunohistochemical staining The transcription factor Sox2 controls the fate of pluripotent stem cells and neural stem cells. qRT-PCR,qPCR,ChIP,3C 29320736 chr15 41514637 41516637 RPAP1 We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. human,mouse Connective tissue High+Lowthroughput The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity 否 maintaining cell identity stem cell E_02_0012 ChIP-qPCR,ChIP-Seq,RNA-Seq,qRT-PCR We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. Enhancer RPAP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. Immunohistochemical staining We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. ChIP-qPCR,ChIP-Seq,RNA-Seq,qRT-PCR 29320702 chr1 3066690 3068690 PRDM16 These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. human,mouse Adipose Tissue High+Lowthroughput Repression of Adipose Tissue Fibrosis through a PRDM16-GTF2IRD1 Complex Improves Systemic Glucose Homeostasis 否 obesity or type 2 diabetes fat cell E_02_0013 RNA-Seq,ChIP These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Enhancer PRDM16 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Immunohistochemical staining These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. RNA-Seq,ChIP 29320702 chr7 74450980 74452980 GTF2IRD1 These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. human,mouse Adipose Tissue High+Lowthroughput Repression of Adipose Tissue Fibrosis through a PRDM16-GTF2IRD1 Complex Improves Systemic Glucose Homeostasis 否 obesity or type 2 diabetes fat cell E_02_0013 RNA-Seq,ChIP These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Enhancer GTF2IRD1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Immunohistochemical staining These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. RNA-Seq,ChIP 29320702 chr9 137616279 137618279 EHMT1 These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. human,mouse Adipose Tissue High+Lowthroughput Repression of Adipose Tissue Fibrosis through a PRDM16-GTF2IRD1 Complex Improves Systemic Glucose Homeostasis 否 obesity or type 2 diabetes fat cell E_02_0013 RNA-Seq,ChIP These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Enhancer EHMT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. Immunohistochemical staining These results suggest a mechanism by which repression of obesity-associated adipose tissue fibrosis through the PRDM16 complex leads to an improvement in systemic glucose homeostasis. RNA-Seq,ChIP 29316219 chr9 81580914 81582914 TLE1 These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis. human Brain High+Lowthroughput Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma-initiating cells 否 Glioblastoma glioblastoma-initiating cells E_01_0016 ChIP-Seq,RNA-Seq,RT-qPCR These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis. Immunohistochemical staining These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis. TLE1 ChIP-Seq,RNA-Seq,RT-qPCR These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis. 29311615 chr12 54030827 54032827 HOXC5 Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. human Somatic tissue High+Lowthroughput HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis 否 Tumor somatic cell E_01_0017 Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. Immunohistochemical staining Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. HOXC5 Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. 29309299 chr19 19143072 19145072 MEF2B Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. human Lymphoid tissue High+Lowthroughput Comparison of Myocyte Enhancer Factor 2B Versus Other Germinal Center-associated Antigens in the Differential Diagnosis of B-Cell Non-Hodgkin Lymphomas 否 Lymphomas B cell E_01_0018 Immunohistochemical Staining Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Enhancer MEF2B qRT-PCR,qPCR,ChIP,3C RNA-Seq Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Immunohistochemical staining Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Immunohistochemical Staining 29307778 chr17 43750876 43752876 SOST The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. human Bone High+Lowthroughput Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis 是 rs1230399, rs7220711, rs1107748, rs75901553 osteoporosis Germinal center B-cells E_01_0019 Luciferase reporter assay,ChIP,qPCR The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Enhancer SOST qRT-PCR,qPCR,ChIP,3C RNA-Seq The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Immunohistochemical staining The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Luciferase reporter assay,ChIP,qPCR 29307778 chr16 67559199 67561199 CTCF The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. human Bone High+Lowthroughput Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis 是 rs1230399, rs7220711, rs1107748, rs75901553 osteoporosis Germinal center B-cells E_01_0019 Luciferase reporter assay,ChIP,qPCR The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Immunohistochemical staining The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. CTCF Luciferase reporter assay,ChIP,qPCR The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. 29304378 chr6 151654024 151656024 ESR1 Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. human Bone High+Lowthroughput Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects 是 rs2982562-C osteoporosis osteocyte E_01_0020 Knockout Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. Immunohistochemical staining Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. ESR1 Knockout Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age. 29303507 chr11 68036369 68038369 TCIRG1 These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells. human HCC tissue High+Lowthroughput T-cell immune regulator 1 enhances metastasis in hepatocellular carcinoma 否 hepatocellular carcinoma HCC cell lines E_01_0021 Western blot,transfection These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells. Enhancer TCIRG1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells. These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells. Immunohistochemical staining These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells. Western blot,transfection 29302059 chr1 133246792 133248792 Kiss1 Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. human,mouse Hypothalamic tissue High+Lowthroughput Trithorax dependent changes in chromatin landscape at enhancer and promoter regions drive female puberty 否 female puberty Automatic Recognition of Cells E_02_0014 qPCR,RNA-seq,ChIP Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. Enhancer Kiss1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. Immunohistochemical staining Polycomb group (PcG) proteins control the timing of puberty by repressing the Kiss1 gene in hypothalamic arcuate nucleus (ARC) neurons. qPCR,RNA-seq,ChIP 29301908 chr6 6874986 6876986 Dlx5 Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. mouse Inner ear High+Lowthroughput Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice 否 inner ear dysmorphologies inner hair cells E_02_0015 DNA-seq Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Enhancer Dlx5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Immunohistochemical staining Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. DNA-seq 29301908 chr6 6038754 6040754 Slc25a13 Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. mouse Inner ear High+Lowthroughput Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice 否 inner ear dysmorphologies inner hair cells E_02_0015 DNA-seq Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Enhancer Slc25a13 qRT-PCR,qPCR,ChIP,3C RNA-Seq Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. Immunohistochemical staining Slc25a13hspn/hspn mice provide a new animal 40 model for studying long-range enhancer effects on Dlx5 expression in the developing inner ear. DNA-seq 29300379 chr15 67061032 67063032 SMAD3 These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3. human Thyroid High+Lowthroughput The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma 是 rs17293632,rs4562997 papillary thyroid carcinoma thyroid cancer cell lines E_01_0022 ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3. Immunohistochemical staining These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3. SMAD3 ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3. 29300379 chr5 142307853 142309853 SPRY4 The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene human Thyroid High+Lowthroughput The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma 是 rs17293632,rs4562997 papillary thyroid carcinoma thyroid cancer cell lines E_01_0022 ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene Enhancer SPRY4 qRT-PCR,qPCR,ChIP,3C RNA-Seq The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene Immunohistochemical staining The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR 29300302 chrX 129537551 129539551 OCRL The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain human Kidney High+Lowthroughput Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease 否 Lowe syndrome and Dent-2 disease COS7 cells E_01_0023 Transfection,RT-PCR The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain Enhancer OCRL qRT-PCR,qPCR,ChIP,3C RNA-Seq The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain Immunohistochemical staining The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain Transfection,RT-PCR 29297498 chr16 29880412 29882412 Hes1 Thus, our results support that IEC-intrinsic Hes1 maintains gut homeostasis by preventing microbial dysbiosis partially through regulating mucosal microhabitats. mouse Small intestine High+Lowthroughput Epithelial Hes1 maintains gut homeostasis by preventing microbial dysbiosis 否 intestinal microbial dysbiosis and disturbed homeostasis enterocyte E_02_0016 qPCR,Western blot Thus, our results support that IEC-intrinsic Hes1 maintains gut homeostasis by preventing microbial dysbiosis partially through regulating mucosal microhabitats. Enhancer Hes1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, our results support that IEC-intrinsic Hes1 maintains gut homeostasis by preventing microbial dysbiosis partially through regulating mucosal microhabitats. Thus, our results support that IEC-intrinsic Hes1 maintains gut homeostasis by preventing microbial dysbiosis partially through regulating mucosal microhabitats. Immunohistochemical staining Thus, our results support that IEC-intrinsic Hes1 maintains gut homeostasis by preventing microbial dysbiosis partially through regulating mucosal microhabitats. qPCR,Western blot 29294297 chr7 148804388 148806388 EZH2 We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs. human Dental pulp tissue High+Lowthroughput EZH2 Impairs Human Dental Pulp Cell Mineralization via the Wnt/β-Catenin Pathway 否 Oral Diseases dental pulp cell E_01_0024 ChIP We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs. Immunohistochemical staining We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs. EZH2 ChIP We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs. 29294065 chr19 33297489 33299489 CEBPA Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter. human Adrenal tissues High+Lowthroughput Purkinje Cell Protein 4 Expression Is Associated With DNA Methylation Status in Aldosterone-Producing Adenoma 否 adrenocortical adenoma cortical cell of adrenal gland E_01_0025 qPCR,ChIP Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter. Immunohistochemical staining Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter. CEBPA qPCR,ChIP Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter. 29286144 chr7 148804229 148806229 EZH2 Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c. human Melanoma tissue High+Lowthroughput Effect of long non-coding RNA PVT1 on cell proliferation and migration in melanoma 否 Melanoma melanoma cells E_01_0026 Western blot,ChIP Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c. Immunohistochemical staining Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c. EZH2 Western blot,ChIP Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c. 29286132 chr7 148804179 148806179 EZH2 Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC human Kidney High+Lowthroughput EZH2 enhances the invasive capability of renal cell carcinoma cells via activation of STAT3 否 renal cell carcinoma nephrocyte E_01_0027 Western blot Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC Immunohistochemical staining Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC EZH2 Western blot Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC 29259014 chr7 55016411 55018411 EGFR We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. human Lung High+Lowthroughput "ER Stress Signaling Promotes the Survival of Cancer ""Persister Cells"" Tolerant to EGFR Tyrosine Kinase Inhibitors" 否 Tumor PC9 cells E_01_0028 qRT-PCR,RNA-seq We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. Immunohistochemical staining We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. EGFR qRT-PCR,RNA-seq We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting. 29257325 chr5 88714072 88716072 MEF2C The present study investigated whether cardiomyocytes from mouse fibroblasts may be reprogrammed in vitro with four cardiac transcription factors, including GATA binding protein 4, myocyte‑specific enhancer factor 2C, T-box transcription factor 5, and heartand neural crest derivatives-expressed protein 2 (GMTH) human,mouse Heart tissue High+Lowthroughput Optimization and enrichment of induced cardiomyocytes derived from mouse fibroblasts by reprogramming with cardiac transcription factors 否 Ischemic heart disease cardiac muscle cell (sensu Arthopoda) E_02_0017 RT-qPCR,qPCR,Immunostaining The present study investigated whether cardiomyocytes from mouse fibroblasts may be reprogrammed in vitro with four cardiac transcription factors, including GATA binding protein 4, myocyte‑specific enhancer factor 2C, T-box transcription factor 5, and heartand neural crest derivatives-expressed protein 2 (GMTH) Enhancer MEF2C qRT-PCR,qPCR,ChIP,3C RNA-Seq The present study investigated whether cardiomyocytes from mouse fibroblasts may be reprogrammed in vitro with four cardiac transcription factors, including GATA binding protein 4, myocyte‑specific enhancer factor 2C, T-box transcription factor 5, and heartand neural crest derivatives-expressed protein 2 (GMTH) The present study investigated whether cardiomyocytes from mouse fibroblasts may be reprogrammed in vitro with four cardiac transcription factors, including GATA binding protein 4, myocyte‑specific enhancer factor 2C, T-box transcription factor 5, and heartand neural crest derivatives-expressed protein 2 (GMTH) Immunohistochemical staining The present study investigated whether cardiomyocytes from mouse fibroblasts may be reprogrammed in vitro with four cardiac transcription factors, including GATA binding protein 4, myocyte‑specific enhancer factor 2C, T-box transcription factor 5, and heartand neural crest derivatives-expressed protein 2 (GMTH) RT-qPCR,qPCR,Immunostaining 29256825 chr4 108045000 108047000 LEF1 β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells human Liver High+Lowthroughput Salvianolic Acid B Enhances Hepatic Differentiation of Human Embryonic Stem Cells Through Upregulation of WNT Pathway and Inhibition of Notch Pathway 否 Liver disease Hepatocytes E_01_0029 qRT-PCR,Immunofluorescence staining,PCR,Western blot β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells Immunohistochemical staining β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells LEF1 qRT-PCR,Immunofluorescence staining,PCR,Western blot β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells 29256171 chr10 24357349 24375452 CCN2 CCN2 is a critical matricellular protein that is expressed in several cells with major implications in physiology and different pathologies. mouse Connective tissue Low+High throughput Multiple enhancer regions govern the transcription of CCN2 during embryonic development 否 -- -- endothelial cell E_02_0018 Transgenic mice,ChIP-seq,DNase I Hypersensitivity Assay Four functional enhancers were identified, with each driving distinct, tissue-specific patterns of transgene expression. An enhancer located -100 kb from the CCN2 transcription start site facilitated expression within vascular tissue. An enhancer -135 kb upstream of CCN2 drove expression within the articular chondrocytes of synovial joints.The other two enhancers, located at -198 kb and -229 kb, mediated transgene expression within dermal fibroblasts, however the most prevalent activity was found within hypertrophic chondrocytes and periosteal tissue, respectively. Enhancer Ccn2 -- PCR,Transgenic mice Four functional enhancers were identified, with each driving distinct, tissue-specific patterns of transgene expression. An enhancer located -100 kb from the CCN2 transcription start site facilitated expression within vascular tissue. An enhancer -135 kb upstream of CCN2 drove expression within the articular chondrocytes of synovial joints.The other two enhancers, located at -198 kb and -229 kb, mediated transgene expression within dermal fibroblasts, however the most prevalent activity was found within hypertrophic chondrocytes and periosteal tissue, respectively. Ctgf,Fisp12,Hcs24,fisp-12 -- -- -- -- -- -- -- -- -- 29255029 chr5 28659278 28661278 Shh Transcriptome analysis indicates that ectopic expression of Shh up-regulates Chordin (Chrd) that antagonizes bone morphogenetic protein signaling in the interdigital region. mouse Toe High+Lowthroughput Enhancer adoption caused by genomic insertion elicits interdigital Shh expression and syndactyly in mouse 否 syndactyly interdigital cell E_02_0019 ATAC-seq,PCR Transcriptome analysis indicates that ectopic expression of Shh up-regulates Chordin (Chrd) that antagonizes bone morphogenetic protein signaling in the interdigital region. Enhancer Shh qRT-PCR,qPCR,ChIP,3C RNA-Seq Transcriptome analysis indicates that ectopic expression of Shh up-regulates Chordin (Chrd) that antagonizes bone morphogenetic protein signaling in the interdigital region. Transcriptome analysis indicates that ectopic expression of Shh up-regulates Chordin (Chrd) that antagonizes bone morphogenetic protein signaling in the interdigital region. Immunohistochemical staining Transcriptome analysis indicates that ectopic expression of Shh up-regulates Chordin (Chrd) that antagonizes bone morphogenetic protein signaling in the interdigital region. ATAC-seq,PCR 29249800 chr18 27930050 27932050 CDH2 DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. human CRPC tissues High+Lowthroughput DBC1 promotes castration-resistant prostate cancer by positively regulating DNA binding and stability of AR-V7 否 castration-resistant prostate cancer castration-resistant prostate cancer cell E_01_0030 qRT-PCR,ChIP,3C DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. Immunohistochemical staining DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. CDH2 qRT-PCR,ChIP,3C DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression. 29248547 chr7 148804663 148806663 EZH2 Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL. human PCALCL tissue High+Lowthroughput Dual Role of EZH2 in Cutaneous Anaplastic Large Cell Lymphoma: Promoting Tumor Cell Survival and Regulating Tumor Microenvironment 否 cutaneous CD30+ lymphoproliferative disease Primary cutaneous anaplastic T cell lymphoma cell E_01_0031 ChIP,qRT-PCR,Western blot Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL. Immunohistochemical staining Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL. EZH2 ChIP,qRT-PCR,Western blot Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL. 29245050 chr13 83649881 83651881 Mef2c Interestingly, senescence and NANOG had dramatic effect on the expression level of Mef2c, which regulates myoblast proliferation by exercising transcriptional control of cell cycle related genes human,mouse Skeletal muscle High+Lowthroughput NANOG restores the impaired myogenic differentiation potential of skeletal myoblasts after multiple population doublings 否 impaired myogenic differentiation potential skeletal muscle myoblast E_02_0020 Western blot,Immunohistochemical Staining,qPCR Interestingly, senescence and NANOG had dramatic effect on the expression level of Mef2c, which regulates myoblast proliferation by exercising transcriptional control of cell cycle related genes Enhancer Mef2c qRT-PCR,qPCR,ChIP,3C RNA-Seq Interestingly, senescence and NANOG had dramatic effect on the expression level of Mef2c, which regulates myoblast proliferation by exercising transcriptional control of cell cycle related genes Interestingly, senescence and NANOG had dramatic effect on the expression level of Mef2c, which regulates myoblast proliferation by exercising transcriptional control of cell cycle related genes Immunohistochemical staining Interestingly, senescence and NANOG had dramatic effect on the expression level of Mef2c, which regulates myoblast proliferation by exercising transcriptional control of cell cycle related genes Western blot,Immunohistochemical Staining,qPCR 29244146 chr7 148804295 148806295 EZH2 It is caused by heterozygous mutations in enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for histone H3 at lysine 27 (H3K27) trimethylation. human,mouse Embryonic tissues High+Lowthroughput Ezh2 Mutations Found in the Weaver Overgrowth Syndrome Cause a Partial Loss of H3K27 Histone Methyltransferase Activity 否 Weaver syndrome chondroblast E_02_0021 Transfection,Immunostaining It is caused by heterozygous mutations in enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for histone H3 at lysine 27 (H3K27) trimethylation. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq It is caused by heterozygous mutations in enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for histone H3 at lysine 27 (H3K27) trimethylation. It is caused by heterozygous mutations in enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for histone H3 at lysine 27 (H3K27) trimethylation. Immunohistochemical staining It is caused by heterozygous mutations in enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for histone H3 at lysine 27 (H3K27) trimethylation. Transfection,Immunostaining 29233846 chr6 47504530 47506530 Ezh2 Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8. human Ovarian tissue High+Lowthroughput VE-Cadherin-Mediated Epigenetic Regulation of Endothelial Gene Expression 否 Ovarian carcinoma endothelial cell E_01_0032 Immunofluorescence,Western blot,RNA-seq ,qRT–PCR,ChIP Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8. Enhancer Ezh2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8. Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8. Immunohistochemical staining Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8. Immunofluorescence,Western blot,RNA-seq ,qRT–PCR,ChIP 29231261 chr7 148804801 148806801 EZH2 LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2. human Bladder tissue High+Lowthroughput LncRNA AWPPH inhibits SMAD4 via EZH2 to regulate bladder cancer progression 否 bladder cancer human bladder epithelial cell line E_01_0033 Transfection,qRT-PCR,Western blot,ChIP LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2. Immunohistochemical staining LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2. EZH2 Transfection,qRT-PCR,Western blot,ChIP LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2. 29227829 chr6 135178878 135180878 MYB HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. human Hematopoietic tissue High+Lowthroughput A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression 是 rs66650371 sickle cell disease and β-thalassemia HUDEP-2 cell E_01_0034 RT–PCR,qPCR,Western blot HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. Enhancer MYB qRT-PCR,qPCR,ChIP,3C RNA-Seq HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. Immunohistochemical staining HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. RT–PCR,qPCR,Western blot 29227829 chr6 134957756 134959756 HBS1L HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. human Hematopoietic tissue High+Lowthroughput A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression 否 sickle cell disease and β-thalassemia HUDEP-2 cell E_01_0034 RT–PCR,qPCR,Western blot HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. Enhancer HBS1L qRT-PCR,qPCR,ChIP,3C RNA-Seq HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. Immunohistochemical staining HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia. RT–PCR,qPCR,Western blot 29223978 chr7 148804763 148806763 EZH2 Our results indicate that EZH2 is not required to repress chondrogenesis in the CM downstream of Wnt/b-catenin signaling. mouse Cartilage High+Lowthroughput PRC2 Is Dispensable in Vivo for β-Catenin-Mediated Repression of Chondrogenesis in the Mouse Embryonic Cranial Mesenchyme 否 chondroblast E_02_0022 Immunofluorescencet,RNA-seq ,RT–qPCR,ChIP-seq Our results indicate that EZH2 is not required to repress chondrogenesis in the CM downstream of Wnt/b-catenin signaling. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results indicate that EZH2 is not required to repress chondrogenesis in the CM downstream of Wnt/b-catenin signaling. Our results indicate that EZH2 is not required to repress chondrogenesis in the CM downstream of Wnt/b-catenin signaling. Immunohistochemical staining Our results indicate that EZH2 is not required to repress chondrogenesis in the CM downstream of Wnt/b-catenin signaling. Immunofluorescencet,RNA-seq ,RT–qPCR,ChIP-seq 29220426 chr13 116431913 116433913 Isl1 Insulin enhancer binding protein-1 (Isl1), a member of the LIM-homeodomain family, is a well-known activator of the insulin gene (14,15) and is essential for the development of the pancreas (16). mouse Liver High+Lowthroughput Isl1β Overexpression With Key β Cell Transcription Factors Enhances Glucose-Responsive Hepatic Insulin Production and Secretion 否 diabete b cell E_02_0023 Western blot,Luciferase Reporter Assay,qRT-PCR Insulin enhancer binding protein-1 (Isl1), a member of the LIM-homeodomain family, is a well-known activator of the insulin gene (14,15) and is essential for the development of the pancreas (16). Enhancer Isl1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Insulin enhancer binding protein-1 (Isl1), a member of the LIM-homeodomain family, is a well-known activator of the insulin gene (14,15) and is essential for the development of the pancreas (16). Insulin enhancer binding protein-1 (Isl1), a member of the LIM-homeodomain family, is a well-known activator of the insulin gene (14,15) and is essential for the development of the pancreas (16). Immunohistochemical staining Insulin enhancer binding protein-1 (Isl1), a member of the LIM-homeodomain family, is a well-known activator of the insulin gene (14,15) and is essential for the development of the pancreas (16). Western blot,Luciferase Reporter Assay,qRT-PCR 29207119 chr7 148804312 148806312 EZH2 Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance. human Breast High+Lowthroughput EZH2 inhibition sensitizes tamoxifen?resistant breast cancer cells through cell cycle regulation 否 breast cancer breast cancer cell E_01_0035 Transfection,RT-qPCR,Western blot Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance. Immunohistochemical staining Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance. EZH2 Transfection,RT-qPCR,Western blot Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance. 29207028 chr5 88714236 88716236 MEF2C Within the four key cellular signaling pathways involved in muscle fiber regulation, there are five important signaling factors: p38 MAPK, ERK2, CBP, MEF2C and AMPKα1. human,mouse Muscle High+Lowthroughput Role of the cofilin 2 gene in regulating the myosin heavy chain genes in mouse myoblast C2C12 cells 否 myofibrillar formation. C2C12 cells E_02_0024 RT-qPCR,RT-PCR,Western blot Within the four key cellular signaling pathways involved in muscle fiber regulation, there are five important signaling factors: p38 MAPK, ERK2, CBP, MEF2C and AMPKα1. Enhancer MEF2C qRT-PCR,qPCR,ChIP,3C RNA-Seq Within the four key cellular signaling pathways involved in muscle fiber regulation, there are five important signaling factors: p38 MAPK, ERK2, CBP, MEF2C and AMPKα1. Within the four key cellular signaling pathways involved in muscle fiber regulation, there are five important signaling factors: p38 MAPK, ERK2, CBP, MEF2C and AMPKα1. Immunohistochemical staining Within the four key cellular signaling pathways involved in muscle fiber regulation, there are five important signaling factors: p38 MAPK, ERK2, CBP, MEF2C and AMPKα1. RT-qPCR,RT-PCR,Western blot 29203251 chrX 67541434 67543434 AR Previous studies have shown that PCa development is closely-linked to the androgen receptor (AR) human,mouse Prostate High+Lowthroughput Androgen receptor (AR) degradation enhancer ASC-J9(?) in an FDA-approved formulated solution suppresses castration resistant prostate cancer cell growth 否 prostate cancer prostate cancer cell E_02_0025 Western blot,qPCR Previous studies have shown that PCa development is closely-linked to the androgen receptor (AR) Enhancer AR qRT-PCR,qPCR,ChIP,3C RNA-Seq Previous studies have shown that PCa development is closely-linked to the androgen receptor (AR) Previous studies have shown that PCa development is closely-linked to the androgen receptor (AR) Immunohistochemical staining Previous studies have shown that PCa development is closely-linked to the androgen receptor (AR) Western blot,qPCR 29180489 chr12 114350941 114352941 TBX5 TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells. human Lymphoid tissue High+Lowthroughput Downregulation of NFAT3 Due to Lack of T-Box Transcription Factor TBX5 Is Crucial for Cytokine Expression in T Cells 否 T cell E_01_0036 Transfection TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells. Immunohistochemical staining TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells. TBX5 Transfection TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells. 29180467 chr11 102107486 102109486 YAP1 In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. human,mouse Bladder tissue High+Lowthroughput YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells 否 urothelial carcinoma urothelial cell E_02_0026 Western blot,PCR In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. Enhancer YAP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. Immunohistochemical staining In a mouse xenograft model of UCB, dual inhibition of COX2 and YAP1 elicited a long-lasting therapeutic response by limiting CSC expansion after chemotherapy and EGFR inhibition. Western blot,PCR 29180467 chr3 181708705 181710705 SOX2 Here we report that the pro-inflammatory COX2/PGE2 pathway and the YAP1 growth regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSC. human,mouse Bladder tissue High+Lowthroughput YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells 否 urothelial carcinoma urothelial cell E_02_0026 Western blot,PCR Here we report that the pro-inflammatory COX2/PGE2 pathway and the YAP1 growth regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSC. Enhancer SOX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we report that the pro-inflammatory COX2/PGE2 pathway and the YAP1 growth regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSC. Here we report that the pro-inflammatory COX2/PGE2 pathway and the YAP1 growth regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSC. Immunohistochemical staining Here we report that the pro-inflammatory COX2/PGE2 pathway and the YAP1 growth regulatory pathway cooperate to recruit the stem cell factor SOX2 in expanding and sustaining the accumulation of urothelial CSC. Western blot,PCR 29180399 chr19 15232268 15234268 BRD4 We therefore describe a novel oncogenic pathway featuring IL-15, miR-29b, and BRD4 in CTCL, and suggest targeting of these components as a potentially effective therapy for CTCL patients. human,mouse Skin tissue High+Lowthroughput Diminished microRNA-29b level is associated with BRD4-mediated activation of oncogenes in cutaneous T-cell lymphoma 否 cutaneous T-cell lymphoma T cell E_02_0027 RT-PCR,ChIP,Transfection We therefore describe a novel oncogenic pathway featuring IL-15, miR-29b, and BRD4 in CTCL, and suggest targeting of these components as a potentially effective therapy for CTCL patients. Enhancer BRD4 qRT-PCR,qPCR,ChIP,3C RNA-Seq We therefore describe a novel oncogenic pathway featuring IL-15, miR-29b, and BRD4 in CTCL, and suggest targeting of these components as a potentially effective therapy for CTCL patients. We therefore describe a novel oncogenic pathway featuring IL-15, miR-29b, and BRD4 in CTCL, and suggest targeting of these components as a potentially effective therapy for CTCL patients. Immunohistochemical staining We therefore describe a novel oncogenic pathway featuring IL-15, miR-29b, and BRD4 in CTCL, and suggest targeting of these components as a potentially effective therapy for CTCL patients. RT-PCR,ChIP,Transfection 29177481 chr7 148804952 148806952 EZH2 The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1. human High+Lowthroughput CDYL1 fosters double-strand break-induced transcription silencing and promotes homology-directed repair 否 E_01_0037 Transfection,Immunofluorescence,Western blot,ChIP The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1. Immunohistochemical staining The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1. EZH2 Transfection,Immunofluorescence,Western blot,ChIP The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1. 29175454 chr10 68557509 68559509 TET1 To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. human Tumor High+Lowthroughput Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells 否 iAs-mediated carcinogenesis transformed cell E_01_0038 qRT-PCR,ChIP To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Immunohistochemical staining To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. TET1 qRT-PCR,ChIP To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. 29175454 chr4 105143899 105145899 TET2 To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. human Tumor High+Lowthroughput Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells 否 iAs-mediated carcinogenesis transformed cell E_01_0038 qRT-PCR,ChIP To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Enhancer TET2 qRT-PCR,qPCR,ChIP,3C RNA-Seq To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Immunohistochemical staining To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. qRT-PCR,ChIP 29175454 chr16 67559779 67561779 CTCF To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. human Tumor High+Lowthroughput Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells 否 iAs-mediated carcinogenesis transformed cell E_01_0038 qRT-PCR,ChIP To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. Immunohistochemical staining To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. CTCF qRT-PCR,ChIP To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site. 29162563 chr16 86507790 86509790 FOXF1 We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. human Gastrointestinal tract High+Lowthroughput FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor 否 gastrointestinal stromal tumor gastrointestinal stromal tumor cell E_01_0039 siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. Immunohistochemical staining We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. FOXF1 siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function. 29162563 chr7 13888509 13890509 ETV1 Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis human Gastrointestinal tract High+Lowthroughput FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor 否 gastrointestinal stromal tumor gastrointestinal stromal tumor cell E_01_0039 siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis Immunohistochemical staining Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis ETV1 siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis 29162563 chr4 54654533 54656533 KIT Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis human Gastrointestinal tract High+Lowthroughput FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor 否 gastrointestinal stromal tumor gastrointestinal stromal tumor cell E_01_0039 siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis Immunohistochemical staining Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis KIT siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis 29162511 chr1 11782707 11784707 MTHFR Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis human Thymus High+Lowthroughput The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with Myasthenia Gravis 是 rs1801133 thymic lymphoid hyperplasia B cell E_01_0040 Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Enhancer MTHFR qRT-PCR,qPCR,ChIP,3C RNA-Seq Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Immunohistochemical staining Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis 29162511 chr1 236792078 236794078 MTR Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis human Thymus High+Lowthroughput The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with Myasthenia Gravis 是 rs1805087 thymic lymphoid hyperplasia B cell E_01_0040 Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Enhancer MTR qRT-PCR,qPCR,ChIP,3C RNA-Seq Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Immunohistochemical staining Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis 29162511 chr18 654552 656552 TYMS Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients human Thymus High+Lowthroughput The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with Myasthenia Gravis 是 rs45445694 thymic lymphoid hyperplasia B cell E_01_0040 Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients Enhancer TYMS qRT-PCR,qPCR,ChIP,3C RNA-Seq Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients Immunohistochemical staining Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients 29162511 chr5 7849068 7851068 MTRR Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis human Thymus High+Lowthroughput The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with Myasthenia Gravis 是 rs1801394 thymic lymphoid hyperplasia B cell E_01_0040 Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Enhancer MTRR qRT-PCR,qPCR,ChIP,3C RNA-Seq Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis Immunohistochemical staining Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis 29158184 chr11 112670256 112672256 Sox9 These findings link Sox9 to intrinsic mechanisms of TGF-β signaling in renal fibrosis and may have therapeutic potential for tissue fibrosis mouse Kidney High+Lowthroughput TGF-β-mediated upregulation of Sox9 in fibroblast promotes renal fibrosis 否 renal fibrosis kidney fibroblast cell E_02_0028 Transfection,qPCR,ChIP These findings link Sox9 to intrinsic mechanisms of TGF-β signaling in renal fibrosis and may have therapeutic potential for tissue fibrosis Enhancer Sox9 qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings link Sox9 to intrinsic mechanisms of TGF-β signaling in renal fibrosis and may have therapeutic potential for tissue fibrosis These findings link Sox9 to intrinsic mechanisms of TGF-β signaling in renal fibrosis and may have therapeutic potential for tissue fibrosis Immunohistochemical staining These findings link Sox9 to intrinsic mechanisms of TGF-β signaling in renal fibrosis and may have therapeutic potential for tissue fibrosis Transfection,qPCR,ChIP 29155305 chr3 8725613 8727613 Hey1 Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development mouse Tooth germ High+Lowthroughput Hey1 and Hey2 are differently expressed during mouse tooth development 否 tooth injury dental mesenchymal cell E_02_0029 qRT-PCR Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Enhancer Hey1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Immunohistochemical staining Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development qRT-PCR 29155305 chr10 30705725 30707725 Hey2 Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development mouse Tooth germ High+Lowthroughput Hey1 and Hey2 are differently expressed during mouse tooth development 否 tooth injury dental mesenchymal cell E_02_0029 qRT-PCR Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Enhancer Hey2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development Immunohistochemical staining Our data implied that Hey2 function is restricted to transient amplifying cells of the ameloblast cell lineage and that Hey1 plays a role in the composition of the subodontoblastic layer, in addition to ameloblast differentiation. These findings provide novel clues for the better understanding of tooth development qRT-PCR 29154949 chr12 56115695 56117695 ESYT1 We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. human Lung CF tissue High+Lowthroughput A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic 否 Cystic Fibrosis bronchial epithelial cell E_01_0041 siRNA transfection,Immunostaining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Enhancer ESYT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Immunohistochemical staining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. siRNA transfection,Immunostaining 29154949 chr11 69983331 69985331 ANO1 We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. human Lung CF tissue High+Lowthroughput A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic 否 Cystic Fibrosis bronchial epithelial cell E_01_0041 siRNA transfection,Immunostaining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Immunohistochemical staining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. ANO1 siRNA transfection,Immunostaining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. 29154949 chr11 14440611 14442611 COPB1 We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. human Lung CF tissue High+Lowthroughput A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic 否 Cystic Fibrosis bronchial epithelial cell E_01_0041 siRNA transfection,Immunostaining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Enhancer COPB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. Immunohistochemical staining We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains. siRNA transfection,Immunostaining 29154784 chr16 29880401 29882401 Hes1 Sox9 and Hes1 are downstream targets of Jagged1–Notch signaling and are responsible for the timing of the maturation of primitive ductal structures mouse Liver High+Lowthroughput TGF-β1 signaling regulates mouse hepatic stellate cell differentiation via the Jagged1/Notch pathway 否 liver disease hepatic stellate cell E_02_0030 Western blot,ChIP,Transfection,qRT-PCR,Immunofluorescence Sox9 and Hes1 are downstream targets of Jagged1–Notch signaling and are responsible for the timing of the maturation of primitive ductal structures Enhancer Hes1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Sox9 and Hes1 are downstream targets of Jagged1–Notch signaling and are responsible for the timing of the maturation of primitive ductal structures Sox9 and Hes1 are downstream targets of Jagged1–Notch signaling and are responsible for the timing of the maturation of primitive ductal structures Immunohistochemical staining Sox9 and Hes1 are downstream targets of Jagged1–Notch signaling and are responsible for the timing of the maturation of primitive ductal structures Western blot,ChIP,Transfection,qRT-PCR,Immunofluorescence 29148101 chr3 130901584 130903584 Lef1 Considering that Bmp2, Bmp4, and Lef1 are essential for promoting odontoblast differentiation, our findings are consistent with previous studies. mouse Tooth-germ High+Lowthroughput Homeobox protein MSX-1 inhibits expression of bone morphogenetic protein 2, bone morphogenetic protein 4, and lymphoid enhancer-binding factor 1 via Wnt/β-catenin signaling to prevent differentiation of dental mesenchymal cells during the late bell stage 否 congenital tooth agenesis dental mesenchymal cell E_02_0031 Western blot,qPCR Considering that Bmp2, Bmp4, and Lef1 are essential for promoting odontoblast differentiation, our findings are consistent with previous studies. Enhancer Lef1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Considering that Bmp2, Bmp4, and Lef1 are essential for promoting odontoblast differentiation, our findings are consistent with previous studies. Considering that Bmp2, Bmp4, and Lef1 are essential for promoting odontoblast differentiation, our findings are consistent with previous studies. Immunohistochemical staining Considering that Bmp2, Bmp4, and Lef1 are essential for promoting odontoblast differentiation, our findings are consistent with previous studies. Western blot,qPCR 29142074 chr7 94002773 94005073 STAT3 Yet, a certain threshold level of STAT3 activity is essential to support activation of the COL1A2 enhancer and TGFβ signalling in fibroblasts. human Lung Low throughput STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation 否 -- -- Myofibroblast E_02_0032 Luciferase Reporter Assay,ChIP The structure of the COL1A2 far-upstream enhancer and the HS4 region is shown in Figure 1A.Enhancer activation was determined by measuring luciferase expression. Enhancer COL1A2 -- Luciferase Reporter Assay,ChIP We created two different luciferase reporter gene constructs under the control of the COL1A2 enhancer and proximal promoter.When the enhancer is engaged, it contacts the RNA polymerase complex forming at the collagen promoter. Thus, an RNA polymerase ChIP signal is a direct measure of enhancer engagement. EDSARTH2,EDSCV,OI4 -- -- -- STAT3 ADMIO,ADMIO1,APRF,HIES ChIP-qPCR ChIP analysis using qPCR for the binding of STAT3, JunB, and RNA polymerase II, in the HS4 region of SSc fibroblasts after treatment with SD1029, STAT3 siRNA (siSTAT3), or nontargeting siRNA (siNT). * = p < 0.05. -- -- 29142074 chr7 94002773 94005073 COL1A2 Yet, a certain threshold level of STAT3 activity is essential to support activation of the COL1A2 enhancer and TGFβ signalling in fibroblasts. human Lung Low throughput STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation 否 -- -- Myofibroblast E_02_0032 Luciferase Reporter Assay,ChIP The structure of the COL1A2 far-upstream enhancer and the HS4 region is shown in Figure 1A.Enhancer activation was determined by measuring luciferase expression. Enhancer COL1A2 -- Luciferase Reporter Assay,ChIP We created two different luciferase reporter gene constructs under the control of the COL1A2 enhancer and proximal promoter.When the enhancer is engaged, it contacts the RNA polymerase complex forming at the collagen promoter. Thus, an RNA polymerase ChIP signal is a direct measure of enhancer engagement. EDSARTH2,EDSCV,OI4 -- -- -- STAT3 ADMIO,ADMIO1,APRF,HIES ChIP-qPCR ChIP analysis using qPCR for the binding of STAT3, JunB, and RNA polymerase II, in the HS4 region of SSc fibroblasts after treatment with SD1029, STAT3 siRNA (siSTAT3), or nontargeting siRNA (siNT). * = p < 0.05. -- -- 29141987 chr2 103887795 103888195 Lmo2 T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development mouse Embryo Low+High throughput BRACHYURY directs histone acetylation to target loci during mesoderm development 否 -- -- hematopoietic and endothelial cell E_02_0033 ChIP-seq We overlapped TBS with genome‐wide H3K4me1 peaks from T WT mesodermal cells and found the same trend of decreased H3K27ac within ±1 kb of TBS/H3K4me1 sites (Fig EV4E), suggesting that T functions to coordinate H3K27ac at putative enhancer regions throughout the genome, and may regulate the switch between poised H3K4me1(+) enhancers and active H3K27ac/H3K4me1(+) enhancer regions. Enhancer Lmo2 -- RT-qPCR,ChIP-qPCR,ChIP-seq Both the ?70 enhancer and the TSS of Lmo2 display a decrease in H3K27ac in T Y88A mutant mesodermal cells, in the ChIP‐Seq data and confirmed by ChIP‐qPCR (Figs ?(Figs5A5A and B, and EV5A). We reasoned that T binding to the ?70 enhancer of Lmo2 may recruit permissive chromatin marks to the TSS to regulate expression, and that this regulation is disrupted in T Y88A mutant mesodermal cells. Rbtn-2,Rbtn2,Rhom-2,Ttg2 -- -- -- T Bra,D17Mit170,Low,Lr1,Tbxt,Tl2,Tl3,cou,me75,T ChIP-seq,ChIP-qPCR We performed a co-immunoprecipitation analysis from in vitrodifferentiated mesodermal cells and found an interaction between endogenous T and p300.Strikingly, loss of H3K27ac was found at TBS upstream of the T genomic locus itself by ChIP-Seq . We validated this decrease in H3K27ac at the T genomic locus by ChIP-qPCR in TY88A and TWT mesodermal cells differentiated in vitro. -- -- 29141987 chr2 103887795 103888195 T Here, we show that cooperative function of BRACHYURY (T) with histone-modifying enzymes is essential for mouse embryogenesis. mouse Embryo Low+High throughput BRACHYURY directs histone acetylation to target loci during mesoderm development 否 -- -- hematopoietic and endothelial cell E_02_0033 ChIP-seq We overlapped TBS with genome‐wide H3K4me1 peaks from T WT mesodermal cells and found the same trend of decreased H3K27ac within ±1 kb of TBS/H3K4me1 sites (Fig EV4E), suggesting that T functions to coordinate H3K27ac at putative enhancer regions throughout the genome, and may regulate the switch between poised H3K4me1(+) enhancers and active H3K27ac/H3K4me1(+) enhancer regions. Enhancer Lmo2 -- RT-qPCR,ChIP-qPCR,ChIP-seq Both the ?70 enhancer and the TSS of Lmo2 display a decrease in H3K27ac in T Y88A mutant mesodermal cells, in the ChIP‐Seq data and confirmed by ChIP‐qPCR (Figs ?(Figs5A5A and B, and EV5A). We reasoned that T binding to the ?70 enhancer of Lmo2 may recruit permissive chromatin marks to the TSS to regulate expression, and that this regulation is disrupted in T Y88A mutant mesodermal cells. Rbtn-2,Rbtn2,Rhom-2,Ttg2 -- -- -- T Bra,D17Mit170,Low,Lr1,Tbxt,Tl2,Tl3,cou,me75,T ChIP-seq,ChIP-qPCR We performed a co-immunoprecipitation analysis from in vitrodifferentiated mesodermal cells and found an interaction between endogenous T and p300.Strikingly, loss of H3K27ac was found at TBS upstream of the T genomic locus itself by ChIP-Seq . We validated this decrease in H3K27ac at the T genomic locus by ChIP-qPCR in TY88A and TWT mesodermal cells differentiated in vitro. -- -- 29138985 chr4 108044731 108046731 LEF1 Lymphoid enhancer-binding factor-1 (LEF1) is one of the 48-kD nuclear proteins that is often expressed in the T and pre-B cells and is also a very significant member of the Wnt/β-catenin in embryonic stem cells human,mouse Skin tissue High+Lowthroughput Effects of microRNA-708 on Epithelial-Mesenchymal Transition, Cell Proliferation and Apoptosis in Melanoma Cells by Targeting LEF1 through the Wnt Signaling Pathway 否 Melanoma Melanoma Cell Line E_02_0034 RT-qPCR,Dual-Luciferase Reporter Assay Lymphoid enhancer-binding factor-1 (LEF1) is one of the 48-kD nuclear proteins that is often expressed in the T and pre-B cells and is also a very significant member of the Wnt/β-catenin in embryonic stem cells Enhancer LEF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Lymphoid enhancer-binding factor-1 (LEF1) is one of the 48-kD nuclear proteins that is often expressed in the T and pre-B cells and is also a very significant member of the Wnt/β-catenin in embryonic stem cells Lymphoid enhancer-binding factor-1 (LEF1) is one of the 48-kD nuclear proteins that is often expressed in the T and pre-B cells and is also a very significant member of the Wnt/β-catenin in embryonic stem cells Immunohistochemical staining Lymphoid enhancer-binding factor-1 (LEF1) is one of the 48-kD nuclear proteins that is often expressed in the T and pre-B cells and is also a very significant member of the Wnt/β-catenin in embryonic stem cells RT-qPCR,Dual-Luciferase Reporter Assay 29138798 chr3 8725482 8727482 Hey1 Taken together, the findings indicate that Hey1 may be a positive regulator of odontoblastic differentiation. mouse Dental pulp tissue High+Lowthroughput Hey1 functions as a positive regulator of odontogenic differentiation in odontoblast?lineage cells 否 Oral Disease odontoblast E_02_0035 Western blot,ChIP,Transfection,RT‑qPCR,Immunofluorescence staining Taken together, the findings indicate that Hey1 may be a positive regulator of odontoblastic differentiation. Enhancer Hey1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, the findings indicate that Hey1 may be a positive regulator of odontoblastic differentiation. Taken together, the findings indicate that Hey1 may be a positive regulator of odontoblastic differentiation. Immunohistochemical staining Taken together, the findings indicate that Hey1 may be a positive regulator of odontoblastic differentiation. Western blot,ChIP,Transfection,RT‑qPCR,Immunofluorescence staining 29129693 chr17 76133482 76135482 FOXJ1 FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis. human Bladder cancer tissues High+Lowthroughput FOXJ1 promotes bladder cancer cell growth and regulates Warburg effect 否 bladder cancer bladder cancer cell E_01_0042 Western blot FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis. Immunohistochemical staining FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis. FOXJ1 Western blot FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis. 29127222 chr15 99562705 99564705 MEF2A These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. human Placental tissue High+Lowthroughput MEF2 transcription factors in human placenta and involvement in cytotrophoblast invasion and differentiation 否 placenta-related pregnancy disorders cytotrophoblast cell lines E_01_0043 Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Immunohistochemical staining These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. MEF2A Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. 29127222 chr19 19143005 19145005 MEF2B These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. human Placental tissue High+Lowthroughput MEF2 transcription factors in human placenta and involvement in cytotrophoblast invasion and differentiation 否 placenta-related pregnancy disorders cytotrophoblast cell lines E_01_0043 Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Enhancer MEF2B qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Immunohistochemical staining These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR 29127222 chr5 88714205 88716205 MEF2C These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. human Placental tissue High+Lowthroughput MEF2 transcription factors in human placenta and involvement in cytotrophoblast invasion and differentiation 否 placenta-related pregnancy disorders cytotrophoblast cell lines E_01_0043 Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Immunohistochemical staining These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. MEF2C Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. 29127222 chr1 156460887 156462887 MEF2D These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. human Placental tissue High+Lowthroughput MEF2 transcription factors in human placenta and involvement in cytotrophoblast invasion and differentiation 否 placenta-related pregnancy disorders cytotrophoblast cell lines E_01_0043 Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Enhancer MEF2D qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Immunohistochemical staining These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation. Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR 29113912 chr14 18175266 18186392 Ang2 Importantly, sorafenib treatment, which suppresses H3K27 acetylation and Ang2 expression, profoundly halts the progression of Arid1a-deficient HCCs mouse Liver Low+High throughput Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma 否 -- Hepatocellular Carcinoma HCC cell lines E_02_0036 ChIP-seq Notably, histone modification markers, including H3K4me1,H3K4me3, H3K27me3 and H3K27ac were presented at the Ang2 gene locus in liver tumor cells and were strongly colocal_x0002_ized with the two Arid1a-binding sites, suggesting an associa_x0002_tion between Arid1a binding and histone modification at the Ang2 gene locus (Fig. 4A). ChIP-qPCR analysis showed Arid1a knockdown increased the H3K27ac at the Ang2 proximal and distal regions. Enhancer Ang2 -- ChIP-seq,ChIP-qPCR Notably, histone modification markers, including H3K4me1,H3K4me3, H3K27me3 and H3K27ac were presented at the Ang2 gene locus in liver tumor cells and were strongly colocal_x0002_ized with the two Arid1a-binding sites, suggesting an associa_x0002_tion between Arid1a binding and histone modification at the Ang2 gene locus (Fig. 4A). ChIP-qPCR analysis showed Arid1a knockdown increased the H3K27ac at the Ang2 proximal and distal regions. Angrp,Raa3,Rnase5b -- -- -- Ep300 A430090G16,A730011L11,KAT3B,p300,p300 HAT ChIP-seq,ChIP-PCR Interestingly,published ChIP-seq data also showed that p300 bound to the Ang2 gene locus, as we validated by ChIP-PCR. -- -- 29113912 chr14 18175266 18186392 Arid1a Arid1a-deficiency promotes Ang2- dependent angiogenesis leading to hepatocellular carcinoma progression. mouse Liver Low+High throughput Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma 否 -- Hepatocellular Carcinoma HCC cell lines E_02_0036 ChIP-seq Notably, histone modification markers, including H3K4me1,H3K4me3, H3K27me3 and H3K27ac were presented at the Ang2 gene locus in liver tumor cells and were strongly colocal_x0002_ized with the two Arid1a-binding sites, suggesting an associa_x0002_tion between Arid1a binding and histone modification at the Ang2 gene locus (Fig. 4A). ChIP-qPCR analysis showed Arid1a knockdown increased the H3K27ac at the Ang2 proximal and distal regions. Enhancer Ang2 -- ChIP-seq,ChIP-qPCR Notably, histone modification markers, including H3K4me1,H3K4me3, H3K27me3 and H3K27ac were presented at the Ang2 gene locus in liver tumor cells and were strongly colocal_x0002_ized with the two Arid1a-binding sites, suggesting an associa_x0002_tion between Arid1a binding and histone modification at the Ang2 gene locus (Fig. 4A). ChIP-qPCR analysis showed Arid1a knockdown increased the H3K27ac at the Ang2 proximal and distal regions. Angrp,Raa3,Rnase5b -- -- -- Ep300 A430090G16,A730011L11,KAT3B,p300,p300 HAT ChIP-seq,ChIP-PCR Interestingly,published ChIP-seq data also showed that p300 bound to the Ang2 gene locus, as we validated by ChIP-PCR. -- -- 29107694 chr7 148804477 148806477 EZH2 Notably, EZH2 can catalyze histone H3 lysine 27 tri-methylation (H3K27me3) to inhibit gene transcription human,mouse Pancreas High+Lowthroughput Chaetospirolactone reverses the apoptotic resistance towards TRAIL in pancreatic cancer 否 pancreatic cancer pancreatic cancer cell E_02_0037 Western blot,ChIP,qPCR Notably, EZH2 can catalyze histone H3 lysine 27 tri-methylation (H3K27me3) to inhibit gene transcription Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Notably, EZH2 can catalyze histone H3 lysine 27 tri-methylation (H3K27me3) to inhibit gene transcription Notably, EZH2 can catalyze histone H3 lysine 27 tri-methylation (H3K27me3) to inhibit gene transcription Immunohistochemical staining Notably, EZH2 can catalyze histone H3 lysine 27 tri-methylation (H3K27me3) to inhibit gene transcription Western blot,ChIP,qPCR 29106960 chr7 148804589 148806589 EZH2 Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis. human Liver High+Lowthroughput Carnosol-mediated Sirtuin 1 activation inhibits Enhancer of Zeste Homolog 2 to attenuate liver fibrosis 否 hepatic fibrosis Myofibroblast E_01_0044 Western blot, RT-PCR,Immunofluorescence staining,Transfection Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis. Immunohistochemical staining Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis. EZH2 Western blot, RT-PCR,Immunofluorescence staining,Transfection Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis. 29089464 chr7 148804445 148806445 EZH2 Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation human Breast cancer tissue High+Lowthroughput Correlations of EZH2 and SMYD3 gene polymorphisms with breast cancer susceptibility and prognosis 否 breast cancer breast cancer cell E_01_0045 RT-qPCR,Western blot Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation Immunohistochemical staining Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation EZH2 RT-qPCR,Western blot Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation 29070695 chr17 19492823 19494823 SLC47A1 These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression. human Liver High+Lowthroughput Relationship between DNA Methylation in the 5' CpG Island of the SLC47A1 (Multidrug and Toxin Extrusion Protein MATE1) Gene and Interindividual Variability in MATE1 Expression in the Human Liver 否 HepG2 cell E_01_0046 qRT-PCR These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression. Enhancer SLC47A1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression. These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression. Immunohistochemical staining These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression. qRT-PCR 29059175 chr16 67559364 67561364 CTCF Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA. human Tumor High+Lowthroughput Induction of anti-VEGF therapy resistance by upregulated expression of microseminoprotein (MSMP) 否 Tumor cancer cell E_01_0047 qRT–PCR,Immunostaining,Western blot Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA. Immunohistochemical staining Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA. CTCF qRT–PCR,Immunostaining,Western blot Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA. 29059175 chr9 35749798 35751798 MSMP These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy human Tumor High+Lowthroughput Induction of anti-VEGF therapy resistance by upregulated expression of microseminoprotein (MSMP) 否 Tumor cancer cell E_01_0047 qRT–PCR,Immunostaining,Western blot These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy Enhancer MSMP qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy Immunohistochemical staining These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy qRT–PCR,Immunostaining,Western blot 29059150 chr12 54572339 54574339 PPP1R1A We found that PPP1R1A is one of the top ranked target genes of EWS/FLI, the master regulator of ES, and is upregulated by EWS/FLI via a GGAA microsatellite enhancer element human,mouse Tumor High+Lowthroughput Protein phosphatase 1 regulatory subunit 1A in ewing sarcoma tumorigenesis and metastasis 否 ewing sarcoma ewing sarcoma cell E_02_0038 qRT–PCR,ChIP-Seq,Luciferase reporter assay We found that PPP1R1A is one of the top ranked target genes of EWS/FLI, the master regulator of ES, and is upregulated by EWS/FLI via a GGAA microsatellite enhancer element Enhancer PPP1R1A qRT-PCR,qPCR,ChIP,3C RNA-Seq We found that PPP1R1A is one of the top ranked target genes of EWS/FLI, the master regulator of ES, and is upregulated by EWS/FLI via a GGAA microsatellite enhancer element We found that PPP1R1A is one of the top ranked target genes of EWS/FLI, the master regulator of ES, and is upregulated by EWS/FLI via a GGAA microsatellite enhancer element Immunohistochemical staining We found that PPP1R1A is one of the top ranked target genes of EWS/FLI, the master regulator of ES, and is upregulated by EWS/FLI via a GGAA microsatellite enhancer element qRT–PCR,ChIP-Seq,Luciferase reporter assay 29054992 chr5 69231968 69233968 CDK7 CDK7 is a key regulator of the cell cycle mouse Tumor High+Lowthroughput Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression 否 Tumor cancer cell E_02_0039 RNA-seq,ChIP-Seq,ChIP,RT-PCR CDK7 is a key regulator of the cell cycle Enhancer CDK7 qRT-PCR,qPCR,ChIP,3C RNA-Seq CDK7 is a key regulator of the cell cycle CDK7 is a key regulator of the cell cycle Immunohistochemical staining CDK7 is a key regulator of the cell cycle RNA-seq,ChIP-Seq,ChIP,RT-PCR 29053336 chr7 148804334 148806334 EZH2 These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF. human Lung High+Lowthroughput Interplay between EZH2 and G9a Regulates CXCL10 Gene Repression in Idiopathic Pulmonary Fibrosis 否 Pulmonary Fibrosis E_01_0048 ChIP These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF. Immunohistochemical staining These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF. EZH2 ChIP These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF. 29044515 chr12 32787839 32789839 PKP2 Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters. human Colon tissue High+Lowthroughput The human PKP2/plakophilin-2 gene is induced by Wnt/β-catenin in normal and colon cancer-associated fibroblasts 否 colon cancer colon cancer-associated fibroblast E_01_0049 RNA-Seq,RT-qPCR,Western blot Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters. Enhancer PKP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters. Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters. Immunohistochemical staining Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters. RNA-Seq,RT-qPCR,Western blot 29024000 chr16 29880620 29882620 Hes1 In conclusion, we demonstrate that myeloid Notch1 deficiency promotes the JSAP1- mediated RhoA/ROCK signaling pathway and exacerbates liver damage by depressing its target gene Hes1 in IR-stressed livers. mouse Liver High+Lowthroughput Myeloid Notch1 deficiency activates the RhoA/ROCK pathway and aggravates hepatocellular damage in mouse ischemic livers 否 Liver Injury hepatocyte E_02_0040 Immunohistochemistry staining,qRT-PCR,Immunofluorescence staining In conclusion, we demonstrate that myeloid Notch1 deficiency promotes the JSAP1- mediated RhoA/ROCK signaling pathway and exacerbates liver damage by depressing its target gene Hes1 in IR-stressed livers. Enhancer Hes1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, we demonstrate that myeloid Notch1 deficiency promotes the JSAP1- mediated RhoA/ROCK signaling pathway and exacerbates liver damage by depressing its target gene Hes1 in IR-stressed livers. In conclusion, we demonstrate that myeloid Notch1 deficiency promotes the JSAP1- mediated RhoA/ROCK signaling pathway and exacerbates liver damage by depressing its target gene Hes1 in IR-stressed livers. Immunohistochemical staining In conclusion, we demonstrate that myeloid Notch1 deficiency promotes the JSAP1- mediated RhoA/ROCK signaling pathway and exacerbates liver damage by depressing its target gene Hes1 in IR-stressed livers. Immunohistochemistry staining,qRT-PCR,Immunofluorescence staining 28994199 chr1 47213269 47215269 TAL1 Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation human Haematopoietic tissue High+Lowthroughput Inhibition of MEK/ERK signalling pathway promotes erythroid differentiation and reduces HSCs engraftment in ex?vivo expanded haematopoietic stem cells 否 hematopoietic stem cell E_01_0050 qPCR,Immunohistochemical staining Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation Immunohistochemical staining Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation TAL1 qPCR,Immunohistochemical staining Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation 28974397 chr7 148804688 148806688 EZH2 A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27. human Soft tissue High+Lowthroughput Comprehensive Genomic Sequencing of Urothelial Tumors Identifies Rare SMARCB1 (INI-1)-Deficient Carcinomas of the Urinary?System 否 urothelial carcinoma tumor cell E_01_0051 Immunohistochemical staining A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27. Immunohistochemical staining A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27. EZH2 Immunohistochemical staining A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27. 28974397 chr22 23784056 23786056 SMARCB1 Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation. human Soft tissue High+Lowthroughput Comprehensive Genomic Sequencing of Urothelial Tumors Identifies Rare SMARCB1 (INI-1)-Deficient Carcinomas of the Urinary?System 否 urothelial carcinoma tumor cell E_01_0051 Immunohistochemical staining Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation. Enhancer SMARCB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation. Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation. Immunohistochemical staining Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation. Immunohistochemical staining 28971975 chr17 61449600 61451600 TBX4 Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs. human High+Lowthroughput TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts 否 pathogenesis of respiratory diseases lung fibroblasts cell E_01_0052 RNA-seq,RT-PCR Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs. Immunohistochemical staining Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs. TBX4 RNA-seq,RT-PCR Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs. 28970250 chr7 148804484 148806484 EZH2 Finally, EZH2 inhibition or PPARg activation ameliorated fibrogenesis in cKO mice. human,mouse Liver High+Lowthroughput SIRT1 antagonizes liver fibrosis by blocking hepatic stellate cell activation in mice 否 liver fibrosis hepatic stellate cell E_02_0041 Western blot, qPCR,Transfection,ChIP Finally, EZH2 inhibition or PPARg activation ameliorated fibrogenesis in cKO mice. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Finally, EZH2 inhibition or PPARg activation ameliorated fibrogenesis in cKO mice. Finally, EZH2 inhibition or PPARg activation ameliorated fibrogenesis in cKO mice. Immunohistochemical staining Finally, EZH2 inhibition or PPARg activation ameliorated fibrogenesis in cKO mice. Western blot, qPCR,Transfection,ChIP 28951561 chr17 42697786 42699786 EZH1 Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. human,mouse Bone marrow High+Lowthroughput Dual inhibition of EZH1/2 breaks the quiescence of leukemia stem cells in acute myeloid leukemia 否 Acute myeloid leukemia leukemia stem cell E_02_0042 Western blot Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Enhancer EZH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Immunohistochemical staining Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Western blot 28951561 chr7 148804920 148806920 EZH2 Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. human,mouse Bone marrow High+Lowthroughput Dual inhibition of EZH1/2 breaks the quiescence of leukemia stem cells in acute myeloid leukemia 否 Acute myeloid leukemia leukemia stem cell E_02_0042 Western blot Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Immunohistochemical staining Taken together, these results show that dual inhibition of EZH1/2 is an effective strategy for eliminating AML LSCs. Western blot 28939663 chr7 148804966 148806966 EZH2 As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets human Liver High+Lowthroughput Hepatoma-intrinsic CCRK inhibition diminishes myeloid-derived suppressor cell immunosuppression and enhances immune-checkpoint blockade efficacy 否 hepatocellular carcinoma Myeloid-derived suppressor cell E_01_0053 Transfection As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets Immunohistochemical staining As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets EZH2 Transfection As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets 28925507 chr7 148804490 148806490 EZH2 In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells. human CRC tissue High+Lowthroughput (-)-Epigallocatechin-3-gallate and EZH2 inhibitor GSK343 have similar inhibitory effects and mechanisms of action on colorectal cancer cells 否 colorectal cancer colorectal cancer (CRC) cell line E_01_0054 Western blot,Immunofluorescence In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells. Immunohistochemical staining In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells. EZH2 Western blot,Immunofluorescence In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells. 28925391 chr7 148804797 148806797 EZH2 Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells. human Tumor High+Lowthroughput EZH2 contributes to the response to PARP inhibitors through its PARP-mediated poly-ADP ribosylation in breast cancer 否 breast cancer breast cancer cell E_01_0055 ChIP,qPCR,RT-qPCR,Western blot Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells. Immunohistochemical staining Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells. EZH2 ChIP,qPCR,RT-qPCR,Western blot Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells. 28923345 chr10 67881952 67883952 SIRT1 Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR. human High+Lowthroughput SIRT1 is a transcriptional enhancer of the glucocorticoid receptor acting independently to its deacetylase activity 否 HeLa cell E_01_0056 Transfection,Western blot,RNA-seq,PCR,ChIP Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR. Immunohistochemical staining Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR. SIRT1 Transfection,Western blot,RNA-seq,PCR,ChIP Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR. 28922471 chr19 35742614 35744614 PSENEN The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit. human High+Lowthroughput A phenotype combining hidradenitis suppurativa with Dowling-Degos disease caused by a founder mutation in PSENEN 否 Dowling-Degos disease keratinocyte cell E_01_0057 qRT-PCR The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit. Enhancer PSENEN qRT-PCR,qPCR,ChIP,3C RNA-Seq The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit. The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit. Immunohistochemical staining The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit. qRT-PCR 28902616 chr5 88714680 88716680 MEF2C The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM). human Heart High+Lowthroughput MEF2C loss-of-function mutation associated with familial dilated cardiomyopathy 否 dilated cardiomyopathy HeLa cell E_01_0058 Transfection,dual-luciferase reporter assay The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM). Immunohistochemical staining The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM). MEF2C Transfection,dual-luciferase reporter assay The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM). 28898113 chr1 209782978 209784978 IRF6 Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. human,mouse Salivary gland High+Lowthroughput Interferon Regulatory Factor 6 Is Necessary for Salivary Glands and Pancreas Development 否 xerostomia acinar cell E_02_0043 Immunofluorescent Staining,RNA-Seq Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. Enhancer IRF6 qRT-PCR,qPCR,ChIP,3C RNA-Seq Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. Immunohistochemical staining Interferon regulatory factor 6 (IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. Immunofluorescent Staining,RNA-Seq 28862715 chr7 148804307 148806307 EZH2 EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas. human Tumor High+Lowthroughput Prognostic role of EZH2 in gliomas: a meta-analysis 否 gliomas tumor cell E_01_0059 Meta-analysis EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas. Immunohistochemical staining EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas. EZH2 Meta-analysis EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas. 28858300 chr7 148804693 148806693 EZH2 Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers. human Tumor High+Lowthroughput Development of a high-throughput fluorescence polarization assay for the discovery of EZH2-EED interaction inhibitors 否 Tumor cancer cell E_01_0060 PCR Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers. Immunohistochemical staining Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers. EZH2 PCR Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers. 28811072 chr16 81236 83236 NPRL3 One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. human High+Lowthroughput Evolution of hemoglobin loci and their regulatory elements 否 erythroid cell E_01_0061 One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. Enhancer NPRL3 qRT-PCR,qPCR,ChIP,3C RNA-Seq One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. Immunohistochemical staining One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates. 28810932 chr7 148804688 148806688 EZH2 RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA. human CCA tissue High+Lowthroughput Long Noncoding RNA NEAT1 Promotes Growth and Metastasis of Cholangiocarcinoma Cells 否 cholangiocarcinoma Cholangiocarcinoma Cell E_01_0062 qRT-PCR,ChIP,Western blot RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA. Immunohistochemical staining RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA. EZH2 qRT-PCR,ChIP,Western blot RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA. 28796375 chr7 148804611 148806611 EZH2 Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright. human LA tissue High+Lowthroughput Effects of long noncoding RNA SPRY4-IT1-mediated EZH2 on the invasion and migration of lung adenocarcinoma 否 lung adenocarcinoma lung adenocarcinoma (LA) cell E_01_0063 Western blot,RT-qPCR Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright. Immunohistochemical staining Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright. EZH2 Western blot,RT-qPCR Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright. 28795320 chr7 148804483 148806483 EZH2 Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma. human Laryngeal carcinoma tissue High+Lowthroughput EZH2 promotes cell proliferation by regulating the expression of RUNX3 in laryngeal carcinoma 否 laryngeal carcinoma laryngeal carcinoma cell E_01_0064 Western blot,qRT-PCR Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma. Immunohistochemical staining Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma. EZH2 Western blot,qRT-PCR Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma. 28774779 chr12 57092763 57094763 STAT6 Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages. human High+Lowthroughput Extensive and functional overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte derived differentiating macrophages 否 macrophage E_01_0065 ChIP,ChIP-seq,RNA-Seq,qPCR Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages. Immunohistochemical staining Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages. STAT6 ChIP,ChIP-seq,RNA-Seq,qPCR Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages. 28763207 chr7 148804454 148806454 EZH2 human High+Lowthroughput Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs 否 E_01_0066 Immunofluorescence staining Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Immunohistochemical staining EZH2 Immunofluorescence staining 28763207 chr9 128680837 128682837 SET human High+Lowthroughput Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs 否 E_01_0066 Immunofluorescence staining Enhancer SET qRT-PCR,qPCR,ChIP,3C RNA-Seq Immunohistochemical staining Immunofluorescence staining 28763207 chr12 19401102 19403102 AEBP2 human High+Lowthroughput Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs 否 E_01_0066 Immunofluorescence staining Enhancer AEBP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Immunohistochemical staining Immunofluorescence staining 28752422 chr16 15702106 15704106 Cebpd These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. mouse Bone High+Lowthroughput Regulation of Clock Genes by Adrenergic Receptor Signaling in Osteoblasts 否 cementoblast E_02_0044 These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Enhancer Cebpd qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Immunohistochemical staining These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. 28752422 chr14 46618115 46620115 Bmp4 These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. mouse Bone High+Lowthroughput Regulation of Clock Genes by Adrenergic Receptor Signaling in Osteoblasts 否 cementoblast E_02_0044 These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Enhancer Bmp4 qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Immunohistochemical staining These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. 28752422 chr13 53118269 53120269 Nfil3 These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. mouse Bone High+Lowthroughput Regulation of Clock Genes by Adrenergic Receptor Signaling in Osteoblasts 否 cementoblast E_02_0044 These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Enhancer Nfil3 qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. Immunohistochemical staining These findings suggest that the effects of Cebpd are due to the circadian regulation of Bmp4 expression, at least in part, by the up-regulated expression of the clock gene Nfil3 in response to α1B-AR signaling in osteoblasts. 28744818 chr9 81580972 81582972 TLE1 Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice mouse Small intestine High+Lowthroughput Epigenetic modification of TLE1 induce abnormal differentiation in diabetic mice intestinal epithelium 否 diabetes mellitus enterocyte E_02_0045 Western Blot,RT-PCR,Dual-luciferase reporter assay Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Enhancer TLE1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Immunohistochemical staining Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Western Blot,RT-PCR,Dual-luciferase reporter assay 28744818 chr16 29880216 29882216 Hes1 Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice mouse Small intestine High+Lowthroughput Epigenetic modification of TLE1 induce abnormal differentiation in diabetic mice intestinal epithelium 否 diabetes mellitus enterocyte E_02_0045 Western Blot,RT-PCR,Dual-luciferase reporter assay Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Enhancer Hes1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Immunohistochemical staining Subsequently, TLE1, through the transcriptional suppression on expression of Hes1, contributes to the aberrant differentiation of IECs in DM mice Western Blot,RT-PCR,Dual-luciferase reporter assay 28722764 chr7 148804258 148806258 EZH2 We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis. human High+Lowthroughput 12-O-tetradecanoylphorbol-13-acetate and EZH2 inhibition: A novel approach for promoting myogenic differentiation in embryonal rhabdomyosarcoma cells 否 Rhabdomyosarcoma myocyte E_01_0067 Western blot,Real-Time PCR We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis. Immunohistochemical staining We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis. EZH2 Western blot,Real-Time PCR We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis. 28720764 chr7 148804667 148806667 EZH2 The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. mouse Bone marrow High+Lowthroughput High expression of ABCG2 induced by EZH2 disruption has pivotal roles in MDS pathogenesis 否 myelodysplastic syndromes bone marrow cell E_02_0046 SQ-RT-PCR,ChIP The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. Immunohistochemical staining The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. SQ-RT-PCR,ChIP 28720764 chr6 58558640 58560640 Abcg2 The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. mouse Bone marrow High+Lowthroughput High expression of ABCG2 induced by EZH2 disruption has pivotal roles in MDS pathogenesis 否 myelodysplastic syndromes bone marrow cell E_02_0046 SQ-RT-PCR,ChIP The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. Enhancer Abcg2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. Immunohistochemical staining The present results indicate that Abcg2 derepression induced by EZH2 mutations play crucial roles in MDS pathogenesis. SQ-RT-PCR,ChIP 28718381 chr7 148804593 148806593 EZH2 Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis. human Ectopic endometrial tissue High+Lowthroughput Histological and Immunohistochemical Characterization of the Similarity and Difference Between Ovarian Endometriomas and Deep Infiltrating Endometriosis 否 Ovarian endometrioma (OMA) and deep infiltrating endometriosis (DIE) endothelial cell E_01_0068 immunostaining Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis. Immunohistochemical staining Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis. EZH2 immunostaining Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis. 28681918 chr7 148804320 148806320 EZH2 Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions human Cervical epithelial tissue High+Lowthroughput MicroRNA-137 is negatively associated with clinical outcome and regulates tumor development through EZH2 in cervical cancer 否 cervical cancer CC cell line E_01_0069 qPCR,Dual-luciferase reporter assay Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions Immunohistochemical staining Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions EZH2 qPCR,Dual-luciferase reporter assay Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions 28681114 chr7 148804493 148806493 EZH2 Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression. human Tumor High+Lowthroughput Predicting the Correlation of EZH2 and Cancer Stem Cell Markers in Esophageal Squamous Cell Carcinoma 否 Esophageal Squamous Cell Carcinoma Cancer Stem Cell E_01_0070 qRT-PCR Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression. Immunohistochemical staining Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression. EZH2 qRT-PCR Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression. 28621459 chr1 39078887 39080887 MACF1 Microtubule actin crosslinking factor 1 (MACF1), a key cytoskeletal linker, has been shown to play key roles in signal transduction and in diverse cellular processes human,mouse Bone High+Lowthroughput Microtubule actin crosslinking factor 1 promotes osteoblast differentiation by promoting β-catenin/TCF1/Runx2 signaling axis 否 Osteoblast differentiation cementoblast E_02_0047 Western blot,Real time PCR Microtubule actin crosslinking factor 1 (MACF1), a key cytoskeletal linker, has been shown to play key roles in signal transduction and in diverse cellular processes Enhancer MACF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Microtubule actin crosslinking factor 1 (MACF1), a key cytoskeletal linker, has been shown to play key roles in signal transduction and in diverse cellular processes Microtubule actin crosslinking factor 1 (MACF1), a key cytoskeletal linker, has been shown to play key roles in signal transduction and in diverse cellular processes Immunohistochemical staining Microtubule actin crosslinking factor 1 (MACF1), a key cytoskeletal linker, has been shown to play key roles in signal transduction and in diverse cellular processes Western blot,Real time PCR 28621459 chr4 108044719 108046719 LEF1 It has been demonstrated that TCF1 but not LEF1 binds directly to Runx2 promoter in MC3T3-E1 cells and that Runx2 is a direct target of β-catenin/TCF1 for the stimulation of osteoblast differentiation human,mouse Bone High+Lowthroughput Microtubule actin crosslinking factor 1 promotes osteoblast differentiation by promoting β-catenin/TCF1/Runx2 signaling axis 否 Osteoblast differentiation cementoblast E_02_0047 Western blot,Real time PCR It has been demonstrated that TCF1 but not LEF1 binds directly to Runx2 promoter in MC3T3-E1 cells and that Runx2 is a direct target of β-catenin/TCF1 for the stimulation of osteoblast differentiation Enhancer LEF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq It has been demonstrated that TCF1 but not LEF1 binds directly to Runx2 promoter in MC3T3-E1 cells and that Runx2 is a direct target of β-catenin/TCF1 for the stimulation of osteoblast differentiation It has been demonstrated that TCF1 but not LEF1 binds directly to Runx2 promoter in MC3T3-E1 cells and that Runx2 is a direct target of β-catenin/TCF1 for the stimulation of osteoblast differentiation Immunohistochemical staining It has been demonstrated that TCF1 but not LEF1 binds directly to Runx2 promoter in MC3T3-E1 cells and that Runx2 is a direct target of β-catenin/TCF1 for the stimulation of osteoblast differentiation Western blot,Real time PCR 28462489 chr5 179729425 179731425 MAML1 In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. human Tumor High+Lowthroughput Role of MAML1 and MEIS1 in Esophageal Squamous Cell Carcinoma Depth of Invasion 否 esophageal squamous cell carcinoma tumor cell E_01_0071 qRT-PCR In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. Enhancer MAML1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. Immunohistochemical staining In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. qRT-PCR 28462489 chr2 66430871 66432871 MEIS1 In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. human Tumor High+Lowthroughput Role of MAML1 and MEIS1 in Esophageal Squamous Cell Carcinoma Depth of Invasion 否 esophageal squamous cell carcinoma tumor cell E_01_0071 qRT-PCR In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. Enhancer MEIS1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. Immunohistochemical staining In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients. qRT-PCR 28442495 chr13 27958465 27960465 CDX2 CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin. human High+Lowthroughput Aspirin prevents NF-κB activation and CDX2 expression stimulated by acid and bile salts in oesophageal squamous cells of patients with Barrett's oesophagus 否 Esophageal Diseases oesophageal squamous cell E_01_0072 Western blot CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin. Immunohistochemical staining CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin. CDX2 Western blot CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin. 28115742 chr5 88714348 88716348 MEF2C However, neurodevelopmental factors play an important role in schizophrenia,and alterations in MEF2C and other TF expression may have impacted diseased brains at earlier periods of pre- and postnatal life human,mouse Brain tissue High+Lowthroughput MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice 否 schizophrenia and related disorders pluripotent stem cell E_02_0048 ChIP-seq,ChIP-PCR However, neurodevelopmental factors play an important role in schizophrenia,and alterations in MEF2C and other TF expression may have impacted diseased brains at earlier periods of pre- and postnatal life Enhancer MEF2C qRT-PCR,qPCR,ChIP,3C RNA-Seq However, neurodevelopmental factors play an important role in schizophrenia,and alterations in MEF2C and other TF expression may have impacted diseased brains at earlier periods of pre- and postnatal life However, neurodevelopmental factors play an important role in schizophrenia,and alterations in MEF2C and other TF expression may have impacted diseased brains at earlier periods of pre- and postnatal life Immunohistochemical staining However, neurodevelopmental factors play an important role in schizophrenia,and alterations in MEF2C and other TF expression may have impacted diseased brains at earlier periods of pre- and postnatal life ChIP-seq,ChIP-PCR 28027119 chr4 108044503 108046503 LEF1 Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF human Soft tissue High+Lowthroughput Comparison of β-Catenin and LEF1 Immunohistochemical Stains in Desmoid-type Fibromatosis and its Selected Mimickers, With Unexpected Finding of LEF1 Positivity in Scars 否 desmoid-type fibromatosis E_01_0073 Immunohistochemical staining Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF Immunohistochemical staining Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF LEF1 Immunohistochemical staining Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF 27997051 chr7 44101517 44103517 AEBP1 Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes human Hippocampal tissue High+Lowthroughput Association of adipocyte enhancer-binding protein 1 with Alzheimer's disease pathology in human hippocampi 否 Alzheimer’s disease smooth muscle cell line E_01_0074 Western blot Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes Enhancer AEBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes Immunohistochemical staining Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes Western blot 27845419 chr7 87500277 87502277 ABCB1 These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition. human Liver High+Lowthroughput ABC transporter polymorphisms are associated with irinotecan pharmacokinetics and neutropenia 是 rs12720066,rs6498588 Neutropenia Hep G2 cell E_01_0075 Enhancer Assay These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition. Immunohistochemical staining These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition. ABCB1 Enhancer Assay These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition. 26842780 chr22 39517640 39519640 ATF4 While suppressing general protein translation, eIF2α phosphorylation also promotes the selective translation of some mRNAs, such as ATF4 that induces CCAAT/enhancer binding homologous protein (CHOP), a pro-apoptotic transcription factor. human,mouse Spinal cord tissue High+Lowthroughput Activating Transcription Factor-6α Deletion Modulates the Endoplasmic Reticulum Stress Response after Spinal Cord Injury but Does Not Affect Locomotor Recovery 否 Spinal cord injury Oligodendrocytes E_02_0049 Western blot,RT-PCR While suppressing general protein translation, eIF2α phosphorylation also promotes the selective translation of some mRNAs, such as ATF4 that induces CCAAT/enhancer binding homologous protein (CHOP), a pro-apoptotic transcription factor. Enhancer ATF4 qRT-PCR,qPCR,ChIP,3C RNA-Seq While suppressing general protein translation, eIF2α phosphorylation also promotes the selective translation of some mRNAs, such as ATF4 that induces CCAAT/enhancer binding homologous protein (CHOP), a pro-apoptotic transcription factor. While suppressing general protein translation, eIF2α phosphorylation also promotes the selective translation of some mRNAs, such as ATF4 that induces CCAAT/enhancer binding homologous protein (CHOP), a pro-apoptotic transcription factor. Immunohistochemical staining While suppressing general protein translation, eIF2α phosphorylation also promotes the selective translation of some mRNAs, such as ATF4 that induces CCAAT/enhancer binding homologous protein (CHOP), a pro-apoptotic transcription factor. Western blot,RT-PCR 28860350 chr2 43219398 43221398 ZFP36L2 Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor human Non-malignant oesophagus tissue High+Lowthroughput Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas 否 Oesophageal squamous cell carcinoma (OScc) and adenocarcinoma (Oac) squamous cell line E_01_0076 ChIP-seq,WGBS Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor Enhancer ZFP36L2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor Immunohistochemical staining Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor ChIP-seq,WGBS 29028630 chr7 148804878 148806878 EZH2 EZH2 plays an important role in this inflammatory process of dental pulp. human,mouse dental pulp tissue High+Lowthroughput EZH2 regulates dental pulp inflammation by direct effect on inflammatory factors 否 dental pulp inflammation dental pulp cell E_02_0050 qPCR,ChIP,Western blot EZH2 plays an important role in this inflammatory process of dental pulp. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2 plays an important role in this inflammatory process of dental pulp. EZH2 plays an important role in this inflammatory process of dental pulp. Immunohistochemical staining EZH2 plays an important role in this inflammatory process of dental pulp. qPCR,ChIP,Western blot 31980609 chr1 47213215 47215215 TAL1 Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. mouse lymph High+Lowthroughput Interrogation of enhancer function by enhancer_x0002_targeting CRISPR epigenetic editing 否 无 K562 cell,Jurkat cell E_02_0051 Flow cytometry, cell viability detection, QRT PCR, Western blot, RNA SEQ, chip SEQ, Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Enhancer TAL1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. Immunohistochemical staining Allele-specific targeting of enCRISPRa to oncogenic TAL1 super-enhancer modulates TAL1 expression and cancer progression in xenotransplants. 流式细胞术,细胞活力检测, qRT-PCR ,Western blot,RNA-seq,ChIP-seq, 31980500 chr2 233757381 233759381 UGT1A1 An LXR specific enhancer site on the UGT1A1 gene was identified, along with convincing evidence that LXRα is crucial in maintaining constitutive expression of UGT1A1 in adult hUGT1 mice. mouse Liver, kidney High+Lowthroughput Differential role of LXRα and LXRβ in the regulation of UDP-glucuronosyltransferase 1A1 in humanized UGT1 mice 否 无 hepatic fibrosis HepG2,HK293 cell E_02_0052 QRT PCR, Western blot, glucuronidation assay, transfection, chromatin immunoprecipitation assay, agarose gel electrophoresis An LXR specific enhancer site on the UGT1A1 gene was identified, along with convincing evidence that LXRα is crucial in maintaining constitutive expression of UGT1A1 in adult hUGT1 mice. Enhancer UGT1A1 qRT-PCR,qPCR,ChIP,3C RNA-Seq An LXR specific enhancer site on the UGT1A1 gene was identified, along with convincing evidence that LXRα is crucial in maintaining constitutive expression of UGT1A1 in adult hUGT1 mice. An LXR specific enhancer site on the UGT1A1 gene was identified, along with convincing evidence that LXRα is crucial in maintaining constitutive expression of UGT1A1 in adult hUGT1 mice. Immunohistochemical staining An LXR specific enhancer site on the UGT1A1 gene was identified, along with convincing evidence that LXRα is crucial in maintaining constitutive expression of UGT1A1 in adult hUGT1 mice. qRT-PCR,Western Blot,葡萄糖醛酸化分析,转染,染色质免疫沉淀分析,琼脂糖凝胶电泳 31975641 chr1 118880199 118882199 TBX15 Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk. human bone marrow High+Lowthroughput Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15 是 Rs10494217, rs61730011,rs984222,rs1106529,rs9659323,rs12742627,, rs961470,rs17023223 Osteoporosis cementoblast E_01_0077 RNA SEQ, GWAS derived SNPs and LD analysis Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk. Immunohistochemical staining Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk. TBX15 RNA-seq,GWAS衍生的SNPs和LD分析 Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk. 31969149 chr1 8001716 8003716 ERRFI1 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. human lung High+Lowthroughput An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer 是 rs72635708 psoriasis IMR-90 cell E_01_0078 ChIP-seq The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. Enhancer ERRFI1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. Immunohistochemical staining The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. ChIP-seq 31968281 chr16 88712787 88714787 PIEZO1 Our results first suggested that SNP rs62048221 might mediate the PIEZO1 expression level via modulating the activity of cis-regulatory elements and then further affect the BMD. mouse bone marrow High+Lowthroughput Identification of PIEZO1 polymorphisms for human bone mineral density 是 rs62048221 Osteoporotic fracture mesenchymal stem cell E_02_0053 Luciferase reporter assay, chip qPCR Our results first suggested that SNP rs62048221 might mediate the PIEZO1 expression level via modulating the activity of cis-regulatory elements and then further affect the BMD. Enhancer PIEZO1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results first suggested that SNP rs62048221 might mediate the PIEZO1 expression level via modulating the activity of cis-regulatory elements and then further affect the BMD. Our results first suggested that SNP rs62048221 might mediate the PIEZO1 expression level via modulating the activity of cis-regulatory elements and then further affect the BMD. Immunohistochemical staining Our results first suggested that SNP rs62048221 might mediate the PIEZO1 expression level via modulating the activity of cis-regulatory elements and then further affect the BMD. 荧光素酶报告分析,ChIP-qPCR 31967103 chr7 148804333 148806333 EZH2 We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. human kidney High+Lowthroughput Site-directed targeting of transcriptional activation-associated proteins to repressed chromatin restores CRISPR activity 否 无 HEK293 cell E_01_0079 Transfection, luciferase assay, flow cytometry, chip qPCR, We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. Immunohistochemical staining We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. EZH2 转染,荧光素酶分析,流式细胞术,ChIP-qPCR, We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 31963554 chr10 52311442 52313442 DKK1 Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ. human Bone, mesenchymal tissue High+Lowthroughput DKK1 Induced by 1,25D3 Is Required for the Mineralization of Osteoblasts 否 无 Osteoporosis osteogenitorcell,cementoblast,SaOS2 cell E_01_0080 QPCR, Western blot, immunofluorescence, luciferase assay, chromatin immunoprecipitation assay Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ. Enhancer DKK1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ. Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ. Immunohistochemical staining Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ. qPCR,Western Blot,免疫荧光,荧光素酶分析,染色质免疫沉淀分析 31961892 chr11 55334650 55336650 Atox1 Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer human colon High+Lowthroughput Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer 否 无 Colon cancer SW480 cell E_01_0081 Immunofluorescence, Western blot, transfection, cell colony assay Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer Enhancer Atox1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer Immunohistochemical staining Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer 免疫荧光,Western blot,转染,细胞集落实验 31954402 chr7 148804633 148806633 EZH2 Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection. human blood High+Lowthroughput Differential expression of microRNA, miR-150 and enhancer of zeste homolog 2 (EZH2) in peripheral blood cells as early prognostic markers of severe forms of dengue 否 无 dengue fever E_01_0082 qRT-PCR Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection. Immunohistochemical staining Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection. EZH2 qRT-PCR Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection. 31953940 chr4 108045068 108047068 LEF1 LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs. human High+Lowthroughput Immunohistochemical Expression of Lymphoid Enhancer Binding Factor 1 in CD5-Positive Marginal Zone, Lymphoplasmacytic, and Follicular Lymphomas. 否 无 Lymphoplasmacytoma, follicular lymphoma tumor cell E_01_0083 Immunohistochemistry, flow cytometry, fluorescence in situ hybridization, QRT PCR LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs. Immunohistochemical staining LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs. LEF1 免疫组化,流式细胞术,荧光原位杂交技术,qRT-PCR LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs. 31953319 chr22 39516679 39518679 ATF4 Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. human skeletal muscle High+Lowthroughput Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ 否 无 Skeletal muscle atrophy mouse cell of skeletal muscle E_01_0084 Western blot, transfection, qPCR, agarose gel electrophoresis Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. Immunohistochemical staining Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. ATF4 Western Blot,转染,qPCR,琼脂糖凝胶电泳 Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. 31952907 chr7 148804371 148806371 EZH2 Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA. human Connective tissue, peripheral blood High+Lowthroughput EZH2 deficiency attenuates Treg differentiation in rheumatoid arthritis 否 无 Rheumatoid arthritis synovial cell,peripheral blood mononuclear cell,Jurkat T cell E_01_0085 Western blot,RT-qPCR Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA. Immunohistochemical staining Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA. EZH2 Western blot,RT-qPCR Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA. 31951295 chr15 88633030 88635030 ISG20 Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region. human liver High+Lowthroughput Antiviral activity of interferon-stimulated gene 20, as a putative repressor binding to hepatitis B virus enhancer II and core promoter 否 无 hepatitis B HepG2,HepG2 NTCP,HepAD38 cell E_01_0086 Immunohistochemistry, luciferase analysis, transfection, Southern blot, Northern blot, Western blot, RT-PCR, chromatin immunoprecipitation analysis, microarray data analysis Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region. Enhancer ISG20 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region. Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region. Immunohistochemical staining Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region. 免疫组化,荧光素酶分析,转染,Southern blot ,Northern blot,Western blot,RT-PCR ,染色质免疫沉淀分析,微阵列数据分析 31938642 chr9 81581120 81583120 TLE1 Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study human High+Lowthroughput Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study 否 无 Soft tissue sarcoma E_01_0087 Immunohistochemistry Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study Immunohistochemical staining Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study TLE1 免疫组化 Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study 31937792 chr9 78383023 78385023 Eef1a1 Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus. mouse embryo High+Lowthroughput Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus 否 无 tumour embryonic stem cell E_02_0054 Immunofluorescence, immunohistochemistry, he staining, Southern blot, PCR Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus. Enhancer Eef1a1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus. Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus. Immunohistochemical staining Efficient tissue-type specific expression of target genes in a tetracycline-controlled manner from the ubiquitously active Eef1a1 locus. 免疫荧光,免疫组化,HE染色,Southern blot,PCR 31937612 chr5 69232027 69234027 CDK7 Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor human bone High+Lowthroughput Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor 否 无 Osteosarcoma SJSA-1 cell,U2-OS cell,HOS cell,G-292 cell,MNNG/HOS cell,143B cell,MG-63 cell,cementoblast E_01_0088 Chromatin immunoprecipitation, microarray, transfection, cell viability assay, Transwell, Western blot, RT qPCR Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor Enhancer CDK7 qRT-PCR,qPCR,ChIP,3C RNA-Seq Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor Immunohistochemical staining Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor 染色质免疫沉淀,微阵列,转染,细胞活力检测,Transwell,Western blot,RT-qPCR 31933869 chr11 113406893 113408893 DRD2 This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD. human Peripheral blood High+Lowthroughput Functional tag SNPs inside the DRD2 gene as a genetic risk factor for major depressive disorder in the Chinese Han population 是 rs4648317,rs7131056 Major depressive disorder peripheral blood mononuclear cell E_01_0089 PCR This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD. Enhancer DRD2 qRT-PCR,qPCR,ChIP,3C RNA-Seq This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD. This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD. Immunohistochemical staining This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD. PCR 31933740 chr9 81580946 81582946 TLE1 TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms. human High+Lowthroughput Transducer-like enhancer of split 1 (TLE1) as a novel biomarker for diagnosis of synovial sarcoma correlates with translocation t(X;18): a study of 155 cases in China 否 无 Synovial sarcoma E_01_0090 Immunohistochemistry, fluorescence in situ hybridization TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms. Immunohistochemical staining TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms. TLE1 免疫组化,荧光原位杂交 TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms. 31932307 chr20 21508188 21510188 NKX2-2 The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors mouse brain High+Lowthroughput The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors 否 无 CG4 cell E_02_0055 In situ hybridization, immunohistochemistry, immunofluorescence, CO immunoprecipitation, Western blot The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors Enhancer NKX2-2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors Immunohistochemical staining The transcription factor NKX2-2 regulates oligodendrocyte differentiation through domain-specific interactions with transcriptional corepressors 原位杂交,免疫组化,免疫荧光,免疫共沉淀,Western blot 31929803 chr4 108044497 108046497 LEF1 We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level. human High+Lowthroughput Prognostic Impact of Lymphoid Enhancer Factor 1 Expression and Serum Galectin.3 in Egyptian AML Patients 否 无 Acute myeloid leukemia E_01_0091 RT qPCR, ELISA We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level. Immunohistochemical staining We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level. LEF1 RT-qPCR,联酶免疫吸附反应 We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level. 31928966 chr6 10978082 10980082 ELOVL2 rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression human liver High+Lowthroughput rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression 是 rs953413 liver cancer HepG2 cell E_01_0092 As qPCR, chip SEQ, gene knockdown, QRT PCR, chromatin immunoprecipitation, luciferase reporter rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression Enhancer ELOVL2 qRT-PCR,qPCR,ChIP,3C RNA-Seq rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression Immunohistochemical staining rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression AS-qPCR,ChIP-seq,基因敲除,qRT-PCR,染色质免疫沉淀,荧光素酶报告基因 31927142 chr22 28791896 28793896 XBP1 Thus, XBP1 acts as an osmoprotective protein since it is activated by high osmolarity and upregulates lipid metabolism, membranes generation and the restoration of ER homeostasis. mouse kidney High+Lowthroughput X-box binding protein 1 (XBP1): A key protein for renal osmotic adaptation. Its role in lipogenic program regulation 否 无 MDCK cell E_02_0056 Transfection, RT-PCR, Western blot, immunofluorescence Thus, XBP1 acts as an osmoprotective protein since it is activated by high osmolarity and upregulates lipid metabolism, membranes generation and the restoration of ER homeostasis. Enhancer XBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, XBP1 acts as an osmoprotective protein since it is activated by high osmolarity and upregulates lipid metabolism, membranes generation and the restoration of ER homeostasis. Thus, XBP1 acts as an osmoprotective protein since it is activated by high osmolarity and upregulates lipid metabolism, membranes generation and the restoration of ER homeostasis. Immunohistochemical staining Thus, XBP1 acts as an osmoprotective protein since it is activated by high osmolarity and upregulates lipid metabolism, membranes generation and the restoration of ER homeostasis. 转染,RT-PCR,Western blot,免疫荧光 31915257 chr11 27652693 27654693 BDNF CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons mouse brain High+Lowthroughput CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons 否 无 E_02_0057 RT qPCR, luciferase reporter assay, Western blot, immunocytochemistry, chromatin immunoprecipitation CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons Enhancer BDNF qRT-PCR,qPCR,ChIP,3C RNA-Seq CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons Immunohistochemical staining CREB family transcription factors are major mediators of BDNF transcriptional autoregulation in cortical neurons RT-qPCR ,荧光素酶报告试验,Western blot,免疫细胞化学,染色质免疫沉淀 31914694 chr7 148804420 148806420 EZH2 In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4-dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury. mouse kidney High+Lowthroughput Enhancer of zeste homolog 2 modulates oxidative stress-mediated pyroptosis in vitro and in a mouse kidney ischemia-reperfusion injury model 否 无 Renal ischemia reperfusion injury HK-2 cell E_02_0058 RT-PCR, Western blot, he staining, immunohistochemistry, TUNEL staining, cell viability assay, luciferase reporter assay, transfection, immunofluorescence In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4-dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4-dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury. In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4-dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury. Immunohistochemical staining In conclusion, our results proved that EZH2 inhibition alleviated renal pyroptosis by blocking Nox4-dependent ROS generation through ALK5/Smad2/3 signaling pathway, indicating that EZH2 could be a potential therapeutic target for renal I/R injury. RT-PCR,Western blot,HE染色,免疫组化,TUNEL染色,细胞活力检测,荧光素酶报告分析,转染,免疫荧光 31914533 chr19 19142448 19144448 MEF2B The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. human High+Lowthroughput Expression of myocyte enhancer factor 2B in mantle cell lymphoma and its clinical significance 否 无 Mantle cell lymphoma E_01_0093 He staining, immunohistochemistry, fluorescence in situ hybridization The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. Enhancer MEF2B qRT-PCR,qPCR,ChIP,3C RNA-Seq The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. Immunohistochemical staining The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. HE染色,免疫组化,荧光原位杂交 31914083 chr5 51380063 51382063 ISL1 ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development. human High+Lowthroughput Correlations between ISL1 rs1017 polymorphism and congenital heart disease risk: A PRISMA-compliant meta-analysis 是 rs1017 Congenital heart disease cardiac muscle cell (sensu Arthopoda) E_01_0094 ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development. Immunohistochemical staining ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development. ISL1 ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development. 31910882 chr11 306685 308685 IFITM1 Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. human bone marrow High+Lowthroughput Epigenetic regulation of IFITM1 expression in lipopolysaccharide-stimulated human mesenchymal stromal cells 否 无 hMSC cell E_01_0095 QRT PCR, ELISA, Western blot, immunocytochemistry, chromatin immunoprecipitation PCR, chip SEQ, scratch assay, gene knockdown, luciferase reporter assay Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. Enhancer IFITM1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. Immunohistochemical staining Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. qRT-PCR,酶联免疫吸附试验,Western blot,免疫细胞化学,染色质免疫沉淀PCR,ChIP-seq,划痕实验,基因敲降,荧光素酶报告试验 31909872 chr5 177129035 177131035 NSD1 We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients. mouse High+Lowthroughput Investigating cortical features of Sotos syndrome using mice heterozygous for Nsd1. 否 无 Sotos syndrome E_02_0059 Immunofluorescence, genotyping PCR, qPCR, hematoxylin staining, We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients. Enhancer NSD1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients. We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients. Immunohistochemical staining We also generated a mouse strain lacking one allele of Nsd1 and analyzed morphological and behavioral characteristics in these mice, showing behavioral characteristics reminiscent of some of the deficits seen in Sotos syndrome patients. 免疫荧光,基因分型PCR,qPCR,苏木精染色, 31908011 chr2 199267108 199269108 SATB2 These findings indicate that maternal HFD-induced obesity may be associated with decreasing fetal pre-osteoblastic cell differentiation, under epigenetic control of SATB2 expression via Ezh2-dependent mechanisms. mouse Cord blood, skull High+Lowthroughput Maternal regulation of SATB2 in osteo-progeniters impairs skeletal development in offspring 否 无 Skeletal development mesenchymal stem cell,skull cells E_02_0060 Immunohistochemistry, chromatin immunoprecipitation, chip SEQ, RT qPCR, Western blot These findings indicate that maternal HFD-induced obesity may be associated with decreasing fetal pre-osteoblastic cell differentiation, under epigenetic control of SATB2 expression via Ezh2-dependent mechanisms. Enhancer SATB2 qRT-PCR,qPCR,ChIP,3C RNA-Seq These findings indicate that maternal HFD-induced obesity may be associated with decreasing fetal pre-osteoblastic cell differentiation, under epigenetic control of SATB2 expression via Ezh2-dependent mechanisms. These findings indicate that maternal HFD-induced obesity may be associated with decreasing fetal pre-osteoblastic cell differentiation, under epigenetic control of SATB2 expression via Ezh2-dependent mechanisms. Immunohistochemical staining These findings indicate that maternal HFD-induced obesity may be associated with decreasing fetal pre-osteoblastic cell differentiation, under epigenetic control of SATB2 expression via Ezh2-dependent mechanisms. 免疫组化,染色质免疫沉淀,ChIP-seq,RT-qPCR,Western blot 31902945 chr22 27745785 27747785 MN1 Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) human bone marrow High+Lowthroughput Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) 否 无 Myeloid neoplasms Bone marrow monocytes E_01_0096 Whole genome sequencing, RT-PCR, fluorescence in situ hybridization, Sanger sequencing Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) Enhancer MN1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) Immunohistochemical staining Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12) 全基因组测序,RT-PCR,荧光原位杂交,sanger测序 31900258 chr5 1250197 1252197 TERT Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks. human High+Lowthroughput 否 无 Neuroblastoma neuroblastoma cells,SK-N-AS cell E_01_0097 Chip – qPCR, RT qPCR, Western blot, cell viability assay Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks. Immunohistochemical staining Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks. TERT ChIP–qPCR,RT-qPCR,Western blot,细胞活力检测 Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks. 31899875 chr14 100776332 100778332 MEG3 Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. human ovarian follicle High+Lowthroughput MEG3/MIR-376B-3P/HMGA2 axis is involved in pituitary tumor invasiveness 否 无 Pituitary tumors E_01_0098 Dual luciferase reporter assay, immunofluorescence, IHC, RT qPCR, Western blot, flow cytometry, TUNEL staining, transfection, cell viability assay, Transwell, scratch assay Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. Enhancer MEG3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. Immunohistochemical staining Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P. 双荧光素酶报告基因,免疫荧光,,免疫组化,RT-qPCR,Western blot,流式细胞术,TUNEL染色,转染,细胞活力检测,Transwell,划痕实验 31897846 chr19 2974615 2976615 TLE6 Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations human High+Lowthroughput Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations 否 无 Infertility E_01_0099 Whole exome sequencing, Sanger sequencing Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations Enhancer TLE6 qRT-PCR,qPCR,ChIP,3C RNA-Seq Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations Immunohistochemical staining Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations 全外显子组测序,Sanger测序 31897220 chr1 6098734 6100734 CHD5 In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer. human Stomach, cervix High+Lowthroughput Clinical significance of chromatin remodeling factor CHD5 expression in gastric cancer 否 无 gastric cancer AGS cell, KATO III cell, MKN45 cell, NCI-N87 cell, NUGC-3 cell, OCUM‑1 cell,HeLa cell E_01_0100 Immunohistochemistry, scratch assay, cell viability assay, Transwell, Western blot, RT ^ PCR In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer. Enhancer CHD5 qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer. In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer. Immunohistochemical staining In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer. 免疫组化,划痕实验,细胞活力检测,Transwell,western blot,RT‑PCR 31897216 chr4 7751333 7753333 AFAP1-AS1 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC. human lung High+Lowthroughput AFAP1-AS1 induces cisplatin resistance in non-small cell lung cancer through PI3K/AKT pathway 否 无 Non small cell lung cancer A549 cell E_01_0101 RNA immunoprecipitation, flow cytometry, Western blot, Transwell, RT ‐qpcr In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC. Enhancer AFAP1-AS1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC. In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC. Immunohistochemical staining In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC. RNA免疫沉淀,流式细胞术,Western blot,Transwell,RT‑qPCR 31893185 chr9 81580729 81582729 TLE1 TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies. human High+Lowthroughput Is TLE1 Expression Limited to Synovial Sarcoma? Our Experience at Shifa International Hospital, Pakistan 否 无 Synovial sarcoma E_01_0102 Immunohistochemistry TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies. Immunohistochemical staining TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies. TLE1 免疫组化 TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies. 31892537 chr10 102103573 102105573 LDB1 Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions. human blood High+Lowthroughput Crystal structure of human LDB1 in complex with SSBP2 否 无 erythrocyte E_01_0103 pull-down Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions. Enhancer LDB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions. Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions. Immunohistochemical staining Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions. pull-down 31891591 chr7 148804482 148806482 EZH2 A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy human High+Lowthroughput A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy 否 无 epilepsy E_01_0104 Western blot,qRT-PCR,LC-MS A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy Immunohistochemical staining A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy EZH2 Western blot,qRT-PCR,LC-MS A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy 31890812 chr2 60447611 60449611 BCL11A Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. human Kidney, peripheral blood, bone marrow High+Lowthroughput Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion 否 无 β- Thalassemia disorders HEK293T cell, KU812 cell,KG-1 cell E_01_0105 Agarose gel electrophoresis, QRT PCR Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. Enhancer BCL11A qRT-PCR,qPCR,ChIP,3C RNA-Seq Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. Immunohistochemical staining Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion. 琼脂糖凝胶电泳, qRT-PCR 31888703 chr3 12284215 12286215 PPARG Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression human High+Lowthroughput Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression 是 rs10865710 Traumatic sepsis E_01_0106 Western blot, dual luciferase gene reporter Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression Immunohistochemical staining Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression PPARG Western blot,双荧光素酶基因报告 Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression 31886719 chr11 100684149 100686149 ARHGAP42 First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription. human Aortic smooth muscle, bronchial smooth muscle High+Lowthroughput Transcriptional and posttranscriptional regulation of the SMC-selective blood pressure-associated gene, ARHGAP42 是 rs604723 Blood pressure regulation HUAOSMC cell,HUBRSMC cell E_01_0107 Luciferase assay, immunoprecipitation, QRT PCR, chromatin immunoprecipitation assay, Western blot, electrophoretic mobility shift assay, immunofluorescence First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription. Enhancer ARHGAP42 qRT-PCR,qPCR,ChIP,3C RNA-Seq First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription. First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription. Immunohistochemical staining First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription. 荧光素酶分析,免疫沉淀,qRT-PCR,染色质免疫沉淀实验,Western blot,电泳迁移率分析,免疫荧光 31886200 chr7 148804829 148806829 EZH2 Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution. human bone marrow High+Lowthroughput Aberrant Expression of EZH2 in Pediatric Patients with Myelodysplastic Syndrome: A Potential Biomarker of Leukemic Evolution 否 无 Pediatric myelodysplastic syndrome bone marrow cell E_01_0108 qRT–PCR Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution. Immunohistochemical staining Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution. EZH2 qRT–PCR Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution. 31882553 chr19 15232668 15234668 BRD4 Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma. human lymph High+Lowthroughput BRD4-Regulated Molecular Targets in Mantle Cell Lymphoma: Insights into Targeted Therapeutic Approach 否 无 Mantle cell lymphoma JVM-2 cell,MINO cell,Z138 cell,KPUM-YY1 cell E_01_0109 Cell viability assay, Western blot, QRT PCR, chromatin immunoprecipitation Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma. Immunohistochemical staining Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma. BRD4 细胞活力检测,Western blot,qRT-PCR,染色质免疫沉淀 Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma. 31878072 chr1 153659104 153661104 ILF2 Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein. human Kidney, peripheral blood High+Lowthroughput Enterovirus 71 Represses Interleukin Enhancer-Binding Factor 2 Production and Nucleus Translocation to Antagonize ILF2 Antiviral Effects 否 无 antiviral HEK293T cell、Vero cell、RD cell,thp-1 cell E_01_0110 RT qPCR, Western blot, CO immunoprecipitation, immunofluorescence Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein. Enhancer ILF2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein. Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein. Immunohistochemical staining Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein. RT-qPCR,Western blot,免疫共沉淀,免疫荧光 31866294 chr7 148804551 148806551 EZH2 Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. human colon High+Lowthroughput Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2 否 无 tumour HCT116 cell E_01_0111 Fluorescence polarization assay, Western blot, CO immunoprecipitation Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. Immunohistochemical staining Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. EZH2 荧光偏振分析,Western Blot,共免疫沉淀 Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2. 31866047 chr20 59860441 59862441 SYCP2 SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility human lymph High+Lowthroughput SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility 是 rs568645874, rs199662252,rs45568532, rs551180067, rs11549332 Lymphoblast E_01_0112 QRT PCR, Western blot, Sanger sequencing, PAS staining, hematoxylin staining SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility Enhancer SYCP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility Immunohistochemical staining SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility qRT-PCR,Western Blot,Sanger测序,PAS染色,苏木精染色 31865141 chr3 3142136 3144136 CRBN In conclusion, our study firstly provided a support that CRBN decrease effectively protected LPS-induced ALI against inflammatory response mainly through the repression of oxidative stress and ER stress. mouse lung High+Lowthroughput CRBN knockdown mitigates lipopolysaccharide-induced acute lung injury by suppression of oxidative stress and endoplasmic reticulum (ER) stress associated NF-κB signaling 否 无 acute lung injury A549 cell E_02_0061 Biochemical analysis, he staining, immunofluorescence, ELISA, Western blot, QRT PCR, intracellular reactive oxygen species detection In conclusion, our study firstly provided a support that CRBN decrease effectively protected LPS-induced ALI against inflammatory response mainly through the repression of oxidative stress and ER stress. Enhancer CRBN qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, our study firstly provided a support that CRBN decrease effectively protected LPS-induced ALI against inflammatory response mainly through the repression of oxidative stress and ER stress. In conclusion, our study firstly provided a support that CRBN decrease effectively protected LPS-induced ALI against inflammatory response mainly through the repression of oxidative stress and ER stress. Immunohistochemical staining In conclusion, our study firstly provided a support that CRBN decrease effectively protected LPS-induced ALI against inflammatory response mainly through the repression of oxidative stress and ER stress. 生化分析,HE染色,免疫荧光,ELISA,Western blot,qRT-PCR,细胞内活性氧检测 31864713 chr7 44101569 44103569 AEBP1 Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis human brain High+Lowthroughput Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis 否 无 Gliomas U87MG cell,U251 MG cell E_01_0113 Western blot, immunohistochemistry, QRT PCR, cell viability assay, Transwell, immunofluorescence, flow cytometry Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis Enhancer AEBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis Immunohistochemical staining Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis Western-blot,免疫组化,qRT-PCR,细胞活力检测,Transwell,免疫荧光,流式细胞术 31861475 chr9 36570240 36572240 MELK Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma human bile duct High+Lowthroughput Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma 否 无 Intrahepatic cholangiocarcinoma iCCA cell E_01_0114 RT-PCR, immunohistochemistry Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma Enhancer MELK qRT-PCR,qPCR,ChIP,3C RNA-Seq Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma Immunohistochemical staining Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma RT-PCR,免疫组织化学 31860165 chr4 52709533 52711533 DANCR The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription human breast High+Lowthroughput The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription 否 无 mammary cancer breast cancer cells,mammary gland epithelial cell E_01_0115 QRT PCR, cell viability assay, ELISA, Western blot, RNA immunoprecipitation, chromatin immunoprecipitation, Transwell The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription Enhancer DANCR qRT-PCR,qPCR,ChIP,3C RNA-Seq The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription Immunohistochemical staining The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription qRT-PCR,细胞活力检测,ELISA,Western blot,RNA免疫沉淀,染色质免疫沉淀,Transwell 31858612 chr14 53946742 53948742 BMP4 The expression levels of ALP, runt-related transcription factor 2, bone morphogenetic protein 4, osterix and β-catenin were significantly increased in GSK-137647A-treated group, while the gene and protein levels of peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly reduced. mouse bone marrow High+Lowthroughput Effect of GSK-137647A, the first non-carboxylic FFA4 agonist, on the osteogenic and adipogenic differentiation of bone mesenchymal stem cells in db/db mice 否 无 mesenchymal stem cell of the bone marrow,cementoblast E_02_0062 Flow cytometry, cell viability assay, oil red O staining, Western blot, RT qPCR The expression levels of ALP, runt-related transcription factor 2, bone morphogenetic protein 4, osterix and β-catenin were significantly increased in GSK-137647A-treated group, while the gene and protein levels of peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly reduced. Enhancer BMP4 qRT-PCR,qPCR,ChIP,3C RNA-Seq The expression levels of ALP, runt-related transcription factor 2, bone morphogenetic protein 4, osterix and β-catenin were significantly increased in GSK-137647A-treated group, while the gene and protein levels of peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly reduced. The expression levels of ALP, runt-related transcription factor 2, bone morphogenetic protein 4, osterix and β-catenin were significantly increased in GSK-137647A-treated group, while the gene and protein levels of peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly reduced. Immunohistochemical staining The expression levels of ALP, runt-related transcription factor 2, bone morphogenetic protein 4, osterix and β-catenin were significantly increased in GSK-137647A-treated group, while the gene and protein levels of peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly reduced. 流式细胞术,细胞活力检测,油红O染色,Western blot,RT-Qpcr 31858557 chr15 42735912 42737912 TTBK2 Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy. human brain High+Lowthroughput Circular RNA TTBK2 promotes the development of human glioma cells via miR-520b/EZH2 axis 否 无 Gliomas A172 cell,U251 cell,astrocyte cell E_01_0116 Transfection, QRT PCR, Western blot, flow cytometry, Transwell, dual luciferase reporter assay Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy. Immunohistochemical staining Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy. TTBK2 转染,qRT-PCR,Western Blot,流式细胞术,Transwell,双荧光素酶报告分析 Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy. 31856860 chr20 50188118 50190118 CEBPB Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. human High+Lowthroughput A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock 否 无 Cardiogenic and septic shock E_01_0117 RNA sequencing Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. Immunohistochemical staining Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. CEBPB RNA测序 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend. 31851943 chr19 1606379 1608379 TCF3 Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. human bone marrow High+Lowthroughput Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells 否 无 HPC-7 cell E_01_0118 Dna-fish, Western blot, flow cytometry Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. Immunohistochemical staining Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. TCF7L1 DNA-FISH, Western blot,流式细胞术 Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. 31845224 chr2 26345405 26347405 Notch1 Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC. human gallbladder High+Lowthroughput Notch1 Drives the Formation and Proliferation of Intrahepatic Cholangiocarcinoma 否 无 Intrahepatic cholangiocarcinoma BC-939 cell,RBE cell E_01_0119 Western blot, flow cytometry, Western blot, immunohistochemistry, immunofluorescence, QRT PCR Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC. Enhancer Notch1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC. Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC. Immunohistochemical staining Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC. Western blot, 流式细胞术,Western Blot,免疫组化,免疫荧光,qRT-PCR 31845180 chr8 81475612 81477612 FABP4 Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes mouse High+Lowthroughput Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes 否 无 3T3-LL cell E_02_0063 Oil red O staining, Western blot Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes Enhancer FABP4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes Immunohistochemical staining Exogenous FABP4 interferes with differentiation, promotes lipolysis and inflammation in adipocytes 油红O染色,Western blot 31844321 chr5 129458078 129460078 ADAMTS19 Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance. mouse valve High+Lowthroughput Loss of ADAMTS19 causes progressive non-syndromic heart valve disease 否 无 Valvular heart disease valve interstitial cells E_02_0064 Immunohistochemistry, immunofluorescence, Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance. Enhancer ADAMTS19 qRT-PCR,qPCR,ChIP,3C RNA-Seq Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance. Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance. Immunohistochemical staining Upregulation of endocardial Krüppel-like factor 2 in Adamts19 knockout mice precedes hemodynamic perturbation, showing that a tight balance in the Wnt-Adamts19-Klf2 axis is required for proper valve maturation and maintenance. 免疫组化,免疫荧光, 31843716 chr18 55219904 55221904 TCF4 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells human breast High+Lowthroughput 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells 否 无 mammary cancer MCF-7 cell,MDA-MB-231 cell E_01_0120 Flow cytometry, immunofluorescence, Western blot 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells Immunohistochemical staining 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells TCF4 流式细胞术,免疫荧光,Western blot 3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells 31843273 chr7 148804648 148806648 EZH2 Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues. human High+Lowthroughput Overexpression of enhance of Zeste homolog 2 (EZH2) in endometrial carcinoma: An NRG Oncology/Gynecologic Oncology Group Study 否 无 Endometrial cancer E_01_0121 RT-PCR,Western blot Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues. Immunohistochemical staining Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues. EZH2 RT-PCR,Western blot Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues. 31841397 chr7 148804351 148806351 EZH2 Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation mouse uterus High+Lowthroughput Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation 否 无 Uterine epithelial VAS epithelial cell of uterus E_02_0065 Immunohistochemistry, qPCR Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation Immunohistochemical staining Mice lacking uterine enhancer of zeste homolog 2 have transcriptomic changes associated with uterine epithelial proliferation 免疫组化,qPCR 31840569 chr17 80542354 80544354 RPTOR Ultimately, atg7 rptor double-KO mice displayed decreased lipolysis, restored adipose tissue development, and upregulated thermogenic gene expression in brown and inguinal adipose tissue compared to RPTOR-deficient mice in vivo. mouse Fat High+Lowthroughput Sustained activation of autophagy suppresses adipocyte maturation via a lipolysis-dependent mechanism 否 无 fat cell E_02_0066 Immunofluorescence, flow cytometry, oil red O staining, he staining, immunohistochemistry, Western blot Ultimately, atg7 rptor double-KO mice displayed decreased lipolysis, restored adipose tissue development, and upregulated thermogenic gene expression in brown and inguinal adipose tissue compared to RPTOR-deficient mice in vivo. Enhancer RPTOR qRT-PCR,qPCR,ChIP,3C RNA-Seq Ultimately, atg7 rptor double-KO mice displayed decreased lipolysis, restored adipose tissue development, and upregulated thermogenic gene expression in brown and inguinal adipose tissue compared to RPTOR-deficient mice in vivo. Ultimately, atg7 rptor double-KO mice displayed decreased lipolysis, restored adipose tissue development, and upregulated thermogenic gene expression in brown and inguinal adipose tissue compared to RPTOR-deficient mice in vivo. Immunohistochemical staining Ultimately, atg7 rptor double-KO mice displayed decreased lipolysis, restored adipose tissue development, and upregulated thermogenic gene expression in brown and inguinal adipose tissue compared to RPTOR-deficient mice in vivo. 免疫荧光,流式细胞术,油红O染色,HE染色,免疫组化,western blot 31836590 chr1 145918614 145920614 RBM8A Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. human High+Lowthroughput 1q21.1 deletion and a rare functional polymorphism in siblings with thrombocytopenia-absent radius-like phenotypes 是 rs61746197 Thrombocytopenia, radial hypoplasia E_01_0122 Western blot Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. Enhancer RBM8A qRT-PCR,qPCR,ChIP,3C RNA-Seq Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. Immunohistochemical staining Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. Western blot 31833556 chr7 148804595 148806595 EZH2 By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. mouse High+Lowthroughput Transcription Factor Enrichment Analysis in Enhancers Identifies EZH2 as a Susceptibility Gene for Osteoporosis 是 rs111851041 Osteoporosis E_02_0067 By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. Immunohistochemical staining By conducting TF enrichment analyses, we identified EZH2 as a common TF binding to osteoporosis-associated enhancers, and EZH2 was also associated with BMD in a Chinese population. EZH2 is functionally related to bone phenotypes. 31831267 chr7 148804596 148806596 EZH2 UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system. human Cervix, lymph, kidney High+Lowthroughput Degradation of Polycomb Repressive Complex 2 with an EED-Targeted Bivalent Chemical Degrader 否 无 cancer Hela cell,DB cell,Pfeiffer cell,293T Cell E_01_0123 Western blot, cell viability assay UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system. Immunohistochemical staining UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system. EZH2 Western Blot,细胞活力检测 UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system. 31827084 chrX 113613674 113615674 XACT This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways. human embryo High+Lowthroughput A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans 否 无 embryonic stem cell E_01_0124 Rna-fish, RT qPCR, chromatin immunoprecipitation, Western blot, This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways. Enhancer XACT qRT-PCR,qPCR,ChIP,3C RNA-Seq This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways. This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways. Immunohistochemical staining This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways. RNA-FISH,RT-qPCR,染色质免疫沉淀,western blot, 31826955 chr14 37586693 37588693 FOXA1 Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer. human breast High+Lowthroughput FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer 否 无 mammary cancer MCF7L cell,T47D cell,600MPE cell E_01_0125 Western blot, immunohistochemistry, QRT PCR Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer. Immunohistochemical staining Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer. FOXA1 Western blot,免疫组化,qRT-PCR Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer. 31825847 chr20 64045290 64047290 SOX18 The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. human ovary High+Lowthroughput A Study of High-Grade Serous Ovarian Cancer Origins Implicates the SOX18 Transcription Factor in Tumor Development 否 无 oophoroma FT246,FT282,FT318,CaOV3,COV318,EFO21,Kuramochi,FUOV1,OAW28,OV177,OVSAHO,TykNu,UWB1.289 cell E_01_0126 western blot,qRT-PCR The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. Immunohistochemical staining The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. SOX18 western blot,qRT-PCR The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. 31819273 chr7 148804439 148806439 EZH2 Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2. human breast High+Lowthroughput Discovery of a first-in-class EZH2 selective degrader 否 无 cancer MDA-MB-231,MDA-MB-468,BT549 E_01_0127 Western blot, cell viability assay, crystal violet staining, QRT PCR Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2. Immunohistochemical staining Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2. EZH2 western blot,细胞活力检测,结晶紫染色,qRT-PCR Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2. 31817839 chr1 115283204 115285204 NGF NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis human ovary High+Lowthroughput NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis 否 无 Epithelial ovarian cancer HOSE cell,A2780 cell,SKOV3 cell,OV90 cell,NIH-OVCAR3 cell E_01_0128 Immunohistochemistry, immunocytochemistry, Western blot, QRT PCR, ELISA NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis Enhancer NGF qRT-PCR,qPCR,ChIP,3C RNA-Seq NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis Immunohistochemical staining NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis 免疫组织化学,免疫细胞化学,Western Blot,qRT-PCR, ELISA 31815603 chr6 133886394 133888394 TCF21 These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk. mouse coronary artery High+Lowthroughput Coronary Disease-Associated Gene TCF21 Inhibits Smooth Muscle Cell Differentiation by Blocking the Myocardin-Serum Response Factor Pathway 否 无 coronary artery disease smooth muscle cell E_02_0068 Western blot, chromatin immunoprecipitation sequencing, transfection These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk. Enhancer TCF21 qRT-PCR,qPCR,ChIP,3C RNA-Seq These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk. These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk. Immunohistochemical staining These data indicate that TCF21 antagonizes the MYOCD-SRF pathway through multiple mechanisms, further establishing a role for this coronary artery disease-associated gene in fundamental SMC processes and indicating the importance of smooth muscle response to vascular stress and phenotypic modulation of this cell type in coronary artery disease risk. Western Blot,染色质免疫沉淀测序,转染 31804013 chr5 151027281 151029281 TNIP1 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells. human Peripheral blood High+Lowthroughput Role of Systemic Lupus Erythematosus Risk Variants With Opposing Functional Effects as a Driver of Hypomorphic Expression of TNIP1 and Other Genes Within a Three-Dimensional Chromatin Network 否 无 Systemic lupus erythematosus Jurkat cell,THP-1cell E_01_0129 Dual luciferase reporter assay, electrophoretic mobility shift assay, QRT PCR, Western blot, and pulldown Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells. Immunohistochemical staining Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells. TNIP1 双荧光素酶报告分析,电泳迁移率分析,qRT-PCR,Western blot,pulldown Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells. 31799674 chr12 53959218 53961218 HOTAIR LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells. human bone marrow High+Lowthroughput Effects of lncRNA HOTAIR on proliferation and apoptosis of myeloma cells through NF-κB pathway 否 无 Myeloma Myeloma cell E_01_0130 QRT PCR, flow cytometry, Western blot, cell viability assay, transfection LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells. Immunohistochemical staining LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells. HOTAIR qRT-PCR,流式细胞术,Western blot,细胞活力检测,转染 LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells. 31786140 chr7 27195600 27197600 HOTTIP HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice mouse Kidney, bone marrow High+Lowthroughput HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice 否 无 Acute myeloid leukemia HEK293T cell,OCI-AML3 cell E_02_0069 QRT PCR, rip, flow cytometry, chromatin immunoprecipitation HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice Enhancer HOTTIP qRT-PCR,qPCR,ChIP,3C RNA-Seq HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice Immunohistochemical staining HOTTIP lncRNA Promotes Hematopoietic Stem Cell Self-Renewal Leading to AML-like Disease in Mice qRT-PCR,RIP,流式细胞术,染色质免疫沉淀 33081480 chr18 47806258 47808258 SMAD2 GLGZD was able to inhibit miR-155 upregulation, resulting in down-regulation of miR-155-targeted molecules in MCAO rats, including suppressor of cytokine signaling 1 (SOCS1), inhibitor of nuclear factor kappa-B kinase (IKK), mothers against decapentaplegic homolog 2 (SMAD2) and CCAAT/enhancer binding protein beta (CEBPβ). mouse brain tissue High+Lowthroughput The inhibitory effect of Gualou Guizhi Decoction on post-ischemic neuroinflammation via miR-155 in MCAO rats 否 stroke Inflammatory cell E_02_0070 RT-qPCR,Western blot,Immunohistochemistry GLGZD was able to inhibit miR-155 upregulation, resulting in down-regulation of miR-155-targeted molecules in MCAO rats, including suppressor of cytokine signaling 1 (SOCS1), inhibitor of nuclear factor kappa-B kinase (IKK), mothers against decapentaplegic homolog 2 (SMAD2) and CCAAT/enhancer binding protein beta (CEBPβ). Enhancer SMAD2 qRT-PCR,qPCR,ChIP,3C RNA-Seq GLGZD was able to inhibit miR-155 upregulation, resulting in down-regulation of miR-155-targeted molecules in MCAO rats, including suppressor of cytokine signaling 1 (SOCS1), inhibitor of nuclear factor kappa-B kinase (IKK), mothers against decapentaplegic homolog 2 (SMAD2) and CCAAT/enhancer binding protein beta (CEBPβ). GLGZD was able to inhibit miR-155 upregulation, resulting in down-regulation of miR-155-targeted molecules in MCAO rats, including suppressor of cytokine signaling 1 (SOCS1), inhibitor of nuclear factor kappa-B kinase (IKK), mothers against decapentaplegic homolog 2 (SMAD2) and CCAAT/enhancer binding protein beta (CEBPβ). Immunohistochemical staining GLGZD was able to inhibit miR-155 upregulation, resulting in down-regulation of miR-155-targeted molecules in MCAO rats, including suppressor of cytokine signaling 1 (SOCS1), inhibitor of nuclear factor kappa-B kinase (IKK), mothers against decapentaplegic homolog 2 (SMAD2) and CCAAT/enhancer binding protein beta (CEBPβ). RT-qPCR,Western blot,Immunohistochemistry 29861522 chr3 149159891 149161891 CP The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. mouse Epithelial tissues High+Lowthroughput Effect of diethyldithiocarbamate in cyclophosphamide-induced nephrotoxicity: Immunohistochemical study of superoxide dismutase 1 in rat 否 Renal impairment nephron tubule epithelial cell E_02_0071 Biochemical analyses,Immunohistochemistry The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Enhancer CP qRT-PCR,qPCR,ChIP,3C RNA-Seq The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Immunohistochemical staining The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Biochemical analyses,Immunohistochemistry 29861522 chr21 31656571 31658571 SOD1 The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. mouse Epithelial tissues High+Lowthroughput Effect of diethyldithiocarbamate in cyclophosphamide-induced nephrotoxicity: Immunohistochemical study of superoxide dismutase 1 in rat 否 Renal impairment nephron tubule epithelial cell E_02_0071 Biochemical analyses,Immunohistochemistry The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Enhancer SOD1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Immunohistochemical staining The present study indicates that DEDTC administration further exacerbated the CP-induced kidney damage in rat. Biochemical analyses,Immunohistochemistry 29861296 chr18 26013138 26015138 SS18 These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. human Synovial sarcoma tissues High+Lowthroughput The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma 否 Synovial sarcoma (SS) HEK293T LentiX cell E_01_0131 Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Enhancer SS18 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Immunohistochemical staining These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors 29861296 chr22 23783961 23785961 SMARCB1 These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. human Synovial sarcoma tissues High+Lowthroughput The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma 否 Synovial sarcoma (SS) HEK293T LentiX cell E_01_0131 Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Enhancer SMARCB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Immunohistochemical staining These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors 29859467 chr10 67881752 67883752 SIRT1 Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. mouse Epididymal white adipose tissue High+Lowthroughput Qing Gan Zi Shen Tang alleviates adipose tissue dysfunction with up-regulation of SIRT1 in spontaneously hypertensive rat 否 Hypertension, obesity, hyperlipidemia, insulin resistance fat cell E_02_0072 ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Enhancer SIRT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Immunohistochemical staining Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC 29859467 chr13 40553149 40555149 FOXO1 Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. mouse Epididymal white adipose tissue High+Lowthroughput Qing Gan Zi Shen Tang alleviates adipose tissue dysfunction with up-regulation of SIRT1 in spontaneously hypertensive rat 否 Hypertension, obesity, hyperlipidemia, insulin resistance fat cell E_02_0072 ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Enhancer FOXO1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Immunohistochemical staining Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC 29859467 chr8 81475508 81477508 FABP4 Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. mouse Epididymal white adipose tissue High+Lowthroughput Qing Gan Zi Shen Tang alleviates adipose tissue dysfunction with up-regulation of SIRT1 in spontaneously hypertensive rat 否 Hypertension, obesity, hyperlipidemia, insulin resistance fat cell E_02_0072 ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Enhancer FABP4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. Immunohistochemical staining Collectively, our research demonstrated for the first time that QGZST is able to alleviate eWAT dysfunction with up-regulation of SIRT1 in HFD-fed SHRs, which might supply further insight into QGZST-mediated anti-hypertension and anti-obesity effects. ELISA,Western blot,Quantitative reverse transcription polymerase chain reaction (qRT-PCR),Immunohistochemistry analysis,HPLC 29859124 chr1 11009935 11011935 TARDBP Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA. human Nervous tissue High+Lowthroughput Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis 否 Amyotrophic lateral sclerosis (ALS) SH-SY5Y neuroblastoma cell E_01_0132 Immunocytochemistry,RNA-FISH,RIP,PCR,Western blot,qRT-PCR,Real-time qPCR,transfection,Cell Viability Assay Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA. Enhancer TARDBP qRT-PCR,qPCR,ChIP,3C RNA-Seq Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA. Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA. Immunohistochemical staining Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA. Immunocytochemistry,RNA-FISH,RIP,PCR,Western blot,qRT-PCR,Real-time qPCR,transfection,Cell Viability Assay 31484726 chr12 53959112 53961112 HOTAIR Focusing on a well-known lncRNA, HOTAIR, four distinct epigenetic modification patterns were observed. The majority of HOTAIR binding sites (50.1%) were located within quiescent regions. human,mouse High+Lowthroughput Comprehensive analysis of long noncoding RNA (lncRNA)-chromatin interactions reveals lncRNA functions dependent on binding diverse regulatory elements 否 cervical carcinoma HeLa-S3 cell E_02_0073 PCR,Flow cytometry Focusing on a well-known lncRNA, HOTAIR, four distinct epigenetic modification patterns were observed. The majority of HOTAIR binding sites (50.1%) were located within quiescent regions. Enhancer HOTAIR qRT-PCR,qPCR,ChIP,3C RNA-Seq Focusing on a well-known lncRNA, HOTAIR, four distinct epigenetic modification patterns were observed. The majority of HOTAIR binding sites (50.1%) were located within quiescent regions. Focusing on a well-known lncRNA, HOTAIR, four distinct epigenetic modification patterns were observed. The majority of HOTAIR binding sites (50.1%) were located within quiescent regions. Immunohistochemical staining Focusing on a well-known lncRNA, HOTAIR, four distinct epigenetic modification patterns were observed. The majority of HOTAIR binding sites (50.1%) were located within quiescent regions. PCR,Flow cytometry 31484079 chr7 150942398 150944398 KCNH2 The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. human,mouse liver High+Lowthroughput Identification and Characterization of a Transcribed Distal Enhancer Involved in Cardiac Kcnh2 Regulation 是 rs9640171 liver cancer hepatocellular carcinoma derived cell E_02_0074 PCR,Flow cytometry The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Enhancer KCNH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. Immunohistochemical staining The human ether-a-go-go-related gene KCNH2 encodes the voltage-gated potassium channel underlying IKr, a current critical for the repolarization phase of the cardiac action potential. PCR,Flow cytometry 32517740 chr4 153777966 153779966 SFRP2 We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. human High+Lowthroughput Association between variation of circulating 25-OH vitamin D and methylation of secreted frizzled-related protein 2 in colorectal cancer 否 Colorectal cancer Human colorectal carcinoma cell E_01_0133 PCR We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. Enhancer SFRP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. Immunohistochemical staining We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes. PCR 32517078 chr10 112947720 112949720 TCF7L2 We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease. human High+Lowthroughput Embryonic Program Activated during Blast Crisis of Chronic Myelogenous Leukemia (CML) Implicates a TCF7L2 and MYC Cooperative Chromatin Binding 否 Chronic Myelogenous Leukemia K562 cell E_01_0134 QRT-PCR, We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease. Immunohistochemical staining We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease. TCF7L2 QRT-PCR, We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease. 32514254 chr12 56749082 56751082 HSD17B6 HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. human High+Lowthroughput Downexpression of HSD17B6 correlates with clinical prognosis and tumor immune infiltrates in hepatocellular carcinoma 否 Hepatocellular carcinoma HCC cell E_01_0135 Gene set enrichment analysis,RT‑qPCR,Western blot HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. Enhancer HSD17B6 qRT-PCR,qPCR,ChIP,3C RNA-Seq HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. Immunohistochemical staining HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1. Gene set enrichment analysis,RT‑qPCR,Western blot 29945972 chrX 49025737 49027737 TFE3 The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. human,mouse High+Lowthroughput Protein phosphatase 2A stimulates activation of TFEB and TFE3 transcription factors in response to oxidative stress 否 cancer E_02_0075 Western blot, immunofluorescence staining The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. Enhancer TFE3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. Immunohistochemical staining The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. western blot,免疫荧光染色 29945972 chr14 105848654 105850654 IGHM The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. human,mouse High+Lowthroughput Protein phosphatase 2A stimulates activation of TFEB and TFE3 transcription factors in response to oxidative stress 否 cancer E_02_0075 Western blot, immunofluorescence staining The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. Enhancer IGHM qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. Immunohistochemical staining The transcriptional regulators transcription factor EB (TFEB) and transcription factor binding to IGHM enhancer 3 (TFE3) play a key role in the control of these stress pathways. western blot,免疫荧光染色 29945888 chr11 120233455 120235455 POU2F3 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). human High+Lowthroughput POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer 否 Small cell lung cancer (SCLC) SCLC cell E_01_0136 Rna-fish, human SCLC immunohistochemistry, Western blot, RNA SEQ, GSEA, chip SEQ, immunofluorescence staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Immunohistochemical staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). POU2F3 RNA-FISH,Human SCLC immunohistochemistry,Western blot,RNA-seq,GSEA,ChIP-seq,免疫荧光染色 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). 29945888 chr12 102954806 102956806 ASCL1 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). human High+Lowthroughput POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer 否 Small cell lung cancer (SCLC) SCLC cell E_01_0136 Rna-fish, human SCLC immunohistochemistry, Western blot, RNA SEQ, GSEA, chip SEQ, immunofluorescence staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Immunohistochemical staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). ASCL1 RNA-FISH,Human SCLC immunohistochemistry,Western blot,RNA-seq,GSEA,ChIP-seq,免疫荧光染色 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). 29945888 chr2 181665466 181667466 NEUROD1 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). human High+Lowthroughput POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer 否 Small cell lung cancer (SCLC) SCLC cell E_01_0136 Rna-fish, human SCLC immunohistochemistry, Western blot, RNA SEQ, GSEA, chip SEQ, immunofluorescence staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Immunohistochemical staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). NEUROD1 RNA-FISH,Human SCLC immunohistochemistry,Western blot,RNA-seq,GSEA,ChIP-seq,免疫荧光染色 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). 29945888 chr20 20365577 20367577 INSM1 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). human High+Lowthroughput POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer 否 Small cell lung cancer (SCLC) SCLC cell E_01_0136 Rna-fish, human SCLC immunohistochemistry, Western blot, RNA SEQ, GSEA, chip SEQ, immunofluorescence staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). Immunohistochemical staining An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). INSM1 RNA-FISH,Human SCLC immunohistochemistry,Western blot,RNA-seq,GSEA,ChIP-seq,免疫荧光染色 An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017). 29945296 chr13 31737329 31739329 Foxq1 In particular, the Fox transcription factor binding motif was frequently observed within EWS FLI1 peaks and Foxq1 was identified as the cooperative partner that interacts with the EWS portion of EWS FLI1.  human,mouse High+Lowthroughput EWS-FLI1 regulates a transcriptional program in cooperation with Foxq1 in mouse Ewing sarcoma 否 Ewing sarcoma E_02_0076 Real ‐ time quantitative PCR, luciferase assay, chip ‐ SEQ, statistical analysis In particular, the Fox transcription factor binding motif was frequently observed within EWS FLI1 peaks and Foxq1 was identified as the cooperative partner that interacts with the EWS portion of EWS FLI1.  Enhancer Foxq1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In particular, the Fox transcription factor binding motif was frequently observed within EWS FLI1 peaks and Foxq1 was identified as the cooperative partner that interacts with the EWS portion of EWS FLI1.  In particular, the Fox transcription factor binding motif was frequently observed within EWS FLI1 peaks and Foxq1 was identified as the cooperative partner that interacts with the EWS portion of EWS FLI1.  Immunohistochemical staining In particular, the Fox transcription factor binding motif was frequently observed within EWS FLI1 peaks and Foxq1 was identified as the cooperative partner that interacts with the EWS portion of EWS FLI1.  Real‐time quantitative PCR,Luciferase assay,ChIP‐Seq,统计分析 29941955 chr1 186441221 186443221 PDC Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. mouse High+Lowthroughput Elucidating the hypoxic stress response in barley (Hordeum vulgare L.) during waterlogging: A proteomics approach 否 E_02_0077 QRT PCR, Western blot, statistical analysis Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Enhancer PDC qRT-PCR,qPCR,ChIP,3C RNA-Seq Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. Immunohistochemical staining Pyruvate decarboxylase (PDC), 1-amino cyclopropane 1-carboxylic acid oxidase (ACO), glutamine synthetase (GS), glutathione S-transferases (GST) and beta-1, 3-glucanase in adventitious, nodal and seminal roots were more abundant in TF58 than those in TF57 under waterlogging stress. qRT-PCR,Western blot,统计分析 29594316 chr1 26690341 26692341 ARID1A In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. human,mouse Lymphoid tissue, liver tissue High+Lowthroughput ARID1A loss in adult hepatocytes activates β-catenin-mediated erythropoietin transcription 否 erythrocyte,stem cell E_02_0078 Immunohistochemistry and in situ hybridization experiments, enzyme-linked immunosorbent assay (ELISA), cell transfection, stimulation and luciferase assays, RNA extraction and quantitative RT-PCR, protein extracts and Western blotting, electrophoretic mobility shift assay (EMSA), flow cytometry and forming unit erythroid (CFU-E) assays, chromatin immunoprecipitation (chip) and ATAC qPCR assays were performed In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. Enhancer ARID1A qRT-PCR,qPCR,ChIP,3C RNA-Seq In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. Immunohistochemical staining In mice with Apc-Arid1a gene invalidations in single hepatocytes, Epo de novo synthesis led to its secretion, to splenic erythropoiesis and to dramatic erythrocytosis. 免疫组化和原位杂交实验,酶联免疫吸附测定(ELISA),细胞转染、刺激和荧光素酶检测,RNA 提取和定量 RT-PCR,蛋白质提取物和蛋白质印迹,电泳迁移率移位测定 (EMSA),流式细胞术和成形单元红系 (CFU-E) 检测,染色质免疫沉淀 (ChIP) 和 ATAC-qPCR 检测 29593713 chr17 27054976 27056976 Nkx2-5 We have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. mouse Musculature High+Lowthroughput Divergent Transcription of the Nkx2-5 Locus Generates Two Enhancer RNAs with Opposing Functions 否 heart failure cardiac muscle cell (sensu Arthopoda) E_02_0079 RNA sequencing (RNA SEQ), quantitative PCR (qPCR), cell fractionation, rna-fish, Western blotting, fluorescent immunoassay We have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. Enhancer Nkx2-5 qRT-PCR,qPCR,ChIP,3C RNA-Seq We have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. We have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. Immunohistochemical staining We have identified an autoregulatory loop controlling expression of the master cardiac TF NKX2-5, in which one eRNA represses transcription. RNA测序(RNA-seq),定量PCR(qPCR),细胞分馏,RNA-FISH,蛋白质印记,荧光免疫分析 29592873 chr13 73052423 73054423 KLF5 These results suggest that CLU is a novel regulator of adipocyte differentiation by modulating the protein stability of the adipogenic transcription factor KLF5. mouse connective tissue High+Lowthroughput Regulation of adipocyte differentiation by clusterin-mediated Krüppel-like factor 5 stabilization 否 fat cell,mesenchymal stem cell E_02_0080 RNA isolation and quantitative real_x0002_time PCR (qRT-PCR),Luciferase reporter assay,20S proteasome activity assay These results suggest that CLU is a novel regulator of adipocyte differentiation by modulating the protein stability of the adipogenic transcription factor KLF5. Enhancer KLF5 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results suggest that CLU is a novel regulator of adipocyte differentiation by modulating the protein stability of the adipogenic transcription factor KLF5. These results suggest that CLU is a novel regulator of adipocyte differentiation by modulating the protein stability of the adipogenic transcription factor KLF5. Immunohistochemical staining These results suggest that CLU is a novel regulator of adipocyte differentiation by modulating the protein stability of the adipogenic transcription factor KLF5. RNA isolation and quantitative real_x0002_time PCR (qRT-PCR),Luciferase reporter assay,20S proteasome activity assay 29583017 chr6 47504032 47506032 Ezh2 Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. mouse Bone marrow High+Lowthroughput Hematopoietic stem/progenitor cell senescence is associated with altered expression profiles of cellular memory-involved gene 否 senescence associated disease progenitor cell E_02_0081 qRT-PCR Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Enhancer Ezh2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. Immunohistochemical staining Ezh2 is a key member of the PcG family. It can promote the survival of HSCs. qRT-PCR 29580634 chr5 173229639 173231639 NKX2-5 NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. human Vascular tissue High+Lowthroughput Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis 是 rs3095870 scleroderma associated pulmonary hypertensio smooth muscle cell of the pulmonary artery E_01_0137 Western blot,qPCR NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. Immunohistochemical staining NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. NKX2-5 Western blot,qPCR NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling. 29579222 chr11 12671903 12673903 TEAD1 TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease human Vascular tissue High+Lowthroughput Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis 是 rs3095870 scleroderma associated pulmonary hypertensio smooth muscle cell of the pulmonary artery E_01_0138 Western blot,qPCR TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease Immunohistochemical staining TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease TEAD1 Western blot,qPCR TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease 29579159 chr15 61854370 61856370 Myc The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies mouse Haematopoietic tissue High+Lowthroughput A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies 否 haematopoietic malignancies hematopoietic stem cell E_02_0082 RT–qPCR,ATAC-seq,RNA-seq, The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies Enhancer Myc qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies Immunohistochemical staining The transcription factor Myc is essential for the regulation of haematopoietic stem cells and progenitors and has a critical function in haematopoietic malignancies RT–qPCR,ATAC-seq,RNA-seq, 29576612 chr17 42310573 42312573 STAT3 Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity human High+Lowthroughput Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity 否 E_01_0139 EZH2 Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity Immunohistochemical staining Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity STAT3 EZH2 Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity 29572261 chr12 54030375 54032375 HOXC5 Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. human Somatic tissue High+Lowthroughput HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis 否 Tumor somatic cell E_01_0140 Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. Immunohistochemical staining Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. HOXC5 Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers. 29570423 chr19 19143043 19145043 MEF2B Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. human Lymphoid tissue High+Lowthroughput Comparison of Myocyte Enhancer Factor 2B Versus Other Germinal Center-associated Antigens in the Differential Diagnosis of B-Cell Non-Hodgkin Lymphomas 否 Lymphomas B cell E_01_0141 Immunohistochemical Staining Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Enhancer MEF2B qRT-PCR,qPCR,ChIP,3C RNA-Seq Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Immunohistochemical staining Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells. Immunohistochemical Staining 29569934 chr17 43751254 43753254 SOST The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. human Bone High+Lowthroughput Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis 是 rs1230399, rs7220711, rs1107748, rs75901553 osteoporosis Germinal center B-cells E_01_0142 Luciferase reporter assay,ChIP,qPCR The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Enhancer SOST qRT-PCR,qPCR,ChIP,3C RNA-Seq The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Immunohistochemical staining The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling. Luciferase reporter assay,ChIP,qPCR 29568244 chr2 103785432 103787432 Lmo2 T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development mouse Embryo High+Lowthroughput BRACHYURY directs histone acetylation to target loci during mesoderm development 否 congenital diseases hematopoietic and endothelial cell E_02_0083 ChIP-Seq,RNA-Seq ,ChIP-qPCR T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development Enhancer Lmo2 qRT-PCR,qPCR,ChIP,3C RNA-Seq T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development Immunohistochemical staining T controls the expression of Lmo2, a master regulator of hematopoietic and endothelial development ChIP-Seq,RNA-Seq ,ChIP-qPCR 29564771 chr7 148804053 148806053 EZH2 EZH2 plays an important role in this inflammatory process of dental pulp. human,mouse dental pulp tissue High+Lowthroughput EZH2 regulates dental pulp inflammation by direct effect on inflammatory factors 否 dental pulp inflammation dental pulp cell E_02_0084 qPCR,ChIP,Western blot EZH2 plays an important role in this inflammatory process of dental pulp. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2 plays an important role in this inflammatory process of dental pulp. EZH2 plays an important role in this inflammatory process of dental pulp. Immunohistochemical staining EZH2 plays an important role in this inflammatory process of dental pulp. qPCR,ChIP,Western blot 29563873 chr14 100892224 100894224 MEG8 "Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer." human High+Lowthroughput MEG8 long noncoding RNA contributes to epigenetic progression of the epithelial-mesenchymal transition of lung and pancreatic cancer cells 否 Lung and pancreatic cancer A549 cell, LC-2/ad cell,Panc1 cell E_01_0143 "Quantitative PCR,Cell migration assay,Chromatin immunoprecipitation (ChIP) assays,RNA immunoprecipitation (RIP),Chromatin isolation by RNA purification (ChIRP) assays" "Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer." Enhancer MEG8 qRT-PCR,qPCR,ChIP,3C RNA-Seq "Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer." "Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer." Immunohistochemical staining "Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer." "Quantitative PCR,Cell migration assay,Chromatin immunoprecipitation (ChIP) assays,RNA immunoprecipitation (RIP),Chromatin isolation by RNA purification (ChIRP) assays" 29563767 chr12 55740444 55742444 GDF11 Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. human High+Lowthroughput GDF11 Antagonizes Psoriasis-like Skin Inflammation via Suppression of NF-κB Signaling Pathway 否 Psoriasiform skin inflammation Mouse leukemic monocyte macrophages E_01_0144 miRNA transfection,Real-Time PCR,Western Blot,Immunofluorescence,ELISA Assays Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. Immunohistochemical staining Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. GDF11 miRNA transfection,Real-Time PCR,Western Blot,Immunofluorescence,ELISA Assays Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 29563503 chr8 127077409 127079409 PRNCR1 Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. human High+Lowthroughput LncRNA PRNCR1 interacts with HEY2 to abolish miR-448-mediated growth inhibition in non-small cell lung cancer 否 Non small cell lung cancer A549 cell, SK-MES-1 cell, Calu-3 cell,H1299 cell,NHBE cell E_01_0145 Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Enhancer PRNCR1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Immunohistochemical staining Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay 29563503 chr6 125744658 125746658 HEY2 Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. human High+Lowthroughput LncRNA PRNCR1 interacts with HEY2 to abolish miR-448-mediated growth inhibition in non-small cell lung cancer 否 Non small cell lung cancer A549 cell, SK-MES-1 cell, Calu-3 cell,H1299 cell,NHBE cell E_01_0145 Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. Immunohistochemical staining Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. HEY2 Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 29563192 chr16 67559679 67561679 CTCF The expression frequencycorrelates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in un_x0002_derstanding the interplay between cellular differenti_x0002_ation and stochastic gene choice. mouse High+Lowthroughput Stochastic Gene Choice during Cellular Differentiation 否 embryonic stem cell E_02_0085 Single-Cell qRT-PCR,Chromatin Immunoprecipitation,Bisulfite Sequencing The expression frequencycorrelates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in un_x0002_derstanding the interplay between cellular differenti_x0002_ation and stochastic gene choice. Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq The expression frequencycorrelates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in un_x0002_derstanding the interplay between cellular differenti_x0002_ation and stochastic gene choice. The expression frequencycorrelates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in un_x0002_derstanding the interplay between cellular differenti_x0002_ation and stochastic gene choice. Immunohistochemical staining The expression frequencycorrelates highly with CTCF binding to the promoters and follows dynamically the changes in the binding during the differentiation. These findings aid in un_x0002_derstanding the interplay between cellular differenti_x0002_ation and stochastic gene choice. Single-Cell qRT-PCR,Chromatin Immunoprecipitation,Bisulfite Sequencing 29563176 chr16 67559907 67561907 CTCF These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. human blood High+Lowthroughput The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance 否 K562 cell E_01_0146 PCR These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. Immunohistochemical staining These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. CTCF PCR These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. 29563122 chr9 21074270 21076270 IFNB1 We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). human uterus High+Lowthroughput The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers 否 HeLa cell E_01_0147 PCR, Western blot, flow cytometry, immunofluorescence staining We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). Immunohistochemical staining We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). IFNB1 PCR,Western blot,Flow cytometry,免疫荧光染色 We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). 29563115 chr17 42310596 42312596 STAT3 Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. human,mouse connective tissue High+Lowthroughput Generation of Nanog reporter mice that distinguish pluripotent stem cells from unipotent primordial germ cells 否 pluripotent stem cell E_02_0086 PCR, flow cytometry, immunofluorescence staining Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Enhancer STAT3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Immunohistochemical staining Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. PCR,Flow cytometry,免疫荧光染色 29559957 chr7 99754049 99756049 CYP3A4 The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. human High+Lowthroughput DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression 否 HepG2 cell E_01_0148 Plasmid construction,In vitro methylation,Luciferase reporter assay,Transfection and rifampicin induction,RNA isolation and real-time quantitative polymerase chain reaction (RT-qPCR) ,ChIP assay The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Enhancer CYP3A4 qRT-PCR,qPCR,ChIP,3C RNA-Seq The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Immunohistochemical staining The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Plasmid construction,In vitro methylation,Luciferase reporter assay,Transfection and rifampicin induction,RNA isolation and real-time quantitative polymerase chain reaction (RT-qPCR) ,ChIP assay 29557377 chr1 156460952 156462952 MEF2D We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). human High+Lowthroughput A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts 否 T, B, NK cell E_01_0149 Gene array capture,Seq,Gene array capture We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). Enhancer MEF2D qRT-PCR,qPCR,ChIP,3C RNA-Seq We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). Immunohistochemical staining We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). Gene array capture,Seq,Gene array capture 29556394 chr8 144311848 144313848 DGAT1 Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. mouse High+Lowthroughput Butyric acid induces spontaneous adipocytic differentiation of porcine bone marrow-derived mesenchymal stem cells 否 mesenchymal stem cell E_02_0087 Proliferation study,Differentiation study,Differentiation study,Cytochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Enhancer DGAT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Immunohistochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Proliferation study,Differentiation study,Differentiation study,Cytochemical staining 29556394 chr10 88950906 88952906 FAS Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. mouse High+Lowthroughput Butyric acid induces spontaneous adipocytic differentiation of porcine bone marrow-derived mesenchymal stem cells 否 mesenchymal stem cell E_02_0087 Proliferation study,Differentiation study,Differentiation study,Cytochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Enhancer FAS qRT-PCR,qPCR,ChIP,3C RNA-Seq Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Immunohistochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Proliferation study,Differentiation study,Differentiation study,Cytochemical staining 29556394 chr1 53193789 53195789 CPT2 Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. mouse High+Lowthroughput Butyric acid induces spontaneous adipocytic differentiation of porcine bone marrow-derived mesenchymal stem cells 否 mesenchymal stem cell E_02_0087 Proliferation study,Differentiation study,Differentiation study,Cytochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Enhancer CPT2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Immunohistochemical staining Treatment with BA modulated the expression of adipocytic differentiation markers: peroxisome proliferator-activated receptor γ and CCAAT/enhancer binding protein α were significantly increased by both BA-2.5 and BA-5 throughout the study, while lipoprotein lipase and fatty acid-binding protein 4 were increased by BA-5 at day 3, and decreased by both BA-5 and BA- 2.5 later throughout the study. Proliferation study,Differentiation study,Differentiation study,Cytochemical staining 29556082 chr11 65494664 65496664 MALAT1 MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. human High+Lowthroughput Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells 否 Primary endothelial cell E_01_0150 GRO-Seq and RNA-Seq, MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. Immunohistochemical staining MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. MALAT1 GRO-Seq and RNA-Seq, MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 29554889 chr3 133743314 133745314 TF Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. human High+Lowthroughput Genomic analysis of transcriptional networks directing progression of cell states during MGE development. 否 E_01_0151 RT qPCR, in situ hybridization analysis, gene knockdown, chip SEQ, immunofluorescence staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Enhancer TF qRT-PCR,qPCR,ChIP,3C RNA-Seq Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Immunohistochemical staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. RT-qPCR,原位杂交分析,基因敲降,ChIP-seq ,免疫荧光染色 29554889 chr9 122199817 122201817 LHX6 Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. human High+Lowthroughput Genomic analysis of transcriptional networks directing progression of cell states during MGE development. 否 E_01_0151 RT qPCR, in situ hybridization analysis, gene knockdown, chip SEQ, immunofluorescence staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Enhancer LHX6 qRT-PCR,qPCR,ChIP,3C RNA-Seq Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Immunohistochemical staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. RT-qPCR,原位杂交分析,基因敲降,ChIP-seq ,免疫荧光染色 29554889 chr1 75125927 75127927 LHX8 Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. human High+Lowthroughput Genomic analysis of transcriptional networks directing progression of cell states during MGE development. 否 E_01_0151 RT qPCR, in situ hybridization analysis, gene knockdown, chip SEQ, immunofluorescence staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Enhancer LHX8 qRT-PCR,qPCR,ChIP,3C RNA-Seq Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. Immunohistochemical staining Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8. RT-qPCR,原位杂交分析,基因敲降,ChIP-seq ,免疫荧光染色 29552163 chr2 132413869 132415869 GPR39 Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). human,mouse adipose tissue High+Lowthroughput Improvement of Duchenne muscular dystrophy phenotype following obestatin treatment. 否 Duchenne muscular dystrophy (DMD) satellite cell E_02_0088 Real ‐ time PCR, Weston blot, immunofluorescence staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Enhancer GPR39 qRT-PCR,qPCR,ChIP,3C RNA-Seq Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Immunohistochemical staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). real‐time PCR,weston blot,免疫荧光染色 29552153 chr2 132413957 132415957 GPR39 Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). human,mouse High+Lowthroughput Improvement of Duchenne muscular dystrophy phenotype following obestatin treatment. 否 Duchenne muscular dystrophy (DMD) muscle cell E_02_0089 Real ‐ time PCR, Weston blot, immunofluorescence staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Enhancer GPR39 qRT-PCR,qPCR,ChIP,3C RNA-Seq Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Immunohistochemical staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). real‐time PCR,weston blot,免疫荧光染色 29549111 chr14 21495511 21497511 METTL3 The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. human High+Lowthroughput Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development 否 Bone marrow stem cell E_01_0152 flow cytometry ,Real-time quantitative PCR , staining ,Protein extraction ,Western blot ,Cell transfection ,Immunofluorescence assay ,Quantitative analysis ,Chromatin immunoprecipitation assay ,Luciferase reporter assay The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. Enhancer METTL3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. Immunohistochemical staining The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. flow cytometry ,Real-time quantitative PCR , staining ,Protein extraction ,Western blot ,Cell transfection ,Immunofluorescence assay ,Quantitative analysis ,Chromatin immunoprecipitation assay ,Luciferase reporter assay 29545900 chr2 226728889 226730889 IRS1 Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). human High+Lowthroughput Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis 否 HeLa cell E_01_0153 Nuclear magnetic resonance (NMR) spectroscopy analysis ,RNA extraction and real-time PCR ,Western blot analysis ,Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Enhancer IRS1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Immunohistochemical staining Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Nuclear magnetic resonance (NMR) spectroscopy analysis ,RNA extraction and real-time PCR ,Western blot analysis ,Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function 29540569 chr7 148804523 148806523 EZH2 We report a distinct mechanism whereby p53-regulated MDM2 works together with MDMX to modulate sensitivity to DNA damage by controlling EZH2 (enhancer of zeste homolog 2) turnover. mouse, p53-dependent tissue High+Lowthroughput An EZH2-mediated epigenetic mechanism behind p53-dependent tissue sensitivity to DNA damage 否 Cancer cell E_02_0090 qRT-PCR. We report a distinct mechanism whereby p53-regulated MDM2 works together with MDMX to modulate sensitivity to DNA damage by controlling EZH2 (enhancer of zeste homolog 2) turnover. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We report a distinct mechanism whereby p53-regulated MDM2 works together with MDMX to modulate sensitivity to DNA damage by controlling EZH2 (enhancer of zeste homolog 2) turnover. We report a distinct mechanism whereby p53-regulated MDM2 works together with MDMX to modulate sensitivity to DNA damage by controlling EZH2 (enhancer of zeste homolog 2) turnover. Immunohistochemical staining We report a distinct mechanism whereby p53-regulated MDM2 works together with MDMX to modulate sensitivity to DNA damage by controlling EZH2 (enhancer of zeste homolog 2) turnover. qRT-PCR. 29540468 chr17 66299977 66301977 PRKCA The PRKCA enhancer contains two common genetic variants and 4 haplotypes; human High+Lowthroughput Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects 是 rs9912468 non-cardiac cell E_01_0154 PCR The PRKCA enhancer contains two common genetic variants and 4 haplotypes; Enhancer PRKCA qRT-PCR,qPCR,ChIP,3C RNA-Seq The PRKCA enhancer contains two common genetic variants and 4 haplotypes; The PRKCA enhancer contains two common genetic variants and 4 haplotypes; Immunohistochemical staining The PRKCA enhancer contains two common genetic variants and 4 haplotypes; PCR 29535816 chr4 108044694 108046694 LEF1 The transcription factor lymphoid enhancer factor 1 (LEF1) and the secreted ligand WNT5A, expressed in NPC, were increased in EBV-infected NOK with sustained expression for more than 20 passages after viral loss. Increased LEF1 levels involved four LEF1 variants, and EBV-infected NOK showed a lack of responsiveness to 尾-catenin activation. Although forced expression of WNT5A and LEF1 enhanced the invasiveness of parental NOK, LEF1 knockdown reversed the invasive phenotype of EBV-infected NOK in the presence of WNT5A. human,mouse High+Lowthroughput Epstein-Barr virus stably confers an invasive phenotype to epithelial cells through reprogramming of the WNT pathway 否 gastric cancer cell E_02_0091  RT-qPCR  The transcription factor lymphoid enhancer factor 1 (LEF1) and the secreted ligand WNT5A, expressed in NPC, were increased in EBV-infected NOK with sustained expression for more than 20 passages after viral loss. Increased LEF1 levels involved four LEF1 variants, and EBV-infected NOK showed a lack of responsiveness to 尾-catenin activation. Although forced expression of WNT5A and LEF1 enhanced the invasiveness of parental NOK, LEF1 knockdown reversed the invasive phenotype of EBV-infected NOK in the presence of WNT5A. Enhancer LEF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The transcription factor lymphoid enhancer factor 1 (LEF1) and the secreted ligand WNT5A, expressed in NPC, were increased in EBV-infected NOK with sustained expression for more than 20 passages after viral loss. Increased LEF1 levels involved four LEF1 variants, and EBV-infected NOK showed a lack of responsiveness to 尾-catenin activation. Although forced expression of WNT5A and LEF1 enhanced the invasiveness of parental NOK, LEF1 knockdown reversed the invasive phenotype of EBV-infected NOK in the presence of WNT5A. The transcription factor lymphoid enhancer factor 1 (LEF1) and the secreted ligand WNT5A, expressed in NPC, were increased in EBV-infected NOK with sustained expression for more than 20 passages after viral loss. Increased LEF1 levels involved four LEF1 variants, and EBV-infected NOK showed a lack of responsiveness to 尾-catenin activation. Although forced expression of WNT5A and LEF1 enhanced the invasiveness of parental NOK, LEF1 knockdown reversed the invasive phenotype of EBV-infected NOK in the presence of WNT5A. Immunohistochemical staining The transcription factor lymphoid enhancer factor 1 (LEF1) and the secreted ligand WNT5A, expressed in NPC, were increased in EBV-infected NOK with sustained expression for more than 20 passages after viral loss. Increased LEF1 levels involved four LEF1 variants, and EBV-infected NOK showed a lack of responsiveness to 尾-catenin activation. Although forced expression of WNT5A and LEF1 enhanced the invasiveness of parental NOK, LEF1 knockdown reversed the invasive phenotype of EBV-infected NOK in the presence of WNT5A.  RT-qPCR  29534682 chrX 21370203 21372203 CNKSR2  The multi-functional scaffold protein Connector enhancer of kinase suppressor of ras 2 (CNKSR2) plays a key role in regulating cell proliferation, and differentiation through multiple receptor tyrosine kinase pathways. human, High+Lowthroughput Regulation of CNKSR2 protein stability by the HECT E3 ubiquitin ligase Smurf2, and its role in breast cancer progression 否 E_02_0092 RT-PCR  The multi-functional scaffold protein Connector enhancer of kinase suppressor of ras 2 (CNKSR2) plays a key role in regulating cell proliferation, and differentiation through multiple receptor tyrosine kinase pathways. Enhancer CNKSR2 qRT-PCR,qPCR,ChIP,3C RNA-Seq  The multi-functional scaffold protein Connector enhancer of kinase suppressor of ras 2 (CNKSR2) plays a key role in regulating cell proliferation, and differentiation through multiple receptor tyrosine kinase pathways.  The multi-functional scaffold protein Connector enhancer of kinase suppressor of ras 2 (CNKSR2) plays a key role in regulating cell proliferation, and differentiation through multiple receptor tyrosine kinase pathways. Immunohistochemical staining  The multi-functional scaffold protein Connector enhancer of kinase suppressor of ras 2 (CNKSR2) plays a key role in regulating cell proliferation, and differentiation through multiple receptor tyrosine kinase pathways. RT-PCR 29533787 chr2 132414173 132416173 GPR39 Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). human,mouse High+Lowthroughput Improvement of Duchenne muscular dystrophy phenotype following obestatin treatment. 否 muscle cell E_02_0093 Real ‐ time PCR, Weston blot, immunofluorescence staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Enhancer GPR39 qRT-PCR,qPCR,ChIP,3C RNA-Seq Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). Immunohistochemical staining Methods and results Using a multidisciplinary approach, we characterized the ageing related preproghrelin/GPR39 expression patterns in tibialis anterior (TA) muscles of 4 , 8 , and 18 week old mdx mice (n = 3/group) and established the effects of obestatin administration at this level in 8 week old mdx mice (n = 5/group). real‐time PCR,weston blot,免疫荧光染色 29531042 chr2 42492054 42494054 MTA3 The effect of NO on DNA accessibility is mediated in part by S_x005f_x0002_nitrosylation of nuclear proteins, including MTA3, a subunit of Nucleosome Remodeling Deacetylase (NuRD) complex. human,mouse Epithelial tissues High+Lowthroughput Acute and Cumulative Effects of Haze Fine Particles on Mortality and the Seasonal Characteristics in Beijing, China, 2005-2013: A Time-Stratified Case-Crossover Study 否 endothelial cell E_02_0094 PCR, Western blot, gel electrophoresis The effect of NO on DNA accessibility is mediated in part by S_x005f_x0002_nitrosylation of nuclear proteins, including MTA3, a subunit of Nucleosome Remodeling Deacetylase (NuRD) complex. Enhancer MTA3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The effect of NO on DNA accessibility is mediated in part by S_x005f_x0002_nitrosylation of nuclear proteins, including MTA3, a subunit of Nucleosome Remodeling Deacetylase (NuRD) complex. The effect of NO on DNA accessibility is mediated in part by S_x005f_x0002_nitrosylation of nuclear proteins, including MTA3, a subunit of Nucleosome Remodeling Deacetylase (NuRD) complex. Immunohistochemical staining The effect of NO on DNA accessibility is mediated in part by S_x005f_x0002_nitrosylation of nuclear proteins, including MTA3, a subunit of Nucleosome Remodeling Deacetylase (NuRD) complex. PCR,Western blot,凝胶电泳 29531012 chr6 36591744 36593744 SRSF3 SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. human,mouse kidney High+Lowthroughput The ameliorative effect of Protaetia brevitarsis Larvae in HFD-induced obese mice 否 HEK293T cell E_02_0095 Western blot, gel electrophoresis, clip seq SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. Enhancer SRSF3 qRT-PCR,qPCR,ChIP,3C RNA-Seq SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. Immunohistochemical staining SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes. Western blot,凝胶电泳,CLIP-seq 29530927 chr12 113389472 113391472 SDS Equal amounts (20 _xd835_g) of protein sample were separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, fol_x0002_lowed by being transferred onto a polyvinylidene fuoride (PVDF) membrane. human,mouse High+Lowthroughput Dephosphorylation of HDAC4 by PP2A-Bδ unravels a new role for the HDAC4/MEF2 axis in myoblast fusion 否 mesenchymal stem cell E_02_0096 PCR, Western blot, gel electrophoresis Equal amounts (20 _xd835_g) of protein sample were separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, fol_x0002_lowed by being transferred onto a polyvinylidene fuoride (PVDF) membrane. Enhancer SDS qRT-PCR,qPCR,ChIP,3C RNA-Seq Equal amounts (20 _xd835_g) of protein sample were separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, fol_x0002_lowed by being transferred onto a polyvinylidene fuoride (PVDF) membrane. Equal amounts (20 _xd835_g) of protein sample were separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, fol_x0002_lowed by being transferred onto a polyvinylidene fuoride (PVDF) membrane. Immunohistochemical staining Equal amounts (20 _xd835_g) of protein sample were separated on a sodium dodecyl sulfate (SDS) polyacrylamide gel, fol_x0002_lowed by being transferred onto a polyvinylidene fuoride (PVDF) membrane. PCR,Western blot,凝胶电泳 29530320 chr3 181709448 181711448 SOX2 Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma human lung High+Lowthroughput Synthetically Scalable Poly(ampholyte) Which Dramatically Enhances Cellular Cryopreservation 否 Lung squamous cell E_01_0155 Western blot, chip SEQ, RNA SEQ, flow cytometry, gene knockdown Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma Immunohistochemical staining Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma SOX2 Western blot,ChIP-seq,RNA-seq,流式细胞术,基因敲降 Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma 29529279 chr8 94246645 94248645 GEM In this study, a bacterium (Lactococcus lactis)- like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). human,mouse liver High+Lowthroughput Toll-like receptor 2 stimulation augments esophageal barrier integrity 否 Huh 7 cell E_02_0097 PCR, flow cytometry, gene knockdown, Western blot, gel electrophoresis, immunofluorescence staining In this study, a bacterium (Lactococcus lactis)- like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). Enhancer GEM qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, a bacterium (Lactococcus lactis)- like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). In this study, a bacterium (Lactococcus lactis)- like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). Immunohistochemical staining In this study, a bacterium (Lactococcus lactis)- like particle (BLP) vaccine displaying the MERS-CoV receptor-binding domain (RBD) was developed, and gram-positive enhancer matrix (GEM) particles were used as substrates to externally bind to the MERS-CoV RBD through a protein anchor (PA). PCR,流式细胞术,基因敲降,Western blot,凝胶电泳,免疫荧光染色 29526278 chr21 33540351 33542351 SON Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs). human High+Lowthroughput Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease 否 E_01_0156 RT-PCR Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs). Enhancer SON qRT-PCR,qPCR,ChIP,3C RNA-Seq Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs). Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs). Immunohistochemical staining Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs). RT-PCR 29525407 chr7 148804989 148806989 EZH2  It was shown that O-GlcNAcylation stabilizes histone methyltransferase enhancer of zeste homolog 2 (EZH2), which facilitates the formation of the trimethylation of histone 3 at lysine 27 (H3K27me3) thereby repressing gene expression in human MCF-7 cells [41]. human,mouse  adipose tissue High+Lowthroughput Skeletal muscle O-GlcNAc transferase is important for muscle energy homeostasis and whole-body insulin sensitivity 否 E_02_0098 qPCR  It was shown that O-GlcNAcylation stabilizes histone methyltransferase enhancer of zeste homolog 2 (EZH2), which facilitates the formation of the trimethylation of histone 3 at lysine 27 (H3K27me3) thereby repressing gene expression in human MCF-7 cells [41]. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq  It was shown that O-GlcNAcylation stabilizes histone methyltransferase enhancer of zeste homolog 2 (EZH2), which facilitates the formation of the trimethylation of histone 3 at lysine 27 (H3K27me3) thereby repressing gene expression in human MCF-7 cells [41].  It was shown that O-GlcNAcylation stabilizes histone methyltransferase enhancer of zeste homolog 2 (EZH2), which facilitates the formation of the trimethylation of histone 3 at lysine 27 (H3K27me3) thereby repressing gene expression in human MCF-7 cells [41]. Immunohistochemical staining  It was shown that O-GlcNAcylation stabilizes histone methyltransferase enhancer of zeste homolog 2 (EZH2), which facilitates the formation of the trimethylation of histone 3 at lysine 27 (H3K27me3) thereby repressing gene expression in human MCF-7 cells [41]. qPCR 29524130 chr14 21495467 21497467 METTL3 The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. human High+Lowthroughput Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development 否 Bone marrow stem cell E_01_0157 flow cytometry ,Real-time quantitative PCR , staining ,Protein extraction ,Western blot ,Cell transfection ,Immunofluorescence assay ,Quantitative analysis ,Chromatin immunoprecipitation assay ,Luciferase reporter assay The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. Enhancer METTL3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. Immunohistochemical staining The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. flow cytometry ,Real-time quantitative PCR , staining ,Protein extraction ,Western blot ,Cell transfection ,Immunofluorescence assay ,Quantitative analysis ,Chromatin immunoprecipitation assay ,Luciferase reporter assay 29523836 chr2 226728284 226730284 IRS1 Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). human High+Lowthroughput Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis 否 HeLa cell E_01_0158 Nuclear magnetic resonance (NMR) spectroscopy analysis ,RNA extraction and real-time PCR ,Western blot analysis ,Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Enhancer IRS1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Immunohistochemical staining Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). Nuclear magnetic resonance (NMR) spectroscopy analysis ,RNA extraction and real-time PCR ,Western blot analysis ,Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function 29521509 chr7 116522460 116524460 CAV1 CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. mouse lymphoid tissue High+Lowthroughput Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene 否 Lymphoblast E_02_0099 Immunoblotting, fluorescent quantitative PCR (RT-PCR), immunocytochemistry, live cell imaging CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. Enhancer CAV1 qRT-PCR,qPCR,ChIP,3C RNA-Seq CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. Immunohistochemical staining CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. 免疫印迹,荧光定量 PCR(RT-PCR),免疫细胞化学,活细胞成像 29515369 chr1 145668268 145670268 PDZK1  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  human,fish High+Lowthroughput A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression 否 rs1967017,rs1471633 hyperuricemia HepG2 cell E_02_0100 Quantitative PCR, immunoblot analysis, chip PCR, statistical analysis, Weston blot  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Enhancer PDZK1 qRT-PCR,qPCR,ChIP,3C RNA-Seq  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.   siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Immunohistochemical staining  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Quantitative PCR,Immunoblot analysis, ChIP-PCR,统计分析,weston blot 29515369 chr20 44353272 44355272 HNF4A  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  human,fish High+Lowthroughput A non-coding genetic variant maximally associated with serum urate levels is functionally linked to HNF4A-dependent PDZK1 expression 否 rs1967017,rs1471633 hyperuricemia HepG2 cell E_02_0100 Quantitative PCR, immunoblot analysis, chip PCR, statistical analysis, Weston blot  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Enhancer HNF4A qRT-PCR,qPCR,ChIP,3C RNA-Seq  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.   siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Immunohistochemical staining  siRNA depletion of HNF4A reduced endogenous PDZK1 expression in HepG2 cells.  Quantitative PCR,Immunoblot analysis, ChIP-PCR,统计分析,weston blot 29514910 chr11 73215408 73217408 P2RY2 P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer.  human, High+Lowthroughput Enhancer RNA - P2RY2e induced by estrogen promotes malignant behaviors of bladder cancer 否 Breast, bladder, stomach, pancreas, prostate, lung T24 cell E_02_0101 RT qPCR, flow cytometry, ELISA, statistical analysis P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer.  Enhancer P2RY2 qRT-PCR,qPCR,ChIP,3C RNA-Seq P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer.  P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer.  Immunohistochemical staining P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer.  RT-qPCR,流式细胞术,ELISA,统计分析 29514101 chrX 67541320 67543320 AR  For example, one human AR is an enhancer with putative roles in the evolution of the human thumb (Prabhakar et al., 2008).  human,mouse High+Lowthroughput Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance 否 E_02_0102 DNase-seq  For example, one human AR is an enhancer with putative roles in the evolution of the human thumb (Prabhakar et al., 2008).  Enhancer AR qRT-PCR,qPCR,ChIP,3C RNA-Seq  For example, one human AR is an enhancer with putative roles in the evolution of the human thumb (Prabhakar et al., 2008).   For example, one human AR is an enhancer with putative roles in the evolution of the human thumb (Prabhakar et al., 2008).  Immunohistochemical staining  For example, one human AR is an enhancer with putative roles in the evolution of the human thumb (Prabhakar et al., 2008).  DNase-seq 29899112 chr6 47504499 47506499 Ezh2 Hence, genetic loss of Ezh2 in mouse pre-osteoblasts inhibits osteogenesis in part by inducing cell cycle changes. Our results suggest that Ezh2 serves a bifunctional role during bone formation by suppressing osteogenic lineage commitment while simultaneously facilitating proliferative expansion of osteoprogenitor cells. mouse Nervous tissue High+Lowthroughput Enhancer of zeste homolog 2 (Ezh2) controls bone formation and cell cycle progression during osteogenesis in mice 否 mesenchymal stem cell of the bone marrow E_02_0103 "RNA-Seq,Western blot,staining,RT-qPCR,MTS assays,Flow cytometric analysis,Ex vivo assays,Histology,histomorphometric analysis,Micro-computed tomography analysis,Alkaline Phosphatase and Alizarin Red Staining,Hoechst staining," Hence, genetic loss of Ezh2 in mouse pre-osteoblasts inhibits osteogenesis in part by inducing cell cycle changes. Our results suggest that Ezh2 serves a bifunctional role during bone formation by suppressing osteogenic lineage commitment while simultaneously facilitating proliferative expansion of osteoprogenitor cells. Enhancer Ezh2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Hence, genetic loss of Ezh2 in mouse pre-osteoblasts inhibits osteogenesis in part by inducing cell cycle changes. Our results suggest that Ezh2 serves a bifunctional role during bone formation by suppressing osteogenic lineage commitment while simultaneously facilitating proliferative expansion of osteoprogenitor cells. Hence, genetic loss of Ezh2 in mouse pre-osteoblasts inhibits osteogenesis in part by inducing cell cycle changes. Our results suggest that Ezh2 serves a bifunctional role during bone formation by suppressing osteogenic lineage commitment while simultaneously facilitating proliferative expansion of osteoprogenitor cells. Immunohistochemical staining Hence, genetic loss of Ezh2 in mouse pre-osteoblasts inhibits osteogenesis in part by inducing cell cycle changes. Our results suggest that Ezh2 serves a bifunctional role during bone formation by suppressing osteogenic lineage commitment while simultaneously facilitating proliferative expansion of osteoprogenitor cells. "RNA-Seq,Western blot,staining,RT-qPCR,MTS assays,Flow cytometric analysis,Ex vivo assays,Histology,histomorphometric analysis,Micro-computed tomography analysis,Alkaline Phosphatase and Alizarin Red Staining,Hoechst staining," 29898989 chr3 36999364 37001216 CTCF A CTCF-bound region within the MLH1-35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. human Connective tissue Low throughput Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells 否 -- Lynch Syndrome E_02_0104 ChIP-qPCR,3C,Luciferase Reporter Assay,CRISPR/Cas9 We provide the first description of an enhancer for the MLH1 gene. This -35kb enhancer was CTCF-bound, and disruption of the consensus binding site within the enhancer significantly impairs MLH1 expression in SW620 colorectal carcinoma cells. Enhancer MLH1 3C,CRISPR/Cas9 ChIP-qPCR,Luciferase Reporter Assay We deleted a DNA fragment corresponding to the -35kb region from SW620 cells,showed that the -35kb region functions as an MLH1 Enhancer in SW620 colorectal cells. COCA2,FCC2,HNPCC,HNPCC2,hMLH1 -- -- -- CTCF MRD21 CRISPR/Cas9 To evaluate the impact on endogenous MLH1 expression, we next deleted a region containing the CTCF binding motif in SW620 and K562 cells using CRISPR-Cas9 (Fig 3A, ΔCTCF). Similar to deletion of the entire Enhancer, we noted significant reduction in MLH1 expression in SW620 but not in K562 cells. -- -- 29898989 chr3 36999364 37001216 MLH1 A CTCF-bound region within the MLH1-35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. human Connective tissue Low throughput Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells 否 -- Lynch Syndrome E_02_0104 ChIP-qPCR,3C,Luciferase Reporter Assay,CRISPR/Cas9 We provide the first description of an enhancer for the MLH1 gene. This -35kb enhancer was CTCF-bound, and disruption of the consensus binding site within the enhancer significantly impairs MLH1 expression in SW620 colorectal carcinoma cells. Enhancer MLH1 3C,CRISPR/Cas9 ChIP-qPCR,Luciferase Reporter Assay We deleted a DNA fragment corresponding to the -35kb region from SW620 cells,showed that the -35kb region functions as an MLH1 Enhancer in SW620 colorectal cells. COCA2,FCC2,HNPCC,HNPCC2,hMLH1 -- -- -- CTCF MRD21 CRISPR/Cas9 To evaluate the impact on endogenous MLH1 expression, we next deleted a region containing the CTCF binding motif in SW620 and K562 cells using CRISPR-Cas9 (Fig 3A, ΔCTCF). Similar to deletion of the entire Enhancer, we noted significant reduction in MLH1 expression in SW620 but not in K562 cells. -- -- 29510148 chr14 30871809 30873809 COCH COCH is the most abundantly expressed gene in the cochlea. human,mouse High+Lowthroughput Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss 否 MDCK cell E_02_0105 RT-PCR,PCR COCH is the most abundantly expressed gene in the cochlea. Enhancer COCH qRT-PCR,qPCR,ChIP,3C RNA-Seq COCH is the most abundantly expressed gene in the cochlea. COCH is the most abundantly expressed gene in the cochlea. Immunohistochemical staining COCH is the most abundantly expressed gene in the cochlea. RT-PCR,PCR 29503092 chr14 100235564 100237564 YY1  We sorted YY1 peaks by H3K4me1 and H3K4me3 to distinguish enhancers from promoters, and observed that both enhancer and promoter regions enriched for YY1 were co-bound by SMARCA4 and OSN (Figure 5D).  human,  adult tissue High+Lowthroughput YY1 Positively Regulates Transcription by Targeting Promoters and Super-Enhancers through the BAF Complex in Embryonic Stem Cells 否 pre-B cell E_02_0106 qPCR  We sorted YY1 peaks by H3K4me1 and H3K4me3 to distinguish enhancers from promoters, and observed that both enhancer and promoter regions enriched for YY1 were co-bound by SMARCA4 and OSN (Figure 5D).  Enhancer YY1 qRT-PCR,qPCR,ChIP,3C RNA-Seq  We sorted YY1 peaks by H3K4me1 and H3K4me3 to distinguish enhancers from promoters, and observed that both enhancer and promoter regions enriched for YY1 were co-bound by SMARCA4 and OSN (Figure 5D).   We sorted YY1 peaks by H3K4me1 and H3K4me3 to distinguish enhancers from promoters, and observed that both enhancer and promoter regions enriched for YY1 were co-bound by SMARCA4 and OSN (Figure 5D).  Immunohistochemical staining  We sorted YY1 peaks by H3K4me1 and H3K4me3 to distinguish enhancers from promoters, and observed that both enhancer and promoter regions enriched for YY1 were co-bound by SMARCA4 and OSN (Figure 5D).  qPCR 31223056 chr16 71843198 71845198 IST1 we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation human connective tissue High+Lowthroughput MAPT/Tau accumulation represses autophagy flux by disrupting IST1-regulated ESCRT-III complex formation: a vicious cycle in Alzheimer neurodegeneration 否 macrophage E_01_0159 PCR we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation Enhancer IST1 qRT-PCR,qPCR,ChIP,3C RNA-Seq we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation Immunohistochemical staining we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation PCR 31221974 chr7 148804781 148806781 EZH2 We have previously shown that the Enhancer-of-zeste-like protein Ezl1 is essential for programmed DNA elimination and viability of the sexual progeny 25 . Here, we provide evidence that, Paramecium Ezl1, which exhibits significant sequence and structural similarities with human EZH2, displays distinct enzy- matic properties. mouse connective tissue High+Lowthroughput The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium 否 embryonic stem cell E_02_0107 PCR We have previously shown that the Enhancer-of-zeste-like protein Ezl1 is essential for programmed DNA elimination and viability of the sexual progeny 25 . Here, we provide evidence that, Paramecium Ezl1, which exhibits significant sequence and structural similarities with human EZH2, displays distinct enzy- matic properties. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We have previously shown that the Enhancer-of-zeste-like protein Ezl1 is essential for programmed DNA elimination and viability of the sexual progeny 25 . Here, we provide evidence that, Paramecium Ezl1, which exhibits significant sequence and structural similarities with human EZH2, displays distinct enzy- matic properties. We have previously shown that the Enhancer-of-zeste-like protein Ezl1 is essential for programmed DNA elimination and viability of the sexual progeny 25 . Here, we provide evidence that, Paramecium Ezl1, which exhibits significant sequence and structural similarities with human EZH2, displays distinct enzy- matic properties. Immunohistochemical staining We have previously shown that the Enhancer-of-zeste-like protein Ezl1 is essential for programmed DNA elimination and viability of the sexual progeny 25 . Here, we provide evidence that, Paramecium Ezl1, which exhibits significant sequence and structural similarities with human EZH2, displays distinct enzy- matic properties. PCR 31219650 chr7 44101654 44103654 AEBP1 In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. human Epithelial tissues High+Lowthroughput AEBP1, a prognostic indicator, promotes colon adenocarcinoma cell growth and metastasis through the NF-κB pathway 否 colon cancer cell E_01_0160 PCR In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. Enhancer AEBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. Immunohistochemical staining In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. PCR 31219209 chr7 148805028 148807028 EZH2 And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l human connective tissue High+Lowthroughput Long noncoding RNA OIP5-AS1 aggravates cell proliferation, migration in gastric cancer by epigenetically silencing NLRP6 expression via binding EZH2 否 Colon cancer gastric cancer cell E_01_0161 PCR And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l Immunohistochemical staining And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l EZH2 PCR And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l 31217031 chr1 26690366 26692366 ARID1A We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. mouse connective tissue High+Lowthroughput ARID1A facilitates KRAS signaling-regulated?enhancer activity in an AP1-dependent manner in colorectal cancer cells 否 tumor cell E_02_0108 PCR We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Enhancer ARID1A qRT-PCR,qPCR,ChIP,3C RNA-Seq We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Immunohistochemical staining We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. PCR 31216773 chr13 27958003 27960003 CDX2 It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. human Colon tissue High+Lowthroughput HNF4α and CDX2 Regulate Intestinal YAP1 Promoter Activity 否 intestinal cell E_01_0162 PCR It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. Immunohistochemical staining It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. CDX2 PCR It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells. 31216559 chr12 49973763 49975763 RACGAP1 Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. human connective tissue High+Lowthroughput Rac GTPase-Activating Protein 1 (RACGAP1) as an Oncogenic Enhancer in Esophageal Carcinoma 否 cancer cell E_01_0163 PCR Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. Immunohistochemical staining Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. RACGAP1 PCR Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 31216030 chr19 4171371 4173371 SIRT6 SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress human connective tissue High+Lowthroughput SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170 否 stem cell E_01_0164 PCR SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress Enhancer SIRT6 qRT-PCR,qPCR,ChIP,3C RNA-Seq SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress Immunohistochemical staining SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress PCR 31215771 chr20 56626718 56628718 TFAP2C We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. human connective tissue High+Lowthroughput Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer 否 mammary cancer breast cancer cell E_01_0165 PCR We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. Immunohistochemical staining We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. TFAP2C PCR We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 31213123 chr7 148804377 148806377 EZH2 Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC. human connective tissue High+Lowthroughput Diosgenin exhibits tumor suppressive function via down-regulation of EZH2 in pancreatic cancer cells 否 tumour tumor cell E_01_0166 PCR Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC. Immunohistochemical staining Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC. EZH2 PCR Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC. 31205561 chr7 148804432 148806432 EZH2 Enhancer of zeste homolog 2 (EZH2) and Bcl-2 gene rearrangement or protein upregulation played pivotal roles in the carcinogenesis of various malignancies including lymphomas. mouse connective tissue High+Lowthroughput EZH2/Bcl-2 Coexpression Predicts Worse Survival in Diffuse Large B-cell Lymphomas and Demonstrates Poor Efficacy to Rituximab in Localized Lesions 否 tumour tumor cell E_02_0109 PCR Enhancer of zeste homolog 2 (EZH2) and Bcl-2 gene rearrangement or protein upregulation played pivotal roles in the carcinogenesis of various malignancies including lymphomas. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homolog 2 (EZH2) and Bcl-2 gene rearrangement or protein upregulation played pivotal roles in the carcinogenesis of various malignancies including lymphomas. Enhancer of zeste homolog 2 (EZH2) and Bcl-2 gene rearrangement or protein upregulation played pivotal roles in the carcinogenesis of various malignancies including lymphomas. Immunohistochemical staining Enhancer of zeste homolog 2 (EZH2) and Bcl-2 gene rearrangement or protein upregulation played pivotal roles in the carcinogenesis of various malignancies including lymphomas. PCR 31202798 chr7 148804013 148806013 EZH2 Enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, has been recognized to play a pivotal role in regulating the immune response in various diseases. mouse connective tissue High+Lowthroughput EZH2 inhibitor DZNep modulates microglial activation and protects against ischaemic brain injury after experimental stroke 否 microglial cell E_02_0110 PCR Enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, has been recognized to play a pivotal role in regulating the immune response in various diseases. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, has been recognized to play a pivotal role in regulating the immune response in various diseases. Enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, has been recognized to play a pivotal role in regulating the immune response in various diseases. Immunohistochemical staining Enhancer of zeste homolog-2 (EZH2), a histone methyltransferase, has been recognized to play a pivotal role in regulating the immune response in various diseases. PCR 31201420 chr7 148804563 148806563 EZH2 In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy and cystic endometrial hyperplasia, indicating a critical role in uterine development and function mouse connective tissue High+Lowthroughput The histone methyltransferase EZH2 is required for normal uterine development and function in mice? 否 epithelial cell of uterus E_02_0111 PCR In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy and cystic endometrial hyperplasia, indicating a critical role in uterine development and function Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy and cystic endometrial hyperplasia, indicating a critical role in uterine development and function In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy and cystic endometrial hyperplasia, indicating a critical role in uterine development and function Immunohistochemical staining In summary, uterine EZH2 expression is developmentally and hormonally regulated, and its loss causes aberrant uterine epithelial proliferation, uterine hypertrophy and cystic endometrial hyperplasia, indicating a critical role in uterine development and function PCR 31189106 chrX 137563628 137565628 ZIC3 Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation human connective tissue High+Lowthroughput ZIC3 Controls the Transition from Naive to Primed Pluripotency 否 embryonic stem cell E_01_0167 PCR Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation Enhancer ZIC3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation Immunohistochemical staining Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation PCR 31186776 chr1 205594870 205596870 ELK4 In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets. human connective tissue High+Lowthroughput ceRNA network analysis reveals prognostic markers for glioblastoma 否 cancer cancer cell E_01_0168 PCR In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets. Immunohistochemical staining In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets. ELK4 PCR In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets. 31186707 chr20 22578327 22580327 FOXA2 Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T human connective tissue High+Lowthroughput Long non-coding RNA-neighboring enhancer of FOXA2 inhibits the migration and invasion of small cell lung carcinoma cells by downregulating transforming growth factor-β1 否 lung cancer Lung cancer cell E_01_0169 PCR Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T Immunohistochemical staining Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T FOXA2 PCR Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T 31182783 chr6 31161443 31163443 POU5F1 OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6 human connective tissue High+Lowthroughput lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells 否 stem cell E_01_0170 PCR OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6 Immunohistochemical staining OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6 POU5F1 PCR OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6 31176714 chr18 63868870 63870870 SERPINB2 However, the further analysis demonstrated that the expression of the enhancer RNA encoded by the region of DNA 20 kbp upstream from the SERPINB2 gene was AhR-dependent mouse connective tissue High+Lowthroughput Expression of Serpin Peptidase Inhibitor B2 (SERPINB2) is regulated by Aryl hydrocarbon receptor (AhR) 否 tumour tumor cell E_02_0112 PCR However, the further analysis demonstrated that the expression of the enhancer RNA encoded by the region of DNA 20 kbp upstream from the SERPINB2 gene was AhR-dependent Enhancer SERPINB2 qRT-PCR,qPCR,ChIP,3C RNA-Seq However, the further analysis demonstrated that the expression of the enhancer RNA encoded by the region of DNA 20 kbp upstream from the SERPINB2 gene was AhR-dependent However, the further analysis demonstrated that the expression of the enhancer RNA encoded by the region of DNA 20 kbp upstream from the SERPINB2 gene was AhR-dependent Immunohistochemical staining However, the further analysis demonstrated that the expression of the enhancer RNA encoded by the region of DNA 20 kbp upstream from the SERPINB2 gene was AhR-dependent PCR 31174563 chr11 65495199 65497199 MALAT1 Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. human connective tissue High+Lowthroughput Long noncoding RNA MALAT1 potentiates growth and inhibits senescence by antagonizing ABI3BP in gallbladder cancer cells 否 Gallbladder cancer Gallbladder cancer cell E_01_0171 PCR Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. Immunohistochemical staining Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. MALAT1 PCR Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 31173852 chr5 132437801 132439801 IRF1 In conclusion, the interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma progression by promoting interferon response through a positive regulatory loop with IRF1 mouse connective tissue High+Lowthroughput Interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma by promoting interferon response 否 ESCC Esophageal squamous cell carcinoma cell E_02_0113 PCR In conclusion, the interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma progression by promoting interferon response through a positive regulatory loop with IRF1 Enhancer IRF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In conclusion, the interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma progression by promoting interferon response through a positive regulatory loop with IRF1 In conclusion, the interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma progression by promoting interferon response through a positive regulatory loop with IRF1 Immunohistochemical staining In conclusion, the interferon-inducible lncRNA IRF1-AS represses esophageal squamous cell carcinoma progression by promoting interferon response through a positive regulatory loop with IRF1 PCR 31171769 chr7 148803892 148805892 EZH2 We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. human connective tissue High+Lowthroughput Silencing of microRNA-708 promotes cell growth and epithelial-to-mesenchymal transition by activating the SPHK2/AKT/β-catenin pathway in glioma 否 Gliomas Glioma cell E_01_0172 PCR We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. Immunohistochemical staining We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. EZH2 PCR We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 31164154 chr4 105142775 105144775 TET2 Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2. mouse connective tissue High+Lowthroughput Phosphorylation of TET2 by AMPK is indispensable in myogenic differentiation 否 myocyte E_02_0114 PCR Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2. Enhancer TET2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2. Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2. Immunohistochemical staining Together, our data demonstrated that AMPK is a critical regulator of myogenesis, partly through phosphorylating TET2. PCR 31164150 chr16 67559426 67561426 CTCF Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity human epithelial cells High+Lowthroughput p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes 否 glial cell E_01_0173 PCR Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity Immunohistochemical staining Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity CTCF PCR Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity 31162630 chr7 148804276 148806276 EZH2 EZH2 inhibition might be a potential therapeutic target for restenosis. human Myotome High+Lowthroughput Inhibition of polycomb repressor complex 2 ameliorates neointimal hyperplasia by suppressing trimethylation of H3K27 in vascular smooth muscle cells 否 smooth muscle cell E_01_0174 PCR EZH2 inhibition might be a potential therapeutic target for restenosis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq EZH2 inhibition might be a potential therapeutic target for restenosis. Immunohistochemical staining EZH2 inhibition might be a potential therapeutic target for restenosis. EZH2 PCR EZH2 inhibition might be a potential therapeutic target for restenosis. 31160593 chr7 148804085 148806085 EZH2 We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a human connective tissue High+Lowthroughput Targeting EZH2 histone methyltransferase activity alleviates experimental intestinal inflammation 否 Colon cancer colon cancer cell E_01_0175 PCR We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a Immunohistochemical staining We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a EZH2 PCR We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a 31155838 chr11 69767717 69769717 FGF4 Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly human connective tissue High+Lowthroughput Critical role of the fibroblast growth factor signalling pathway in Ewing's sarcoma octamer-binding transcription factor 4-mediated cell proliferation and tumorigenesis 否 tumour tumor cell E_01_0176 PCR Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly Enhancer FGF4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly Immunohistochemical staining Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly PCR 31141090 chr19 33297251 33299251 CEBPA Moreover, this translocation is detected in 50% of T-ALL patients with gamma/delta T cell receptor rearrangement, frequently associated with low expression of transcription factor CCAAT/enhancer-binding protein alpha (CEBPA). mouse connective tissue High+Lowthroughput CCAAT/enhancer-binding protein alpha (CEBPA) gene haploinsufficiency does not alter hematopoiesis or induce leukemia in Lck-CALM/AF10 transgenic mice 否 hematopoietic stem cell E_02_0115 PCR Moreover, this translocation is detected in 50% of T-ALL patients with gamma/delta T cell receptor rearrangement, frequently associated with low expression of transcription factor CCAAT/enhancer-binding protein alpha (CEBPA). Enhancer CEBPA qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, this translocation is detected in 50% of T-ALL patients with gamma/delta T cell receptor rearrangement, frequently associated with low expression of transcription factor CCAAT/enhancer-binding protein alpha (CEBPA). Moreover, this translocation is detected in 50% of T-ALL patients with gamma/delta T cell receptor rearrangement, frequently associated with low expression of transcription factor CCAAT/enhancer-binding protein alpha (CEBPA). Immunohistochemical staining Moreover, this translocation is detected in 50% of T-ALL patients with gamma/delta T cell receptor rearrangement, frequently associated with low expression of transcription factor CCAAT/enhancer-binding protein alpha (CEBPA). PCR 31081034 chr18 55219304 55221304 TCF4 The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder. human connective tissue High+Lowthroughput Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine 否 neural cell E_01_0177 PCR The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder. Immunohistochemical staining The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder. TCF4 PCR The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder. 30995827 chr20 22578226 22580226 FOXA2 The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC). human connective tissue High+Lowthroughput Transcriptional Regulation Factors of the Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 (SLC25A13): USF1 as Basal Factor and FOXA2 as Activator in Liver Cells 否 cancer cell E_01_0178 PCR The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC). Immunohistochemical staining The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC). FOXA2 PCR The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC). 31127282 chr16 67559749 67561749 CTCF CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13). human connective tissue High+Lowthroughput Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping 否 E_01_0179 PCR CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13). Immunohistochemical staining CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13). CTCF PCR CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13). 31064204 chr19 33297418 33299418 CEBPA In this study, the coding domain sequences (CDS) of pigeon C/EBP-α and βwere cloned, mouse connective tissue High+Lowthroughput Molecular cloning, characterisation, and expression patterns of pigeon CCAAT/enhancer binding protein-α and -β genes 否 cancer cancer cell E_02_0116 PCR In this study, the coding domain sequences (CDS) of pigeon C/EBP-α and βwere cloned, Enhancer CEBPA qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, the coding domain sequences (CDS) of pigeon C/EBP-α and βwere cloned, In this study, the coding domain sequences (CDS) of pigeon C/EBP-α and βwere cloned, Immunohistochemical staining In this study, the coding domain sequences (CDS) of pigeon C/EBP-α and βwere cloned, PCR 31053723 chr11 2126891 2128891 IGF2 This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. human connective tissue High+Lowthroughput Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis 是 neural cell E_01_0180 PCR This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. Enhancer IGF2 qRT-PCR,qPCR,ChIP,3C RNA-Seq This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. Immunohistochemical staining This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. PCR 31053176 chrX 153441659 153443659 TREX2 The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. human connective tissue High+Lowthroughput DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer 是 laryngeal carcinoma cell E_01_0181 PCR The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. Enhancer TREX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. Immunohistochemical staining The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. PCR 31721105 chr12 117450290 117452290 KSR2 In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. human liver High+Lowthroughput Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii 否 无 liver cancer HCC cell E_01_0182 In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. Enhancer KSR2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. Immunohistochemical staining In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii. 31719045 chr13 63653269 63655269 Ptch1 We confirmed that, in comparison to wild-type (WT) littermates, SHH signalling was significantly decreased in the developing tongue of ShhMFCS4/− mice by E11.5, as demonstrated by reduced Shh and patched 1 (Ptch1) expression (Fig. 1A-D) and consistent with the known period of MFCS4 activity (Sagai et al., 2009). human,mouse Musculature High+Lowthroughput Temporospatial sonic hedgehog signalling is essential for neural crest-dependent patterning of the intrinsic tongue musculature 否 无 muscle precursor cell E_02_0117 PCR、Western blot We confirmed that, in comparison to wild-type (WT) littermates, SHH signalling was significantly decreased in the developing tongue of ShhMFCS4/− mice by E11.5, as demonstrated by reduced Shh and patched 1 (Ptch1) expression (Fig. 1A-D) and consistent with the known period of MFCS4 activity (Sagai et al., 2009). Enhancer Ptch1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We confirmed that, in comparison to wild-type (WT) littermates, SHH signalling was significantly decreased in the developing tongue of ShhMFCS4/− mice by E11.5, as demonstrated by reduced Shh and patched 1 (Ptch1) expression (Fig. 1A-D) and consistent with the known period of MFCS4 activity (Sagai et al., 2009). We confirmed that, in comparison to wild-type (WT) littermates, SHH signalling was significantly decreased in the developing tongue of ShhMFCS4/− mice by E11.5, as demonstrated by reduced Shh and patched 1 (Ptch1) expression (Fig. 1A-D) and consistent with the known period of MFCS4 activity (Sagai et al., 2009). Immunohistochemical staining We confirmed that, in comparison to wild-type (WT) littermates, SHH signalling was significantly decreased in the developing tongue of ShhMFCS4/− mice by E11.5, as demonstrated by reduced Shh and patched 1 (Ptch1) expression (Fig. 1A-D) and consistent with the known period of MFCS4 activity (Sagai et al., 2009). PCR、Western blot 31718595 chr7 148804304 148806304 EZH2 Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma. human connective tissue High+Lowthroughput EZH2 upregulation by ERα induces proliferation and migration of papillary thyroid carcinoma 否 无 cancer Cancer Stem Cell E_01_0183 PCR, Western blot, immunofluorescence staining Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma. Immunohistochemical staining Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma. EZH2 PCR、Western blot、免疫荧光染色 Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma. 31718447 chr9 117701356 117703356 TLR4 Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD2) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. human,mouse connective tissue High+Lowthroughput Sphingomyelin Synthase 2 Inhibition Ameliorates Cerebral Ischemic Reperfusion Injury Through Reducing the Recruitment of Toll-Like Receptor 4 to Lipid Rafts 否 无 cerebral ischemia B cell E_02_0118 PCR、Western blot Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD2) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Enhancer TLR4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD2) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD2) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Immunohistochemical staining Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD2) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. PCR、Western blot 31718447 chr1 223106431 223108431 TLR5 Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD3) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. human,mouse brain High+Lowthroughput Sphingomyelin Synthase 2 Inhibition Ameliorates Cerebral Ischemic Reperfusion Injury Through Reducing the Recruitment of Toll-Like Receptor 5 to Lipid Rafts 否 无 cerebral ischemia brain cell  E_02_0118 PCR、Western blot Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD3) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Enhancer TLR5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD3) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD3) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. Immunohistochemical staining Activation of the TLR4 signaling pathway is initiated by the binding of its ligands to TLR4, causing TLR4 to relocate to lipid rafts, and then forming TLR4/myeloid differentiation factor 2 (MD3) complex in lipid rafts, leading to activation of nuclear factorkappa-light-chain-enhancer of activated B cells (NF-jB)and overproduction of proinflammatory cytokines. PCR、Western blot 31718444 chr3 43283601 43285601 SNRK The SNRK (sucrose-nonfermenting–related kinase) enzyme is critical for cardiac function. human,mouse connective tissue High+Lowthroughput Cardiomyocyte-Specific Snrk Prevents Inflammation in the Heart 否 无 cancer B cell E_02_0119 PCR、Western blot The SNRK (sucrose-nonfermenting–related kinase) enzyme is critical for cardiac function. Enhancer SNRK qRT-PCR,qPCR,ChIP,3C RNA-Seq The SNRK (sucrose-nonfermenting–related kinase) enzyme is critical for cardiac function. The SNRK (sucrose-nonfermenting–related kinase) enzyme is critical for cardiac function. Immunohistochemical staining The SNRK (sucrose-nonfermenting–related kinase) enzyme is critical for cardiac function. PCR、Western blot 31714653 chrX 123856867 123858867 XIAP "In addition, expression of phospho-ERK (p-ERK), NF-κB p65 (Ser536), and tumor progression-associated proteins, such as matrix metallopeptidase 9 (MMP-9), vascular endothelial growth factor (VEGF), X-linked inhibitor of apoptosis protein (XIAP), and CyclinD1 were all significantly decreased by magnolol." human,mouse connective tissue High+Lowthroughput Apoptosis induction and ERK/NF-κB inactivation are associated with magnolol-inhibited tumor progression in hepatocellular carcinoma in vivo 否 无 liver cancer B cell E_02_0120 PCR "In addition, expression of phospho-ERK (p-ERK), NF-κB p65 (Ser536), and tumor progression-associated proteins, such as matrix metallopeptidase 9 (MMP-9), vascular endothelial growth factor (VEGF), X-linked inhibitor of apoptosis protein (XIAP), and CyclinD1 were all significantly decreased by magnolol." Enhancer XIAP qRT-PCR,qPCR,ChIP,3C RNA-Seq "In addition, expression of phospho-ERK (p-ERK), NF-κB p65 (Ser536), and tumor progression-associated proteins, such as matrix metallopeptidase 9 (MMP-9), vascular endothelial growth factor (VEGF), X-linked inhibitor of apoptosis protein (XIAP), and CyclinD1 were all significantly decreased by magnolol." "In addition, expression of phospho-ERK (p-ERK), NF-κB p65 (Ser536), and tumor progression-associated proteins, such as matrix metallopeptidase 9 (MMP-9), vascular endothelial growth factor (VEGF), X-linked inhibitor of apoptosis protein (XIAP), and CyclinD1 were all significantly decreased by magnolol." Immunohistochemical staining "In addition, expression of phospho-ERK (p-ERK), NF-κB p65 (Ser536), and tumor progression-associated proteins, such as matrix metallopeptidase 9 (MMP-9), vascular endothelial growth factor (VEGF), X-linked inhibitor of apoptosis protein (XIAP), and CyclinD1 were all significantly decreased by magnolol." PCR 31713877 chr17 27753488 27755488 NOS2 Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS2 and TNF expression in diabetic mice. human,mouse connective tissue High+Lowthroughput Comparative effectiveness of different antiplatelet agents at reducing TNF-driven inflammatory responses in a mouse model 否 无 Ischemic disease immune cell E_02_0121 PCR、Western blot Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS2 and TNF expression in diabetic mice. Enhancer NOS2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS2 and TNF expression in diabetic mice. Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS2 and TNF expression in diabetic mice. Immunohistochemical staining Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS2 and TNF expression in diabetic mice. PCR、Western blot 31713877 chr7 150988213 150990213 NOS3 Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS3 and TNF expression in diabetic mice. human,mouse Epithelial tissues High+Lowthroughput Comparative effectiveness of different antiplatelet agents at reducing TNF-driven inflammatory responses in a mouse model 否 无 Ischemic disease blood vessel endothelial cell E_02_0121 PCR、Western blot Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS3 and TNF expression in diabetic mice. Enhancer NOS3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS3 and TNF expression in diabetic mice. Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS3 and TNF expression in diabetic mice. Immunohistochemical staining Clopidogrel reduced serum TNF and IL‐1β release in rats with coronary microembolization and experimental LPS-induced mouse model (25, 26). Sarpogrelate decreased immune cell infiltration and NOS3 and TNF expression in diabetic mice. PCR、Western blot 31712448 chr11 108808163 108810163 Axin2 In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells human,mouse Epithelial tissues High+Lowthroughput Hepatocyte nuclear factor-1β regulates Wnt signaling through genome-wide competition with β-catenin/lymphoid enhancer binding factor 否 无 Cystic kidney disease epithelial cell E_02_0122 In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells Enhancer Axin2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells Immunohistochemical staining In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells 31712448 chr16 44910716 44912716 Ccdc80 In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells human,mouse Epithelial tissues High+Lowthroughput Hepatocyte nuclear factor-1β regulates Wnt signaling through genome-wide competition with β-catenin/lymphoid enhancer binding factor 否 无 Cystic kidney disease epithelial cell E_02_0122 In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells Enhancer Ccdc80 qRT-PCR,qPCR,ChIP,3C RNA-Seq In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells Immunohistochemical staining In contrast, the expression of Axin2 and Ccdc80 was strongly up-regulated in Wnt3a-treated HNF-1β mutant cells compared to wild-type cells 31712269 chr3 52218227 52220227 TLR9 pylori-induced NF-κB activation and IL-8 secretion are attributed to T4SS-dependent delivery of lipopolysaccharide metabolites and peptidoglycan into host cells, and Toll-like receptor 9 (TLR9) activation is attributed to delivery of bacterial DNA. human,mouse stomach High+Lowthroughput Bacterial Energetic Requirements for Helicobacter pylori Cag Type IV Secretion System-Dependent Alterations in Gastric Epithelial Cells 否 无 cancer epithelial cell of stomach E_02_0123 pylori-induced NF-κB activation and IL-8 secretion are attributed to T4SS-dependent delivery of lipopolysaccharide metabolites and peptidoglycan into host cells, and Toll-like receptor 9 (TLR9) activation is attributed to delivery of bacterial DNA. Enhancer TLR9 qRT-PCR,qPCR,ChIP,3C RNA-Seq pylori-induced NF-κB activation and IL-8 secretion are attributed to T4SS-dependent delivery of lipopolysaccharide metabolites and peptidoglycan into host cells, and Toll-like receptor 9 (TLR9) activation is attributed to delivery of bacterial DNA. pylori-induced NF-κB activation and IL-8 secretion are attributed to T4SS-dependent delivery of lipopolysaccharide metabolites and peptidoglycan into host cells, and Toll-like receptor 9 (TLR9) activation is attributed to delivery of bacterial DNA. Immunohistochemical staining pylori-induced NF-κB activation and IL-8 secretion are attributed to T4SS-dependent delivery of lipopolysaccharide metabolites and peptidoglycan into host cells, and Toll-like receptor 9 (TLR9) activation is attributed to delivery of bacterial DNA. 31711897 chr14 54839063 54841063 GCH1 GCH1 feedback regulatory protein (GFRP) inhibits GCH1 activity when BH4 levels increase [14]; dihydropteridin reductase (DHPR) and dihydrofolate reductase (DHFR) ensure the re_x0002_cycling of dihydrobiopterin (BH2) into BH4 [15], BH2 being an oxi_x0002_dized and inactive form of BH4. mouse High+Lowthroughput Tetrahydrobiopterin administration facilitates amphetamine-induced dopamine release and motivation in mice 否 E_02_0124 PCR,Western blot GCH1 feedback regulatory protein (GFRP) inhibits GCH1 activity when BH4 levels increase [14]; dihydropteridin reductase (DHPR) and dihydrofolate reductase (DHFR) ensure the re_x0002_cycling of dihydrobiopterin (BH2) into BH4 [15], BH2 being an oxi_x0002_dized and inactive form of BH4. Enhancer GCH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq GCH1 feedback regulatory protein (GFRP) inhibits GCH1 activity when BH4 levels increase [14]; dihydropteridin reductase (DHPR) and dihydrofolate reductase (DHFR) ensure the re_x0002_cycling of dihydrobiopterin (BH2) into BH4 [15], BH2 being an oxi_x0002_dized and inactive form of BH4. GCH1 feedback regulatory protein (GFRP) inhibits GCH1 activity when BH4 levels increase [14]; dihydropteridin reductase (DHPR) and dihydrofolate reductase (DHFR) ensure the re_x0002_cycling of dihydrobiopterin (BH2) into BH4 [15], BH2 being an oxi_x0002_dized and inactive form of BH4. Immunohistochemical staining GCH1 feedback regulatory protein (GFRP) inhibits GCH1 activity when BH4 levels increase [14]; dihydropteridin reductase (DHPR) and dihydrofolate reductase (DHFR) ensure the re_x0002_cycling of dihydrobiopterin (BH2) into BH4 [15], BH2 being an oxi_x0002_dized and inactive form of BH4. PCR,Western blot 31711520 chr7 148804473 148806473 EZH2 We noticed that enhancer of zeste homologue 2 (EZH2) could afect the self-renewal and dif_x0002_ferentiation of hematopoietic stem cells [5] and may be an independent prognostic factor [6] related to a poor progno_x0002_sis [7]. human,mouse connective tissue High+Lowthroughput HO-1 promotes resistance to an EZH2 inhibitor through the pRB-E2F pathway: correlation with the progression of myelodysplastic syndrome into acute myeloid leukemia 否 leukemia tumor cell E_02_0125 PCR, Western blot, immunofluorescence staining We noticed that enhancer of zeste homologue 2 (EZH2) could afect the self-renewal and dif_x0002_ferentiation of hematopoietic stem cells [5] and may be an independent prognostic factor [6] related to a poor progno_x0002_sis [7]. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We noticed that enhancer of zeste homologue 2 (EZH2) could afect the self-renewal and dif_x0002_ferentiation of hematopoietic stem cells [5] and may be an independent prognostic factor [6] related to a poor progno_x0002_sis [7]. We noticed that enhancer of zeste homologue 2 (EZH2) could afect the self-renewal and dif_x0002_ferentiation of hematopoietic stem cells [5] and may be an independent prognostic factor [6] related to a poor progno_x0002_sis [7]. Immunohistochemical staining We noticed that enhancer of zeste homologue 2 (EZH2) could afect the self-renewal and dif_x0002_ferentiation of hematopoietic stem cells [5] and may be an independent prognostic factor [6] related to a poor progno_x0002_sis [7]. PCR,Western blot,免疫荧光染色 31709534 chr1 164552565 164554565 PBX1 Low Nfe2l1 mRNA expression is unlikely caused by reduced mTOR signaling but could be the result of diminished pre‐B‐cell leukemia homeobox-1 transcription factor (PBX1) levels. human,mouse connective tissue High+Lowthroughput Decreased levels of constitutive proteasomes in experimental autoimmune encephalomyelitis may be caused by a combination of subunit displacement and reduced Nfe2l1 expression 否 inflammation B cell E_02_0126 PCR, Western blot, immunofluorescence staining Low Nfe2l1 mRNA expression is unlikely caused by reduced mTOR signaling but could be the result of diminished pre‐B‐cell leukemia homeobox-1 transcription factor (PBX1) levels. Enhancer PBX1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Low Nfe2l1 mRNA expression is unlikely caused by reduced mTOR signaling but could be the result of diminished pre‐B‐cell leukemia homeobox-1 transcription factor (PBX1) levels. Low Nfe2l1 mRNA expression is unlikely caused by reduced mTOR signaling but could be the result of diminished pre‐B‐cell leukemia homeobox-1 transcription factor (PBX1) levels. Immunohistochemical staining Low Nfe2l1 mRNA expression is unlikely caused by reduced mTOR signaling but could be the result of diminished pre‐B‐cell leukemia homeobox-1 transcription factor (PBX1) levels. PCR,Western blot,免疫荧光染色 31709175 chr9 127084657 127086657 ANGPTL2 Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. human,mouse connective tissue High+Lowthroughput Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures 否 leukemia B cell E_02_0127 PCR,Flow cytometry Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Enhancer ANGPTL2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Immunohistochemical staining Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. PCR,Flow cytometry 31709175 chr7 22115708 22117708 RAPGEF5 Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. human,mouse connective tissue High+Lowthroughput Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures 否 leukemia B cell E_02_0127 PCR,Flow cytometry Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Enhancer RAPGEF5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Immunohistochemical staining Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG,RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. PCR,Flow cytometry 31709175 chr17 35868982 35870982 CCL5 Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. human,mouse connective tissue High+Lowthroughput Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures 否 leukemia T cell E_02_0127 PCR,Flow cytometry Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Enhancer CCL5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Immunohistochemical staining Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. PCR,Flow cytometry 31709175 chr5 35849791 35851791 IL7R Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. human,mouse connective tissue High+Lowthroughput Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures 否 leukemia T cell E_02_0127 PCR,Flow cytometry Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Enhancer IL7R qRT-PCR,qPCR,ChIP,3C RNA-Seq Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Immunohistochemical staining Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. PCR,Flow cytometry 31709175 chr3 39260841 39262841 CX3CR1 Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. human,mouse connective tissue High+Lowthroughput Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures 否 leukemia T cell E_02_0127 PCR,Flow cytometry Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Enhancer CX3CR1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. Immunohistochemical staining Genes involved in lymphocyte and T-cell apoptotic processes (CCL5, CD3G,IL7R, PLAC8) were over-presented, as well as two others,CX3CR1, RORA, corresponding to macrophage migration. PCR,Flow cytometry 31708105 chr5 136274432 136276432 Cux1 Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b human,mouse connective tissue High+Lowthroughput Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex 否 autism immune cell E_02_0128 PCR, flow cytometry, immunofluorescence staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Enhancer Cux1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Immunohistochemical staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b PCR,Flow cytometry,免疫荧光染色 31708105 chr5 121991850 121993850 Cux2 Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b human,mouse connective tissue High+Lowthroughput Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex 否 autism immune cell E_02_0128 PCR, flow cytometry, immunofluorescence staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Enhancer Cux2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Immunohistochemical staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b PCR,Flow cytometry,免疫荧光染色 31708105 chrX 72233135 72235135 Xlr3b Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b human,mouse connective tissue High+Lowthroughput Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex 否 autism immune cell E_02_0128 PCR, flow cytometry, immunofluorescence staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Enhancer Xlr3b qRT-PCR,qPCR,ChIP,3C RNA-Seq Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b Immunohistochemical staining Cux1 and Cux2, which are specifically expressed in cortical layer II-IV, have been shown to be involved in synapse formation, dendritic branching, and spine development by directly controlling the expression of Xlr3b and Xlr4b PCR,Flow cytometry,免疫荧光染色 31707045 chr16 56295383 56297383 Abi3bp Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Abi3bp qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr9 65169791 65171791 Cilp Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Cilp qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr9 95516985 95518985 Pcolce2 Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Pcolce2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr1 133962055 133964055 Fmod Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Fmod qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr13 49695201 49697201 Aspn Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Aspn qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr1 71621729 71623729 Fn1 Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Fn1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr17 34876882 34878882 Tnxb Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Tnxb qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31707045 chr15 85088078 85090078 Fbln1 Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). human,mouse connective tissue High+Lowthroughput TonEBP-deficiency accelerates intervertebral disc degeneration underscored by matrix remodeling, cytoskeletal rearrangements, and changes in proinflammatory gene expression 否 cancer cancer cell E_02_0129 PCR, flow cytometry, immunofluorescence staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Enhancer Fbln1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). Immunohistochemical staining Consistent with our histological and FTIR analyses, a number of downregulated extracellular matrix genes in the AF corresponded to collagen assembly and organization. These genes included ABI family member 3 binding protein (Abi3bp), cartilage intermediate layer protein (Cilp, Cilp2), procollagen c-endopeptidase enhancer 2 (Pcolce2), fibromodulin (Fmod), asporin (Aspn), fibronectin 1 (Fn1), tenascin X (Tnxb), and fibulin 1 (Fbln1). PCR,Flow cytometry,免疫荧光染色 31706027 chr16 67559869 67561869 CTCF A popular model explaining loop formation in vertebrates has proposed that the cohesin complex can dynamically bind to DNA and move along the DNA strand, extruding chromatin to form loops until complex movement is stopped by CTCF [14] human,mouse High+Lowthroughput Small Drosophila zinc finger C2H2 protein with an N-terminal zinc finger-associated domain demonstrates the architecture functions 否 S2 cell E_02_0130 PCR, flow cytometry, immunofluorescence staining A popular model explaining loop formation in vertebrates has proposed that the cohesin complex can dynamically bind to DNA and move along the DNA strand, extruding chromatin to form loops until complex movement is stopped by CTCF [14] Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq A popular model explaining loop formation in vertebrates has proposed that the cohesin complex can dynamically bind to DNA and move along the DNA strand, extruding chromatin to form loops until complex movement is stopped by CTCF [14] A popular model explaining loop formation in vertebrates has proposed that the cohesin complex can dynamically bind to DNA and move along the DNA strand, extruding chromatin to form loops until complex movement is stopped by CTCF [14] Immunohistochemical staining A popular model explaining loop formation in vertebrates has proposed that the cohesin complex can dynamically bind to DNA and move along the DNA strand, extruding chromatin to form loops until complex movement is stopped by CTCF [14] PCR,Flow cytometry,免疫荧光染色 31705954 chr3 115620608 115622608 GAP43 The aim of the present study was to evaluate the effect of fluoxetine, a widely used SSRI antidepressant, on the neurogenesis and the expression of Growth-Associated Protein 43 (GAP43), a synaptic protein, in the rat hippocampus exposed to Unpredictable Chronic Mild Stress mouse,hippocampus Nervous tissue High+Lowthroughput Fluoxetine attenuates stress-induced depressive-like behavior through modulation of hippocampal GAP43 and neurogenesis in male rats 否 depression neural progenitor cell E_02_0131 PCR, immunofluorescence staining The aim of the present study was to evaluate the effect of fluoxetine, a widely used SSRI antidepressant, on the neurogenesis and the expression of Growth-Associated Protein 43 (GAP43), a synaptic protein, in the rat hippocampus exposed to Unpredictable Chronic Mild Stress Enhancer GAP43 qRT-PCR,qPCR,ChIP,3C RNA-Seq The aim of the present study was to evaluate the effect of fluoxetine, a widely used SSRI antidepressant, on the neurogenesis and the expression of Growth-Associated Protein 43 (GAP43), a synaptic protein, in the rat hippocampus exposed to Unpredictable Chronic Mild Stress The aim of the present study was to evaluate the effect of fluoxetine, a widely used SSRI antidepressant, on the neurogenesis and the expression of Growth-Associated Protein 43 (GAP43), a synaptic protein, in the rat hippocampus exposed to Unpredictable Chronic Mild Stress Immunohistochemical staining The aim of the present study was to evaluate the effect of fluoxetine, a widely used SSRI antidepressant, on the neurogenesis and the expression of Growth-Associated Protein 43 (GAP43), a synaptic protein, in the rat hippocampus exposed to Unpredictable Chronic Mild Stress PCR,免疫荧光染色 31704972 chr12 55964033 55966033 CDK2 Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). human,mouse High+Lowthroughput CDK2-mediated site-specific phosphorylation of EZH2 drives and maintains triple-negative breast cancer 否 mammary cancer Triple-negative breast cancer cell E_02_0132 PCR,Western blot Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Enhancer CDK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Immunohistochemical staining Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). PCR,Western blot 31704972 chr7 148804376 148806376 EZH2 Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). human,mouse breast High+Lowthroughput CDK2-mediated site-specific phosphorylation of EZH2 drives and maintains triple-negative breast cancer 否 mammary cancer mammary gland epithelial cell E_02_0132 PCR,Western blot Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Immunohistochemical staining Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). PCR,Western blot 31699991 chr17 42697602 42699602 EZH1 Here we report that AML1-ETO-positive patients, with high histone lysine methyl_x0002_transferase Enhancer of zeste homolog 1 (EZH1) expression, show a worse overall survival than those with lower EZH1 expression. EZH1 knockdown impairs survival and proliferation of AML1-ETO-expressing cells in vitro and in vivo. human,mouse connective tissue High+Lowthroughput Protein lysine 43 methylation by EZH1 promotes AML1-ETO transcriptional repression in leukemia 否 cancer stem cell E_02_0133 PCR,Western blot Here we report that AML1-ETO-positive patients, with high histone lysine methyl_x0002_transferase Enhancer of zeste homolog 1 (EZH1) expression, show a worse overall survival than those with lower EZH1 expression. EZH1 knockdown impairs survival and proliferation of AML1-ETO-expressing cells in vitro and in vivo. Enhancer EZH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we report that AML1-ETO-positive patients, with high histone lysine methyl_x0002_transferase Enhancer of zeste homolog 1 (EZH1) expression, show a worse overall survival than those with lower EZH1 expression. EZH1 knockdown impairs survival and proliferation of AML1-ETO-expressing cells in vitro and in vivo. Here we report that AML1-ETO-positive patients, with high histone lysine methyl_x0002_transferase Enhancer of zeste homolog 1 (EZH1) expression, show a worse overall survival than those with lower EZH1 expression. EZH1 knockdown impairs survival and proliferation of AML1-ETO-expressing cells in vitro and in vivo. Immunohistochemical staining Here we report that AML1-ETO-positive patients, with high histone lysine methyl_x0002_transferase Enhancer of zeste homolog 1 (EZH1) expression, show a worse overall survival than those with lower EZH1 expression. EZH1 knockdown impairs survival and proliferation of AML1-ETO-expressing cells in vitro and in vivo. PCR,Western blot 31698854 chrX 25000875 25002875 ARX In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. human,mouse connective tissue High+Lowthroughput Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1 否 epilepsy T cell E_02_0134 PCR In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Enhancer ARX qRT-PCR,qPCR,ChIP,3C RNA-Seq In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Immunohistochemical staining In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. PCR 31698854 chr12 121623759 121625759 ORAI1 In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. human,mouse connective tissue High+Lowthroughput Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1 否 epilepsy T cell E_02_0134 PCR In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Enhancer ORAI1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Immunohistochemical staining In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. PCR 31698854 chrX 159552038 159554038 Cdkl5 In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. human,mouse connective tissue High+Lowthroughput Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1 否 epilepsy T cell E_02_0134 PCR In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Enhancer Cdkl5 qRT-PCR,qPCR,ChIP,3C RNA-Seq In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Immunohistochemical staining In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. PCR 31698854 chr3 55147134 55149134 Dclk1 In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. human,mouse connective tissue High+Lowthroughput Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1 否 epilepsy T cell E_02_0134 PCR In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Enhancer Dclk1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. Immunohistochemical staining In humans, ARX, DCLK1, and CDLK5 were shown to be mutated in some rare epilepsy-associated disorders. We conclude that the occurrence of seizure-like events in aged mice overexpressing ORAI1 might be due to the down-regulation of Arx, and possibly of Cdkl5 and Dclk1 genes. PCR 31698100 chr20 13993019 13995019 MACROD2 Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. human High+Lowthroughput Split hand/foot malformation associated with 20p12.1 deletion: A case report 是 Split hand / foot malformation E_01_0184 PCR Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Enhancer MACROD2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Immunohistochemical staining Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. PCR 31698100 chr20 16269065 16271065 KIF16B Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. human High+Lowthroughput Split hand/foot malformation associated with 20p12.1 deletion: A case report 是 Split hand / foot malformation E_01_0184 PCR Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Enhancer KIF16B qRT-PCR,qPCR,ChIP,3C RNA-Seq Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. Immunohistochemical staining Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. PCR 31697837 chr5 88714150 88716150 MEF2C In this context, SIK3maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), arepressive cofactor of MEF2C. human,mouse connective tissue High+Lowthroughput Salt-inducible kinase inhibition suppresses acute myeloid leukemia progression in vivo 否 Acute myeloid leukemia mutant lymphoma cell E_02_0135 PCR,Flow cytometry,Western blot In this context, SIK3maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), arepressive cofactor of MEF2C. Enhancer MEF2C qRT-PCR,qPCR,ChIP,3C RNA-Seq In this context, SIK3maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), arepressive cofactor of MEF2C. In this context, SIK3maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), arepressive cofactor of MEF2C. Immunohistochemical staining In this context, SIK3maintains MEF2C function by directly phosphorylating histone deacetylase 4 (HDAC4), arepressive cofactor of MEF2C. PCR,Flow cytometry,Western blot 31695501 chr7 148804320 148806320 EZH2 Enhancer of zeste 2 homolog (EZH2) is the catalytic subunit of the polycomb repressive complex 2, which is a complex that methylates lysine 27 of histone H3 (H3K27)to repress its gene expression. human,mouse connective tissue High+Lowthroughput Silencing Of hsa_circ_0008450 Represses Hepatocellular Carcinoma Progression Through Regulation Of microRNA-214-3p/EZH2 Axis 否 liver cancer cancer cell E_02_0136 PCR,Western blot Enhancer of zeste 2 homolog (EZH2) is the catalytic subunit of the polycomb repressive complex 2, which is a complex that methylates lysine 27 of histone H3 (H3K27)to repress its gene expression. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste 2 homolog (EZH2) is the catalytic subunit of the polycomb repressive complex 2, which is a complex that methylates lysine 27 of histone H3 (H3K27)to repress its gene expression. Enhancer of zeste 2 homolog (EZH2) is the catalytic subunit of the polycomb repressive complex 2, which is a complex that methylates lysine 27 of histone H3 (H3K27)to repress its gene expression. Immunohistochemical staining Enhancer of zeste 2 homolog (EZH2) is the catalytic subunit of the polycomb repressive complex 2, which is a complex that methylates lysine 27 of histone H3 (H3K27)to repress its gene expression. PCR,Western blot 31695196 chr17 40016366 40018366 MED24 ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. human,mouse connective tissue High+Lowthroughput Silencing Of hsa_circ_0008450 Represses Hepatocellular Carcinoma Progression Through Regulation Of microRNA-214-3p/EZH2 Axis 否 无 embryonic stem cell E_02_0137 PCR,Flow cytometry ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. Enhancer MED24 qRT-PCR,qPCR,ChIP,3C RNA-Seq ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. Immunohistochemical staining ERK triggers the reversible association and disassociation of RNA polymerase II and associated co-factors from genes and enhancers with the mediator component MED24 having an essential role in ERK-dependent transcriptional regulation. PCR,Flow cytometry 31694243 chr4 186066778 186068778 TLR3 Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα),extracellular regulated kinases (ERK), and p38, in an in vitro model. human,mouse blood High+Lowthroughput Transcriptome analysis reveals a positive effect of brassinosteroids on the photosynthetic capacity of wucai under low temperature 否 无 leukemia B cell E_02_0138 PCR,Western blot Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα),extracellular regulated kinases (ERK), and p38, in an in vitro model. Enhancer TLR3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα),extracellular regulated kinases (ERK), and p38, in an in vitro model. Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα),extracellular regulated kinases (ERK), and p38, in an in vitro model. Immunohistochemical staining Interestingly, the interaction of OAA with IκB kinase α/β (IKKα/β) strongly attenuated the production of certain proteins and inflammatory cytokines in the TLR3 signaling pathway, such as nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IkBα),extracellular regulated kinases (ERK), and p38, in an in vitro model. PCR,Western blot 31694013 chr7 148804620 148806620 EZH2 Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities human intestines High+Lowthroughput Oleanolic Acid Acetate Exerts Anti-Inflammatory Activity via IKKα/β Suppression in TLR3-Mediated NF-κB Activation 否 无 Colon cancer colon cancer cell E_01_0185 PCR Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities Immunohistochemical staining Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities EZH2 PCR Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities 31693890 chr7 148804304 148806304 EZH2 The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation. human breast High+Lowthroughput Enhancer of Zeste Homolog 2 in Colorectal Cancer Development and Progression 否 无 mammary cancer breast cancer cell E_01_0186 PCR,Western blot,Flow cytometry The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation. Immunohistochemical staining The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation. EZH2 PCR,Western blot,Flow cytometry The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation. 31693439 chr15 90963083 90965083 PRC1 Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1 human bone marrow High+Lowthroughput Regulation of EZH2 by SMYD2-Mediated Lysine Methylation Is Implicated in Tumorigenesis 否 无 Myeloma Myeloma cell E_01_0187 PCR,Western blot,Flow cytometry Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1 Enhancer PRC1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1 Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1 Immunohistochemical staining Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1 PCR,Western blot,Flow cytometry 31692936 chr4 1868930 1870930 NSD2 NSD2 (also known as WHSC1 and MMSET) was initially found to be deleted in Wolf-Hirschhorn syndrome (WHS) and rearranged with the immunoglobulin locus in 15%~20% multiple Ivyspring International Publisher myeloma (MM) cases [4-5]. Indeed, NSD2 gene,encoding two main isoforms, NSD2-long (1,365 aminoacid) and NSD2-short (647 amino acid), was located at chromosome 4p16.3, which exhibits strong cancerrelevance human,mouse kidney High+Lowthroughput Investigating the epi-miRNome: identification of epi-miRNAs using transfection experiments 否 无 renal cell carcinoma Renal cell E_02_0139 PCR,Western blot,Flow cytometry NSD2 (also known as WHSC1 and MMSET) was initially found to be deleted in Wolf-Hirschhorn syndrome (WHS) and rearranged with the immunoglobulin locus in 15%~20% multiple Ivyspring International Publisher myeloma (MM) cases [4-5]. Indeed, NSD2 gene,encoding two main isoforms, NSD2-long (1,365 aminoacid) and NSD2-short (647 amino acid), was located at chromosome 4p16.3, which exhibits strong cancerrelevance Enhancer NSD2 qRT-PCR,qPCR,ChIP,3C RNA-Seq NSD2 (also known as WHSC1 and MMSET) was initially found to be deleted in Wolf-Hirschhorn syndrome (WHS) and rearranged with the immunoglobulin locus in 15%~20% multiple Ivyspring International Publisher myeloma (MM) cases [4-5]. Indeed, NSD2 gene,encoding two main isoforms, NSD2-long (1,365 aminoacid) and NSD2-short (647 amino acid), was located at chromosome 4p16.3, which exhibits strong cancerrelevance NSD2 (also known as WHSC1 and MMSET) was initially found to be deleted in Wolf-Hirschhorn syndrome (WHS) and rearranged with the immunoglobulin locus in 15%~20% multiple Ivyspring International Publisher myeloma (MM) cases [4-5]. Indeed, NSD2 gene,encoding two main isoforms, NSD2-long (1,365 aminoacid) and NSD2-short (647 amino acid), was located at chromosome 4p16.3, which exhibits strong cancerrelevance Immunohistochemical staining NSD2 (also known as WHSC1 and MMSET) was initially found to be deleted in Wolf-Hirschhorn syndrome (WHS) and rearranged with the immunoglobulin locus in 15%~20% multiple Ivyspring International Publisher myeloma (MM) cases [4-5]. Indeed, NSD2 gene,encoding two main isoforms, NSD2-long (1,365 aminoacid) and NSD2-short (647 amino acid), was located at chromosome 4p16.3, which exhibits strong cancerrelevance PCR,Western blot,Flow cytometry 31692093 chr17 82215342 82217342 SLC16A3 Moreover, we demonstrate for the first time that HIF-1α directly activates an intronic enhancer in SLC16A3 under hypoxic conditions. human,mouse intervertebral disc High+Lowthroughput Combining GAL4 GFP enhancer trap with split luciferase to measure spatiotemporal promoter activity in Arabidopsis 否 无 Chronic intervertebral pain intervertebral disc cells E_02_0140 PCR, Western blot, flow cytometry, immunofluorescence staining Moreover, we demonstrate for the first time that HIF-1α directly activates an intronic enhancer in SLC16A3 under hypoxic conditions. Enhancer SLC16A3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, we demonstrate for the first time that HIF-1α directly activates an intronic enhancer in SLC16A3 under hypoxic conditions. Moreover, we demonstrate for the first time that HIF-1α directly activates an intronic enhancer in SLC16A3 under hypoxic conditions. Immunohistochemical staining Moreover, we demonstrate for the first time that HIF-1α directly activates an intronic enhancer in SLC16A3 under hypoxic conditions. PCR,Western blot,Flow cytometry,免疫荧光染色 31692040 chr12 55964023 55966023 CDK2 In this study, we show that cyclin‐dependent kinase 2 (CDK2) negatively regulates C/EBPα protein levels in myeloid leukemia cells human,mouse bone marrow High+Lowthroughput Lactate Efflux From Intervertebral Disc Cells Is Required for Maintenance of Spine Health 否 无 Myeloid leukemia myeloid leukemia cells E_02_0141 PCR, Western blot, flow cytometry, immunofluorescence staining In this study, we show that cyclin‐dependent kinase 2 (CDK2) negatively regulates C/EBPα protein levels in myeloid leukemia cells Enhancer CDK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we show that cyclin‐dependent kinase 2 (CDK2) negatively regulates C/EBPα protein levels in myeloid leukemia cells In this study, we show that cyclin‐dependent kinase 2 (CDK2) negatively regulates C/EBPα protein levels in myeloid leukemia cells Immunohistochemical staining In this study, we show that cyclin‐dependent kinase 2 (CDK2) negatively regulates C/EBPα protein levels in myeloid leukemia cells PCR,Western blot,Flow cytometry,免疫荧光染色 31692040 chr19 33297357 33299357 CEBPA Condi_x0002_tional disruption of CEBPA leads to differentiation block(transition from common myeloid to granulocyte mono_x0002_cyte progenitors), granulopoiesis in particular. human,mouse liver High+Lowthroughput Lactate Efflux From Intervertebral Disc Cells Is Required for Maintenance of Spine Health 否 无 tumour hepatocyte E_02_0141 PCR, Western blot, flow cytometry, immunofluorescence staining Condi_x0002_tional disruption of CEBPA leads to differentiation block(transition from common myeloid to granulocyte mono_x0002_cyte progenitors), granulopoiesis in particular. Enhancer CEBPA qRT-PCR,qPCR,ChIP,3C RNA-Seq Condi_x0002_tional disruption of CEBPA leads to differentiation block(transition from common myeloid to granulocyte mono_x0002_cyte progenitors), granulopoiesis in particular. Condi_x0002_tional disruption of CEBPA leads to differentiation block(transition from common myeloid to granulocyte mono_x0002_cyte progenitors), granulopoiesis in particular. Immunohistochemical staining Condi_x0002_tional disruption of CEBPA leads to differentiation block(transition from common myeloid to granulocyte mono_x0002_cyte progenitors), granulopoiesis in particular. PCR,Western blot,Flow cytometry,免疫荧光染色 31691800 chr21 39443054 39445054 SH3BGR Hi-C data show that rs2836411 is located in a sub-domain spanning from a region upstream of P3 till the 3_x0002_ end of ERG, which is part of a larger TAD spanning from the 3_x0002_ end of ERG to SH3BGR. human,mouse Epithelial tissues High+Lowthroughput Berberine Inhibits Adipogenesis in Porcine Adipocytes via AMP-Activated Protein Kinase-Dependent and -Independent Mechanisms 是 rs2836411 Abdominal aortic aneurysm blood vessel endothelial cell E_02_0142 PCR,Flow cytometry Hi-C data show that rs2836411 is located in a sub-domain spanning from a region upstream of P3 till the 3_x0002_ end of ERG, which is part of a larger TAD spanning from the 3_x0002_ end of ERG to SH3BGR. Enhancer SH3BGR qRT-PCR,qPCR,ChIP,3C RNA-Seq Hi-C data show that rs2836411 is located in a sub-domain spanning from a region upstream of P3 till the 3_x0002_ end of ERG, which is part of a larger TAD spanning from the 3_x0002_ end of ERG to SH3BGR. Hi-C data show that rs2836411 is located in a sub-domain spanning from a region upstream of P3 till the 3_x0002_ end of ERG, which is part of a larger TAD spanning from the 3_x0002_ end of ERG to SH3BGR. Immunohistochemical staining Hi-C data show that rs2836411 is located in a sub-domain spanning from a region upstream of P3 till the 3_x0002_ end of ERG, which is part of a larger TAD spanning from the 3_x0002_ end of ERG to SH3BGR. PCR,Flow cytometry 31690584 chr17 72118178 72120178 SOX9 Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase human breast High+Lowthroughput The hTERT-VNTR2-2(nd) alleles are involved in genomic stability in gastrointestinal cancer 否 无 mammary cancer breast cancer cell E_01_0188 PCR, Western blot, gene knockdown Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase Immunohistochemical staining Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase SOX9 PCR,Western blot,基因敲降 Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase 31689455 chr7 100717697 100719697 EPO EPO prevented the reduction of VSMC phenotypic markers, and reversed the increased calcium content and calcium salt deposition in the aortas of CKD rats and cultured calcified VSMCs. human,mouse Musculature High+Lowthroughput Erythropoietin attenuates vascular calcification by inhibiting endoplasmic reticulum stress in rats with chronic kidney disease 否 无 Vascular calcification smooth muscle cell E_02_0143 Western blot,PCR EPO prevented the reduction of VSMC phenotypic markers, and reversed the increased calcium content and calcium salt deposition in the aortas of CKD rats and cultured calcified VSMCs. Enhancer EPO qRT-PCR,qPCR,ChIP,3C RNA-Seq EPO prevented the reduction of VSMC phenotypic markers, and reversed the increased calcium content and calcium salt deposition in the aortas of CKD rats and cultured calcified VSMCs. EPO prevented the reduction of VSMC phenotypic markers, and reversed the increased calcium content and calcium salt deposition in the aortas of CKD rats and cultured calcified VSMCs. Immunohistochemical staining EPO prevented the reduction of VSMC phenotypic markers, and reversed the increased calcium content and calcium salt deposition in the aortas of CKD rats and cultured calcified VSMCs. Western blot,PCR 31689455 chr19 11374596 11376596 EPOR The EPO receptor (EPOR) mediates the pleiotropic effects of EPO in target cells human,mouse connective tissue High+Lowthroughput Erythropoietin attenuates vascular calcification by inhibiting endoplasmic reticulum stress in rats with chronic kidney disease 否 无 Vascular calcification target cell E_02_0143 Western blot,PCR The EPO receptor (EPOR) mediates the pleiotropic effects of EPO in target cells Enhancer EPOR qRT-PCR,qPCR,ChIP,3C RNA-Seq The EPO receptor (EPOR) mediates the pleiotropic effects of EPO in target cells The EPO receptor (EPOR) mediates the pleiotropic effects of EPO in target cells Immunohistochemical staining The EPO receptor (EPOR) mediates the pleiotropic effects of EPO in target cells Western blot,PCR 31686316 chr22 39516753 39518753 ATF4 We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. mouse connective tissue High+Lowthroughput CCAAT/enhancer-binding protein beta (C/EBPβ) knockdown reduces inflammation, ER stress, and apoptosis, and promotes autophagy in oxLDL-treated RAW264.7 macrophage cells 否 无 atherosclerosis macrophage derived foam cell E_02_0144 Western blot,PCR We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Enhancer ATF4 qRT-PCR,qPCR,ChIP,3C RNA-Seq We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Immunohistochemical staining We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Western blot,PCR 31686316 chr1 161763620 161765620 ATF6 We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. mouse connective tissue High+Lowthroughput CCAAT/enhancer-binding protein beta (C/EBPβ) knockdown reduces inflammation, ER stress, and apoptosis, and promotes autophagy in oxLDL-treated RAW264.7 macrophage cells 否 无 atherosclerosis macrophage derived foam cell E_02_0144 Western blot,PCR We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Enhancer ATF6 qRT-PCR,qPCR,ChIP,3C RNA-Seq We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Immunohistochemical staining We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Western blot,PCR 31686316 chr6 106042776 106044776 ATG5 We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. mouse connective tissue High+Lowthroughput CCAAT/enhancer-binding protein beta (C/EBPβ) knockdown reduces inflammation, ER stress, and apoptosis, and promotes autophagy in oxLDL-treated RAW264.7 macrophage cells 否 无 atherosclerosis immune cell E_02_0144 Western blot,PCR We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Enhancer ATG5 qRT-PCR,qPCR,ChIP,3C RNA-Seq We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Immunohistochemical staining We measured key genes CHOP, mTORC1, genes implicated in ERS [activat_x0002_ing transcription factor 4 & 6 (ATF4, ATF6)] and apopto_x0002_sis (caspase 1, caspase-3 and caspase 12), and autophagy (ATG5, LC3A, LC3B) in macrophage cells by qPCR. Western blot,PCR 31686214 chr16 86507862 86509862 FOXF1 Haploinsufciency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. human,mouse Epithelial tissues High+Lowthroughput Association of rare non-coding SNVs in the lung-specific FOXF1 enhancer with a mitigation of the lethal ACDMPV phenotype 是 rs150502618-A Misalignment of pulmonary veins epithelial cell E_02_0145 Flow cytometry,PCR Haploinsufciency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. Enhancer FOXF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Haploinsufciency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. Haploinsufciency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. Immunohistochemical staining Haploinsufciency of FOXF1 causes alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV), a lethal neonatal lung developmental disorder. We describe two similar heterozygous CNV deletions involving the FOXF1 enhancer and re-analyze FOXF1 missense mutation, all associated with an unexpectedly mitigated disease phenotype. Flow cytometry,PCR 31686214 chr16 67559674 67561674 CTCF Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. human,mouse lung High+Lowthroughput Association of rare non-coding SNVs in the lung-specific FOXF1 enhancer with a mitigation of the lethal ACDMPV phenotype 是 rs79301423-T Misalignment of pulmonary veins pneumocyte E_02_0145 Flow cytometry,PCR Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Immunohistochemical staining Sequencing of these alleles revealed two rare SNVs, rs150502618-A and rs79301423-T, mapping to the partially overlapping binding sites for TFAP2s and CTCF in the core region of the enhancer. Flow cytometry,PCR 31684161 chr4 153681439 153683439 TLR2 The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). human,mouse blood High+Lowthroughput HP1717 Contributes to Streptococcus suis Virulence by Inducing an Excessive Inflammatory Response and Influencing the Biosynthesis of the Capsule 否 无 inflammation B cell E_02_0146 Western blot,PCR The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Enhancer TLR2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Immunohistochemical staining The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Western blot,PCR 31684161 chr9 117701075 117703075 TLR4 The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). human,mouse connective tissue High+Lowthroughput HP1717 Contributes to Streptococcus suis Virulence by Inducing an Excessive Inflammatory Response and Influencing the Biosynthesis of the Capsule 否 无 inflammation immune cell E_02_0146 Western blot,PCR The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Enhancer TLR4 qRT-PCR,qPCR,ChIP,3C RNA-Seq The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Immunohistochemical staining The qRT-PCR results show that TLR2 transcription was significantly upregulated in RAW264.7 cells stimulated by HP1717, but TLR4 transcription did not significantly change (Figure 4A). Western blot,PCR 31682213 chr20 44582166 44584166 ADA Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential). human connective tissue High+Lowthroughput An Assessment of the Effects of Azodicarbonamide-containing Diet on Neurobehaviour, Brain Antioxidant Status and Membrane Lipid Peroxidation Status in Rats 否 无 E_01_0189 PCR Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential). Enhancer ADA qRT-PCR,qPCR,ChIP,3C RNA-Seq Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential). Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential). Immunohistochemical staining Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential). PCR 31681405 chr14 100235887 100237887 YY1 The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. human,mouse High+Lowthroughput Enhancer LncRNAs Influence Chromatin Interactions in Different Ways 是 无 GM12878 cell E_02_0147 Flow cytometry The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Enhancer YY1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Immunohistochemical staining The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Flow cytometry 31681009 chr8 19899234 19901234 LPL For instance, lipoprotein lipase (LPL) reveals lipid storage in the early stages of differentiation, whereas fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and glycerol-3-phosphate dehydrogenase (G-3-PDH) are involved in triglyceride metabolism in late stages human,mouse connective tissue High+Lowthroughput Ghrelin Promotes Proliferation and Inhibits Differentiation of 3T3-L1 and Human Primary Preadipocytes 否 无 pluripotent stem cell E_02_0148 Western blot,PCR For instance, lipoprotein lipase (LPL) reveals lipid storage in the early stages of differentiation, whereas fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and glycerol-3-phosphate dehydrogenase (G-3-PDH) are involved in triglyceride metabolism in late stages Enhancer LPL qRT-PCR,qPCR,ChIP,3C RNA-Seq For instance, lipoprotein lipase (LPL) reveals lipid storage in the early stages of differentiation, whereas fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and glycerol-3-phosphate dehydrogenase (G-3-PDH) are involved in triglyceride metabolism in late stages For instance, lipoprotein lipase (LPL) reveals lipid storage in the early stages of differentiation, whereas fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and glycerol-3-phosphate dehydrogenase (G-3-PDH) are involved in triglyceride metabolism in late stages Immunohistochemical staining For instance, lipoprotein lipase (LPL) reveals lipid storage in the early stages of differentiation, whereas fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), and glycerol-3-phosphate dehydrogenase (G-3-PDH) are involved in triglyceride metabolism in late stages Western blot,PCR 31680128 chr11 1155000 1157000 MUC5AC MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases human Epithelial tissues High+Lowthroughput Fipronil upregulates inflammatory cytokines and MUC5AC expression in human nasal epithelial cells 否 无 airway inflammation epithelial cell E_01_0190 Western blot,PCR MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases Enhancer MUC5AC qRT-PCR,qPCR,ChIP,3C RNA-Seq MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases Immunohistochemical staining MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases Western blot,PCR 31679819 chr12 48826675 48828675 DDX23 Even when formed, R-loops may be removed either by RNase H1 ac_x0002_tivity that selectively degrades RNA hybridized to DNA (Cerritelli and Crouch, 2009) or alternatively by various helicases such as Senataxin (SETX; Skourti-Stathaki et al., 2011), Aquarius (Sollier et al., 2014), DDX23 (Sridhara et al., 2017), and DHX9 (Cristini et al., 2018), which have all been shown to restrict R-loop accu_x0002_mulation. human,mouse uterus High+Lowthroughput R-Loops Promote Antisense Transcription across the Mammalian Genome 否 无 HeLa cell E_02_0149 Western blot,PCR,Flow cytometry Even when formed, R-loops may be removed either by RNase H1 ac_x0002_tivity that selectively degrades RNA hybridized to DNA (Cerritelli and Crouch, 2009) or alternatively by various helicases such as Senataxin (SETX; Skourti-Stathaki et al., 2011), Aquarius (Sollier et al., 2014), DDX23 (Sridhara et al., 2017), and DHX9 (Cristini et al., 2018), which have all been shown to restrict R-loop accu_x0002_mulation. Enhancer DDX23 qRT-PCR,qPCR,ChIP,3C RNA-Seq Even when formed, R-loops may be removed either by RNase H1 ac_x0002_tivity that selectively degrades RNA hybridized to DNA (Cerritelli and Crouch, 2009) or alternatively by various helicases such as Senataxin (SETX; Skourti-Stathaki et al., 2011), Aquarius (Sollier et al., 2014), DDX23 (Sridhara et al., 2017), and DHX9 (Cristini et al., 2018), which have all been shown to restrict R-loop accu_x0002_mulation. Even when formed, R-loops may be removed either by RNase H1 ac_x0002_tivity that selectively degrades RNA hybridized to DNA (Cerritelli and Crouch, 2009) or alternatively by various helicases such as Senataxin (SETX; Skourti-Stathaki et al., 2011), Aquarius (Sollier et al., 2014), DDX23 (Sridhara et al., 2017), and DHX9 (Cristini et al., 2018), which have all been shown to restrict R-loop accu_x0002_mulation. Immunohistochemical staining Even when formed, R-loops may be removed either by RNase H1 ac_x0002_tivity that selectively degrades RNA hybridized to DNA (Cerritelli and Crouch, 2009) or alternatively by various helicases such as Senataxin (SETX; Skourti-Stathaki et al., 2011), Aquarius (Sollier et al., 2014), DDX23 (Sridhara et al., 2017), and DHX9 (Cristini et al., 2018), which have all been shown to restrict R-loop accu_x0002_mulation. Western blot,PCR,Flow cytometry 31679819 chr2 144361373 144363373 ZEB2 Similarly, the ZEB2 gene, which is associated with stem celldevelopment and reprogramming, generates a lncRNA (referred to as a native AS RNA or NAT) initiating in the ZEB2 intron 1 that plays a positive role in activating ZEB2 expression. human,mouse connective tissue High+Lowthroughput R-Loops Promote Antisense Transcription across the Mammalian Genome 否 无 stem cell E_02_0149 Western blot,PCR,Flow cytometry Similarly, the ZEB2 gene, which is associated with stem celldevelopment and reprogramming, generates a lncRNA (referred to as a native AS RNA or NAT) initiating in the ZEB2 intron 1 that plays a positive role in activating ZEB2 expression. Enhancer ZEB2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Similarly, the ZEB2 gene, which is associated with stem celldevelopment and reprogramming, generates a lncRNA (referred to as a native AS RNA or NAT) initiating in the ZEB2 intron 1 that plays a positive role in activating ZEB2 expression. Similarly, the ZEB2 gene, which is associated with stem celldevelopment and reprogramming, generates a lncRNA (referred to as a native AS RNA or NAT) initiating in the ZEB2 intron 1 that plays a positive role in activating ZEB2 expression. Immunohistochemical staining Similarly, the ZEB2 gene, which is associated with stem celldevelopment and reprogramming, generates a lncRNA (referred to as a native AS RNA or NAT) initiating in the ZEB2 intron 1 that plays a positive role in activating ZEB2 expression. Western blot,PCR,Flow cytometry 31678303 chr1 156461181 156463181 MEF2D MEF2D protein acetylation and proteins that interact with MEF2D were identified by co-immunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls) were transplanted into BALB/c mice, some mice were given antibodies to deplete T cells. human,mouse liver High+Lowthroughput Disruption of SIRT7 Increases the Efficacy of Checkpoint Inhibitor via MEF2D Regulation of Programmed Cell Death 1 Ligand 1 in Hepatocellular Carcinoma Cells 否 无 liver cancer hepatocellular carcinoma cell E_02_0150 Western blot, PCR, flow cytometry, immunofluorescence staining MEF2D protein acetylation and proteins that interact with MEF2D were identified by co-immunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls) were transplanted into BALB/c mice, some mice were given antibodies to deplete T cells. Enhancer MEF2D qRT-PCR,qPCR,ChIP,3C RNA-Seq MEF2D protein acetylation and proteins that interact with MEF2D were identified by co-immunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls) were transplanted into BALB/c mice, some mice were given antibodies to deplete T cells. MEF2D protein acetylation and proteins that interact with MEF2D were identified by co-immunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls) were transplanted into BALB/c mice, some mice were given antibodies to deplete T cells. Immunohistochemical staining MEF2D protein acetylation and proteins that interact with MEF2D were identified by co-immunoprecipitation and pull-down assays. H22 cells, with MEF2D knockout or without (controls) were transplanted into BALB/c mice, some mice were given antibodies to deplete T cells. Western blot,PCR,Flow cytometry,免疫荧光染色 31678303 chr17 81909215 81911215 SIRT7 Mice bearing orthotopic tumors grown from HCC cells with or without knockout of SIRT7, were given injections of an antibody against PD1. human,mouse blood High+Lowthroughput Disruption of SIRT7 Increases the Efficacy of Checkpoint Inhibitor via MEF2D Regulation of Programmed Cell Death 1 Ligand 1 in Hepatocellular Carcinoma Cells 否 无 liver cancer T cell E_02_0150 Western blot, PCR, flow cytometry, immunofluorescence staining Mice bearing orthotopic tumors grown from HCC cells with or without knockout of SIRT7, were given injections of an antibody against PD1. Enhancer SIRT7 qRT-PCR,qPCR,ChIP,3C RNA-Seq Mice bearing orthotopic tumors grown from HCC cells with or without knockout of SIRT7, were given injections of an antibody against PD1. Mice bearing orthotopic tumors grown from HCC cells with or without knockout of SIRT7, were given injections of an antibody against PD1. Immunohistochemical staining Mice bearing orthotopic tumors grown from HCC cells with or without knockout of SIRT7, were given injections of an antibody against PD1. Western blot,PCR,Flow cytometry,免疫荧光染色 31678303 chr9 5447414 5449414 CD274 MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. human,mouse connective tissue High+Lowthroughput Disruption of SIRT7 Increases the Efficacy of Checkpoint Inhibitor via MEF2D Regulation of Programmed Cell Death 1 Ligand 1 in Hepatocellular Carcinoma Cells 否 无 liver cancer immune cell E_02_0150 Western blot, PCR, flow cytometry, immunofluorescence staining MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. Enhancer CD274 qRT-PCR,qPCR,ChIP,3C RNA-Seq MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. Immunohistochemical staining MEF2D bound the promoter region of the CD274 gene (encodes PD-L1) and activated its transcription. Western blot,PCR,Flow cytometry,免疫荧光染色 31676868 chr20 40683274 40685274 MAFB Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus. human blood High+Lowthroughput The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes 是 rs78037977 diabetes B cell E_01_0191 Flow cytometry,PCR Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus. Immunohistochemical staining Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus. MAFB Flow cytometry,PCR Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus. 31676868 chr16 11251612 11253612 SOCS1 The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. human connective tissue High+Lowthroughput The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes 是 rs193778 diabetes EC cell E_01_0191 Flow cytometry,PCR The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. Immunohistochemical staining The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. SOCS1 Flow cytometry,PCR The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. 31676868 chr16 10925964 10927964 DEXI The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. human connective tissue High+Lowthroughput The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes 是 rs193778 diabetes EC cell E_01_0191 Flow cytometry,PCR The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. Enhancer DEXI qRT-PCR,qPCR,ChIP,3C RNA-Seq The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. Immunohistochemical staining The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32. Flow cytometry,PCR 31676828 chr1 92469783 92471783 GFI1 In erythro–megakaryocyte lineage leukemia cells, activation of the SE of GFI1 (GFI1-SE) is related to induction of myeloid differentiation by LSD1 inhibitors NCD38 and NCD25 and to their antileukemia effect. human,mouse blood High+Lowthroughput LSD1-mediated repression of GFI1 super-enhancer plays an essential role in erythroleukemia 否 无 leukemia leukemic cell E_02_0151 Flow cytometry,PCR In erythro–megakaryocyte lineage leukemia cells, activation of the SE of GFI1 (GFI1-SE) is related to induction of myeloid differentiation by LSD1 inhibitors NCD38 and NCD25 and to their antileukemia effect. Enhancer GFI1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In erythro–megakaryocyte lineage leukemia cells, activation of the SE of GFI1 (GFI1-SE) is related to induction of myeloid differentiation by LSD1 inhibitors NCD38 and NCD25 and to their antileukemia effect. In erythro–megakaryocyte lineage leukemia cells, activation of the SE of GFI1 (GFI1-SE) is related to induction of myeloid differentiation by LSD1 inhibitors NCD38 and NCD25 and to their antileukemia effect. Immunohistochemical staining In erythro–megakaryocyte lineage leukemia cells, activation of the SE of GFI1 (GFI1-SE) is related to induction of myeloid differentiation by LSD1 inhibitors NCD38 and NCD25 and to their antileukemia effect. Flow cytometry,PCR 31676673 chrX 49025404 49027404 TFE3 Our results reveal that Fnip1 coordinates multiple metabolic pathways regulated by AMPK, mTORC1, and transcription factor binding to IgHM enhancer 3 (TFE3) to maintain metabolic ho_x0002_meostasis necessary for pre–B cell survival and differentiation during metabolic stress. human,mouse blood High+Lowthroughput Folliculin Interacting Protein 1 Maintains Metabolic Homeostasis during B Cell Development by Modulating AMPK, mTORC1, and TFE3 否 无 B cell E_02_0152 Flow cytometry,PCR Our results reveal that Fnip1 coordinates multiple metabolic pathways regulated by AMPK, mTORC1, and transcription factor binding to IgHM enhancer 3 (TFE3) to maintain metabolic ho_x0002_meostasis necessary for pre–B cell survival and differentiation during metabolic stress. Enhancer TFE3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results reveal that Fnip1 coordinates multiple metabolic pathways regulated by AMPK, mTORC1, and transcription factor binding to IgHM enhancer 3 (TFE3) to maintain metabolic ho_x0002_meostasis necessary for pre–B cell survival and differentiation during metabolic stress. Our results reveal that Fnip1 coordinates multiple metabolic pathways regulated by AMPK, mTORC1, and transcription factor binding to IgHM enhancer 3 (TFE3) to maintain metabolic ho_x0002_meostasis necessary for pre–B cell survival and differentiation during metabolic stress. Immunohistochemical staining Our results reveal that Fnip1 coordinates multiple metabolic pathways regulated by AMPK, mTORC1, and transcription factor binding to IgHM enhancer 3 (TFE3) to maintain metabolic ho_x0002_meostasis necessary for pre–B cell survival and differentiation during metabolic stress. Flow cytometry,PCR 31675590 chr7 148804429 148806429 EZH2 Our results indicate that Cd at1 mM concentration increases the viability of HepG2 and MCF7 cells and significantly upregulates the expression of PRMT5 and EZH2, leading to an increased global level of symmetric dimethylarginine(SDMA), H4R3me2s, and H3K27me3. human,mouse connective tissue High+Lowthroughput The carcinogen cadmium elevates CpG-demethylation and enrichment of NFYA and E2F1 in the promoter of oncogenic PRMT5 and EZH2 methyltransferases resulting in their elevated expression in?vitro 否 无 cancer HepG2 cell E_02_0153 Western blot,PCR,Flow cytometry Our results indicate that Cd at1 mM concentration increases the viability of HepG2 and MCF7 cells and significantly upregulates the expression of PRMT5 and EZH2, leading to an increased global level of symmetric dimethylarginine(SDMA), H4R3me2s, and H3K27me3. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our results indicate that Cd at1 mM concentration increases the viability of HepG2 and MCF7 cells and significantly upregulates the expression of PRMT5 and EZH2, leading to an increased global level of symmetric dimethylarginine(SDMA), H4R3me2s, and H3K27me3. Our results indicate that Cd at1 mM concentration increases the viability of HepG2 and MCF7 cells and significantly upregulates the expression of PRMT5 and EZH2, leading to an increased global level of symmetric dimethylarginine(SDMA), H4R3me2s, and H3K27me3. Immunohistochemical staining Our results indicate that Cd at1 mM concentration increases the viability of HepG2 and MCF7 cells and significantly upregulates the expression of PRMT5 and EZH2, leading to an increased global level of symmetric dimethylarginine(SDMA), H4R3me2s, and H3K27me3. Western blot,PCR,Flow cytometry 31672165 chr17 47197711 47199711 MYL4 Interestingly, while HEK293 cells are not thought to express MYL4, human MYL4 is known to be slightly larger than the mouse protein. mouse blood High+Lowthroughput Contaminating reactivity of a monoclonal CCAAT/Enhancer Binding Protein β antibody in differentiating myoblasts 否 无 B cell E_02_0154 Western blot Interestingly, while HEK293 cells are not thought to express MYL4, human MYL4 is known to be slightly larger than the mouse protein. Enhancer MYL4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Interestingly, while HEK293 cells are not thought to express MYL4, human MYL4 is known to be slightly larger than the mouse protein. Interestingly, while HEK293 cells are not thought to express MYL4, human MYL4 is known to be slightly larger than the mouse protein. Immunohistochemical staining Interestingly, while HEK293 cells are not thought to express MYL4, human MYL4 is known to be slightly larger than the mouse protein. Western blot 31668620 chr13 118804154 118806154 Fgf10 Analyzing open chromatin revealsdifferentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer ac_x0002_tivity is dependent on a likely Fgf-mediated Ets tran_x0002_scription factor-binding site. mouse Musculature High+Lowthroughput Attenuated Fgf Signaling Underlies the Forelimb Heterochrony in the Emu Dromaius novaehollandiae 否 无 muscle cell E_02_0155 Flow cytometry, PCR, immunofluorescence staining Analyzing open chromatin revealsdifferentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer ac_x0002_tivity is dependent on a likely Fgf-mediated Ets tran_x0002_scription factor-binding site. Enhancer Fgf10 qRT-PCR,qPCR,ChIP,3C RNA-Seq Analyzing open chromatin revealsdifferentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer ac_x0002_tivity is dependent on a likely Fgf-mediated Ets tran_x0002_scription factor-binding site. Analyzing open chromatin revealsdifferentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer ac_x0002_tivity is dependent on a likely Fgf-mediated Ets tran_x0002_scription factor-binding site. Immunohistochemical staining Analyzing open chromatin revealsdifferentially active regulatory elements near Fgf10 and Sall-1 in the emu wing, and the Sall-1 enhancer ac_x0002_tivity is dependent on a likely Fgf-mediated Ets tran_x0002_scription factor-binding site. Flow cytometry,PCR,免疫荧光染色 31666694 chr11 69983276 69985276 ANO1 By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d). human Stomach, gut High+Lowthroughput Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs 否 无 Gastrointestinal stromal tumors GIST-T1 cell E_01_0192 Flow cytometry By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d). Immunohistochemical staining By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d). ANO1 Flow cytometry By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d). 31666665 chr7 148804251 148806251 EZH2 Enhancer of zester homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PCR2), and its-terminal SET domain exhibits methyl transferase activity9 human,mouse lung High+Lowthroughput Cigarette smoke affects the onco-suppressor DAB2IP expression in bronchial epithelial cells of COPD patients 否 无 lung cancer Lung cancer cell E_02_0156 PCR, Western blot, immunofluorescence staining Enhancer of zester homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PCR2), and its-terminal SET domain exhibits methyl transferase activity9 Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zester homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PCR2), and its-terminal SET domain exhibits methyl transferase activity9 Enhancer of zester homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PCR2), and its-terminal SET domain exhibits methyl transferase activity9 Immunohistochemical staining Enhancer of zester homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PCR2), and its-terminal SET domain exhibits methyl transferase activity9 PCR,Western blot,免疫荧光染色 31666509 chr3 38545360 38547360 SCN5A Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia dis_x0002_orders. human,mouse heart High+Lowthroughput An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo 是 rs6810361 Arrhythmia cardiac muscle cell (sensu Arthopoda) E_02_0157 Flow cytometry,PCR Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia dis_x0002_orders. Enhancer SCN5A qRT-PCR,qPCR,ChIP,3C RNA-Seq Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia dis_x0002_orders. Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia dis_x0002_orders. Immunohistochemical staining Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia dis_x0002_orders. Flow cytometry,PCR 31666509 chr3 38694445 38696445 SCN10A The activity of REs is largely limited to target genes that fall within the same TAD8, including SCN5A, SCN10A, EXOG, SCN11A, and WDR48. human,mouse connective tissue High+Lowthroughput An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo 是 rs6781009 Arrhythmia embryonic stem cell E_02_0157 Flow cytometry,PCR The activity of REs is largely limited to target genes that fall within the same TAD8, including SCN5A, SCN10A, EXOG, SCN11A, and WDR48. Enhancer SCN10A qRT-PCR,qPCR,ChIP,3C RNA-Seq The activity of REs is largely limited to target genes that fall within the same TAD8, including SCN5A, SCN10A, EXOG, SCN11A, and WDR48. The activity of REs is largely limited to target genes that fall within the same TAD8, including SCN5A, SCN10A, EXOG, SCN11A, and WDR48. Immunohistochemical staining The activity of REs is largely limited to target genes that fall within the same TAD8, including SCN5A, SCN10A, EXOG, SCN11A, and WDR48. Flow cytometry,PCR 31666072 chr17 50181276 50183276 COL1A1 Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13]. human Epithelial tissues High+Lowthroughput Epigenetic landscapes suggest that genetic risk for intracranial aneurysm operates on the endothelium 是 rs1333040 inflammation endothelial cell E_01_0193 ChIP-Seq Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13]. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13]. Immunohistochemical staining Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13]. COL1A1 ChIP-Seq Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13]. 31665646 chrX 73818246 73820246 XIST "HEK293 are female cells and, therefore, one of the two X chromosomes is subject to X chromosome inactivation, a process that is dependent on the expression of the XIST lncRNA (da Rocha and Heard, 2017; Jégu et al., 2017). Both MapR and RHΔC&R signals are clearly higher than the respective controls at the 5′ end of the XIST gene (Figure 2E). " human,mouse connective tissue High+Lowthroughput Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach 否 无 cancer HEK293 cell E_02_0158 Flow cytometry,PCR "HEK293 are female cells and, therefore, one of the two X chromosomes is subject to X chromosome inactivation, a process that is dependent on the expression of the XIST lncRNA (da Rocha and Heard, 2017; Jégu et al., 2017). Both MapR and RHΔC&R signals are clearly higher than the respective controls at the 5′ end of the XIST gene (Figure 2E). " Enhancer XIST qRT-PCR,qPCR,ChIP,3C RNA-Seq "HEK293 are female cells and, therefore, one of the two X chromosomes is subject to X chromosome inactivation, a process that is dependent on the expression of the XIST lncRNA (da Rocha and Heard, 2017; Jégu et al., 2017). Both MapR and RHΔC&R signals are clearly higher than the respective controls at the 5′ end of the XIST gene (Figure 2E). " "HEK293 are female cells and, therefore, one of the two X chromosomes is subject to X chromosome inactivation, a process that is dependent on the expression of the XIST lncRNA (da Rocha and Heard, 2017; Jégu et al., 2017). Both MapR and RHΔC&R signals are clearly higher than the respective controls at the 5′ end of the XIST gene (Figure 2E). " Immunohistochemical staining "HEK293 are female cells and, therefore, one of the two X chromosomes is subject to X chromosome inactivation, a process that is dependent on the expression of the XIST lncRNA (da Rocha and Heard, 2017; Jégu et al., 2017). Both MapR and RHΔC&R signals are clearly higher than the respective controls at the 5′ end of the XIST gene (Figure 2E). " Flow cytometry,PCR 31665330 chr16 68733997 68735997 CDH1 On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. human,mouse Epithelial tissues High+Lowthroughput Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators 否 无 Infertility epithelial cell E_02_0159 PCR On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. Enhancer CDH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. Immunohistochemical staining On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. PCR 31665330 chr13 73052330 73054330 KLF5 On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. human,mouse Epithelial tissues High+Lowthroughput Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators 否 无 Infertility epithelial cell E_02_0159 PCR On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. Enhancer KLF5 qRT-PCR,qPCR,ChIP,3C RNA-Seq On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. Immunohistochemical staining On the other hand, numerous epithelial cell markers including CDH1, CLDN1, CLDN4, CLDN8, CLDN10, KLF4 and KLF5 were all upregulated during MS. PCR 31665330 chr16 28529423 28531423 NUPR1 Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. mouse blood High+Lowthroughput Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators 否 无 Infertility B cell E_02_0159 PCR Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Enhancer NUPR1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Immunohistochemical staining Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. PCR 31665330 chr12 131947347 131949347 EP400 Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. mouse blood High+Lowthroughput Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators 否 无 Infertility B cell E_02_0159 PCR Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Enhancer EP400 qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. Immunohistochemical staining Additionally, the majority of the epithelial transcription regulators identified in our study have yet to be studied for functional relevance in mediating implantation in the human endometrium, including NUPR1, TBX2, SMARCA4, CEBPA, RABL6 and EP400. Interestingly, the Estrogen Receptors ESR1 and ESR2 showed repression and activation during WOI in the epithelium, respectively. PCR 31665135 chr8 116842944 116844944 RAD21 Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. human,mouse blood High+Lowthroughput EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions 否 无 E_02_0160 Flow cytometry,PCR Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Enhancer RAD21 qRT-PCR,qPCR,ChIP,3C RNA-Seq Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Immunohistochemical staining Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Flow cytometry,PCR 31665135 chr16 67559548 67561548 CTCF Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. human,mouse uterus High+Lowthroughput EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions 否 无 Hela-S3 cell E_02_0160 Flow cytometry,PCR Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Immunohistochemical staining Similarly, CTCF, RAD21, and H3K4me3 occurred more often at interacting pro_x0002_moters than non-interacting promoters (Fig 7). Taken together, histone marks and relevant factors suggested that our prediction of enhancer-target relationships were likely biologically functional. Flow cytometry,PCR 31665067 chr18 55219450 55221450 TCF4 While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42]. human bone High+Lowthroughput CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/RUVBL1 axis to enhance the transcriptional activity of β-catenin/LEF1 complex via effects on chromatin remodeling 否 无 Osteosarcoma osteosarcoma cell E_01_0194 Flow cytometry,PCR,Western blot While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42]. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42]. Immunohistochemical staining While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42]. TCF4 Flow cytometry,PCR,Western blot While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42]. 31665067 chr5 16658965 16660965 MYO10 In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44]. human connective tissue High+Lowthroughput CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/RUVBL1 axis to enhance the transcriptional activity of β-catenin/LEF1 complex via effects on chromatin remodeling 否 无 Osteosarcoma mesenchymal stem cell E_01_0194 Flow cytometry,PCR,Western blot In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44]. Enhancer MYO10 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44]. In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44]. Immunohistochemical staining In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44]. Flow cytometry,PCR,Western blot 31664109 chrX 154007840 154009840 IRAK1 IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. human blood High+Lowthroughput IRAK3 modulates downstream innate immune signalling through its guanylate cyclase activity 是 无 inflammation B cell E_01_0195 PCR IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. Enhancer IRAK1 qRT-PCR,qPCR,ChIP,3C RNA-Seq IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. Immunohistochemical staining IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. PCR 31664109 chr12 43756484 43758484 IRAK4 IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. human blood High+Lowthroughput IRAK3 modulates downstream innate immune signalling through its guanylate cyclase activity 是 无 inflammation B cell E_01_0195 PCR IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. Enhancer IRAK4 qRT-PCR,qPCR,ChIP,3C RNA-Seq IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. Immunohistochemical staining IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. PCR 31662342 chr16 86508235 86510235 FOXF1 Tran_x0002_scriptional profiling of lung samples obtained from normal human fetal lung tissues ranging from 53 to 140 days of gesta_x0002_tion demonstrated that FOXF1 has robust, stable expression throughout early human lung development (online supplemen_x0002_tary figure 4,11). human,mouse Epithelial tissues High+Lowthroughput Disruption of normal patterns of FOXF1 expression in a lethal disorder of lung development 否 无 cancer endothelial cell E_02_0161 Flow cytometry,PCR,Western blot Tran_x0002_scriptional profiling of lung samples obtained from normal human fetal lung tissues ranging from 53 to 140 days of gesta_x0002_tion demonstrated that FOXF1 has robust, stable expression throughout early human lung development (online supplemen_x0002_tary figure 4,11). Enhancer FOXF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Tran_x0002_scriptional profiling of lung samples obtained from normal human fetal lung tissues ranging from 53 to 140 days of gesta_x0002_tion demonstrated that FOXF1 has robust, stable expression throughout early human lung development (online supplemen_x0002_tary figure 4,11). Tran_x0002_scriptional profiling of lung samples obtained from normal human fetal lung tissues ranging from 53 to 140 days of gesta_x0002_tion demonstrated that FOXF1 has robust, stable expression throughout early human lung development (online supplemen_x0002_tary figure 4,11). Immunohistochemical staining Tran_x0002_scriptional profiling of lung samples obtained from normal human fetal lung tissues ranging from 53 to 140 days of gesta_x0002_tion demonstrated that FOXF1 has robust, stable expression throughout early human lung development (online supplemen_x0002_tary figure 4,11). Flow cytometry,PCR,Western blot 31661141 chr12 2855382 2857382 FOXM1 In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). human,mouse uterus High+Lowthroughput Crosstalk between histone modification and DNA methylation orchestrates the epigenetic regulation of the costimulatory factors, Tim?3 and galectin?9, in cervical cancer 否 无 cervical carcinoma HeLa cell E_02_0162 PCR,Western blot In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). Enhancer FOXM1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). Immunohistochemical staining In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). PCR,Western blot 31661141 chr7 148804354 148806354 EZH2 In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). human,mouse blood High+Lowthroughput Crosstalk between histone modification and DNA methylation orchestrates the epigenetic regulation of the costimulatory factors, Tim?3 and galectin?9, in cervical cancer 否 无 cervical carcinoma T cell E_02_0162 PCR,Western blot In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). Immunohistochemical staining In this study, we report that E2F-1 and FOXM1 mediated by HPV18 E6 and E7 can enhance the transcriptional activity of Enhancer of zeste homolog 2 (EZH2) by binding to its promoter region, resulting in the induced expression of the EZH2‑specific target protein, H3K27me3, which consequently reduces the expression of the downstream target gene, DNA (cytosine-5)-methyltransferase 3A (DNMT3A). PCR,Western blot 31661121 chr17 58267209 58269209 MPO Measurement of myeloperoxidase (MPO), malondialde‑hyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) levels. The MPO, MDA, SOD and GSH levels were detected using the related kits (MPO: cat. no. A044; MDA: cat. no. A003; SOD: cat. no. A001; GSH: cat. no. A005; Nanjing Jiancheng Bioengineering Institute). human,mouse Epithelial tissues High+Lowthroughput Dihydroartemisinin attenuates lipopolysaccharide?induced acute lung injury in mice by suppressing NF?κB signaling in an Nrf2?dependent manner 否 无 inflammation epithelial cell E_02_0163 PCR, Western blot, immunofluorescence staining Measurement of myeloperoxidase (MPO), malondialde‑hyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) levels. The MPO, MDA, SOD and GSH levels were detected using the related kits (MPO: cat. no. A044; MDA: cat. no. A003; SOD: cat. no. A001; GSH: cat. no. A005; Nanjing Jiancheng Bioengineering Institute). Enhancer MPO qRT-PCR,qPCR,ChIP,3C RNA-Seq Measurement of myeloperoxidase (MPO), malondialde‑hyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) levels. The MPO, MDA, SOD and GSH levels were detected using the related kits (MPO: cat. no. A044; MDA: cat. no. A003; SOD: cat. no. A001; GSH: cat. no. A005; Nanjing Jiancheng Bioengineering Institute). Measurement of myeloperoxidase (MPO), malondialde‑hyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) levels. The MPO, MDA, SOD and GSH levels were detected using the related kits (MPO: cat. no. A044; MDA: cat. no. A003; SOD: cat. no. A001; GSH: cat. no. A005; Nanjing Jiancheng Bioengineering Institute). Immunohistochemical staining Measurement of myeloperoxidase (MPO), malondialde‑hyde (MDA), superoxide dismutase (SOD) and glutathione (GSH) levels. The MPO, MDA, SOD and GSH levels were detected using the related kits (MPO: cat. no. A044; MDA: cat. no. A003; SOD: cat. no. A001; GSH: cat. no. A005; Nanjing Jiancheng Bioengineering Institute). PCR,Western blot,免疫荧光染色 31659808 chr2 237482764 237484764 MLPH To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues. human prostate High+Lowthroughput Single-nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4 是 rs13426236 prostatic cancer prostate cancer cell E_01_0196 Flow cytometry,Western blot,PCR To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues. Enhancer MLPH qRT-PCR,qPCR,ChIP,3C RNA-Seq To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues. To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues. Immunohistochemical staining To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues. Flow cytometry,Western blot,PCR 31659207 chr11 128455802 128457802 ETS1 ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39. human blood High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs9888739 Systemic lupus erythematosus T cell E_01_0197 Flow cytometry,PCR ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39. Immunohistochemical staining ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39. ETS1 Flow cytometry,PCR ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39. 31659207 chrX 49247778 49249778 FOXP3 Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1). human connective tissue High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs1143679 Systemic lupus erythematosus stem cell E_01_0197 Flow cytometry,PCR Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1). Immunohistochemical staining Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1). FOXP3 Flow cytometry,PCR Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1). 31659207 chr5 151027114 151029114 TNIP1 We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1). human blood High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs10488631 Systemic lupus erythematosus B cell E_01_0197 Flow cytometry,PCR We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1). Immunohistochemical staining We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1). TNIP1 Flow cytometry,PCR We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1). 31659207 chr7 128934736 128936736 IRF5 We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes. human connective tissue High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs4728142 Systemic lupus erythematosus B-lymphoblastoid cells E_01_0197 Flow cytometry,PCR We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes. Immunohistochemical staining We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes. IRF5 Flow cytometry,PCR We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes. 31659207 chrX 12864199 12866199 TLR7 Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45. human connective tissue High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs1128334 Systemic lupus erythematosus immune cell E_01_0197 Flow cytometry,PCR Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45. Enhancer TLR7 qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45. Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45. Immunohistochemical staining Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45. Flow cytometry,PCR 31659207 chr7 128951769 128953769 TNPO3 The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. human blood High+Lowthroughput Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus 是 rs6590330 Systemic lupus erythematosus E_01_0197 Flow cytometry,PCR The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Enhancer TNPO3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Immunohistochemical staining The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share. Flow cytometry,PCR 31659164 chr8 11673920 11675920 GATA4 Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. human connective tissue High+Lowthroughput A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers 否 无 cancer stem cell E_01_0198 PCR,Flow cytometry Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. Immunohistochemical staining Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. GATA4 PCR,Flow cytometry Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. 31659164 chr5 173229614 173231614 NKX2-5 The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. human Musculature High+Lowthroughput A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers 否 无 cancer muscle cell E_01_0198 PCR,Flow cytometry The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. Immunohistochemical staining The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. NKX2-5 PCR,Flow cytometry The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. 31659164 chr15 99562305 99564305 MEF2A The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. human Musculature High+Lowthroughput A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers 否 无 cancer muscle cell E_01_0198 PCR,Flow cytometry The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. Immunohistochemical staining The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. MEF2A PCR,Flow cytometry The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. 31659118 chr7 97849158 97851158 ASNS "Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. " human,mouse tumour High+Lowthroughput Promoter demethylation of the asparagine synthetase gene is required for ATF4-dependent adaptation to asparagine depletion 否 无 acute lymphoblastic leukemia tumor cell E_02_0164 Flow cytometry,Western blot,PCR "Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. " Enhancer ASNS qRT-PCR,qPCR,ChIP,3C RNA-Seq "Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. " "Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. " Immunohistochemical staining "Insufficient expression of ASNS leads to asparagine deficiency, which facilitates an ATF4-independent induction of C/EBP homologous protein (CHOP) that triggers apoptosis. " Flow cytometry,Western blot,PCR 31659118 chr1 28257099 28259099 SESN2 As a control, there was induced recruitment of ATF4 to the promoter region of another target gene, SESN2 (Figure 3E), following asparagine depletion in both the RS4;11 and RS4;11/R cells (Figure 4G, right). human,mouse blood High+Lowthroughput Promoter demethylation of the asparagine synthetase gene is required for ATF4-dependent adaptation to asparagine depletion 否 无 acute lymphoblastic leukemia Nalm-6 cell E_02_0164 Flow cytometry,Western blot,PCR As a control, there was induced recruitment of ATF4 to the promoter region of another target gene, SESN2 (Figure 3E), following asparagine depletion in both the RS4;11 and RS4;11/R cells (Figure 4G, right). Enhancer SESN2 qRT-PCR,qPCR,ChIP,3C RNA-Seq As a control, there was induced recruitment of ATF4 to the promoter region of another target gene, SESN2 (Figure 3E), following asparagine depletion in both the RS4;11 and RS4;11/R cells (Figure 4G, right). As a control, there was induced recruitment of ATF4 to the promoter region of another target gene, SESN2 (Figure 3E), following asparagine depletion in both the RS4;11 and RS4;11/R cells (Figure 4G, right). Immunohistochemical staining As a control, there was induced recruitment of ATF4 to the promoter region of another target gene, SESN2 (Figure 3E), following asparagine depletion in both the RS4;11 and RS4;11/R cells (Figure 4G, right). Flow cytometry,Western blot,PCR 31658410 chr14 48891897 48893897 Otx2 Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. human,mouse connective tissue High+Lowthroughput A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina 否 无 pluripotent stem cell E_02_0165 Flow cytometry, immunofluorescence staining Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Enhancer Otx2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Immunohistochemical staining Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Flow cytometry,免疫荧光染色 31658410 chr11 31781903 31783903 PAX6 In the 392-bp mouse hs1150 element, recognition sites for transcription factors PAX6, CHX10, CRX, BLIMP1, and OTX were found (Fig. 6A, B), suggesting that hs1150 enhancer could be regulated by these transcription factors thatare essential for neuroretinal cell differentiation human,mouse Nervous tissue High+Lowthroughput A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina 否 无 photoreceptor cell E_02_0165 Flow cytometry, immunofluorescence staining In the 392-bp mouse hs1150 element, recognition sites for transcription factors PAX6, CHX10, CRX, BLIMP1, and OTX were found (Fig. 6A, B), suggesting that hs1150 enhancer could be regulated by these transcription factors thatare essential for neuroretinal cell differentiation Enhancer PAX6 qRT-PCR,qPCR,ChIP,3C RNA-Seq In the 392-bp mouse hs1150 element, recognition sites for transcription factors PAX6, CHX10, CRX, BLIMP1, and OTX were found (Fig. 6A, B), suggesting that hs1150 enhancer could be regulated by these transcription factors thatare essential for neuroretinal cell differentiation In the 392-bp mouse hs1150 element, recognition sites for transcription factors PAX6, CHX10, CRX, BLIMP1, and OTX were found (Fig. 6A, B), suggesting that hs1150 enhancer could be regulated by these transcription factors thatare essential for neuroretinal cell differentiation Immunohistochemical staining In the 392-bp mouse hs1150 element, recognition sites for transcription factors PAX6, CHX10, CRX, BLIMP1, and OTX were found (Fig. 6A, B), suggesting that hs1150 enhancer could be regulated by these transcription factors thatare essential for neuroretinal cell differentiation Flow cytometry,免疫荧光染色 31657619 chr1 26690155 26692155 ARID1A "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" human,mouse connective tissue High+Lowthroughput Altered 5-Hydroxymethylcytosine Landscape in Primary Gastric Adenocarcinoma 否 无 gastric cancer embryonic stem cell E_02_0166 PCR "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" Enhancer ARID1A qRT-PCR,qPCR,ChIP,3C RNA-Seq "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" Immunohistochemical staining "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" PCR 31657619 chr10 121475438 121477438 FGFR2 "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" human,mouse connective tissue High+Lowthroughput Altered 5-Hydroxymethylcytosine Landscape in Primary Gastric Adenocarcinoma 否 无 gastric cancer embryonic stem cell E_02_0166 PCR "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" Enhancer FGFR2 qRT-PCR,qPCR,ChIP,3C RNA-Seq "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" Immunohistochemical staining "For example, previous studies have identified several key genetic alterations that are linked to gastric malignancy, including mutations in the chromatin modifier gene AT-rich interaction domain 1A (ARID1A) and amplifications in human epidermal growth factor receptor 2 (HER2), fibroblast growth factor receptor 2 (FGFR2), and mesenchymal–epithelial transition (MET)" PCR 31654083 chr17 44073800 44075800 HDAC5 "HDAC5 is recruited to its target genesthrough interactions with transcription factors, i.e., myocyte en_x0002_hancer factor 2 (MEF2), to repress target gene transcription (Parra and Verdin 2010). " human,mouse blood High+Lowthroughput Early-life blockade of NMDA receptors induces epigenetic abnormalities in the adult medial prefrontal cortex: possible involvement in memory impairment in trace fear conditioning 否 无 Schizophrenia E_02_0167 PCR,Western blot "HDAC5 is recruited to its target genesthrough interactions with transcription factors, i.e., myocyte en_x0002_hancer factor 2 (MEF2), to repress target gene transcription (Parra and Verdin 2010). " Enhancer HDAC5 qRT-PCR,qPCR,ChIP,3C RNA-Seq "HDAC5 is recruited to its target genesthrough interactions with transcription factors, i.e., myocyte en_x0002_hancer factor 2 (MEF2), to repress target gene transcription (Parra and Verdin 2010). " "HDAC5 is recruited to its target genesthrough interactions with transcription factors, i.e., myocyte en_x0002_hancer factor 2 (MEF2), to repress target gene transcription (Parra and Verdin 2010). " Immunohistochemical staining "HDAC5 is recruited to its target genesthrough interactions with transcription factors, i.e., myocyte en_x0002_hancer factor 2 (MEF2), to repress target gene transcription (Parra and Verdin 2010). " PCR,Western blot 31653691 chr12 107873350 107875350 Bcl11b To com_x0002_pare the molecular mechanisms through which Bcl11b controls cell type–specific gene regulation in the two contexts, we first examined the DNA binding patterns of Bcl11b across the genome in pro-T cells with those in ILC2 cells. human,mouse blood High+Lowthroughput Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells 否 无 mutant lymphoma cell E_02_0168 Flow cytometry,Western blot,PCR To com_x0002_pare the molecular mechanisms through which Bcl11b controls cell type–specific gene regulation in the two contexts, we first examined the DNA binding patterns of Bcl11b across the genome in pro-T cells with those in ILC2 cells. Enhancer Bcl11b qRT-PCR,qPCR,ChIP,3C RNA-Seq To com_x0002_pare the molecular mechanisms through which Bcl11b controls cell type–specific gene regulation in the two contexts, we first examined the DNA binding patterns of Bcl11b across the genome in pro-T cells with those in ILC2 cells. To com_x0002_pare the molecular mechanisms through which Bcl11b controls cell type–specific gene regulation in the two contexts, we first examined the DNA binding patterns of Bcl11b across the genome in pro-T cells with those in ILC2 cells. Immunohistochemical staining To com_x0002_pare the molecular mechanisms through which Bcl11b controls cell type–specific gene regulation in the two contexts, we first examined the DNA binding patterns of Bcl11b across the genome in pro-T cells with those in ILC2 cells. Flow cytometry,Western blot,PCR 31653691 chr16 92395674 92397674 Runx1 Thus, globally, Runx1, Runx3, and Bcl11b binding sites across the genome were often coincident within a cell type, but differed markedly between pro-T and ILC2 contexts. human,mouse lymph High+Lowthroughput Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells 否 无 lymphocyte E_02_0168 Flow cytometry,Western blot,PCR Thus, globally, Runx1, Runx3, and Bcl11b binding sites across the genome were often coincident within a cell type, but differed markedly between pro-T and ILC2 contexts. Enhancer Runx1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, globally, Runx1, Runx3, and Bcl11b binding sites across the genome were often coincident within a cell type, but differed markedly between pro-T and ILC2 contexts. Thus, globally, Runx1, Runx3, and Bcl11b binding sites across the genome were often coincident within a cell type, but differed markedly between pro-T and ILC2 contexts. Immunohistochemical staining Thus, globally, Runx1, Runx3, and Bcl11b binding sites across the genome were often coincident within a cell type, but differed markedly between pro-T and ILC2 contexts. Flow cytometry,Western blot,PCR 31653691 chr10 8042938 8044938 GATA3 These results show sharp lineagespecific binding differences both for the Runx factors, usually co-recruited with Bcl11b, and for GATA3, often recruited inde pendently of Bcl11b. They also indicate a likely role for a bZIP family member in defining ILC2-specific occupancy sites of Bcl11b, Runx factors, and GATA3 human,mouse blood High+Lowthroughput Cell type-specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells 否 无 T cell E_02_0168 Flow cytometry,Western blot,PCR These results show sharp lineagespecific binding differences both for the Runx factors, usually co-recruited with Bcl11b, and for GATA3, often recruited inde pendently of Bcl11b. They also indicate a likely role for a bZIP family member in defining ILC2-specific occupancy sites of Bcl11b, Runx factors, and GATA3 Enhancer GATA3 qRT-PCR,qPCR,ChIP,3C RNA-Seq These results show sharp lineagespecific binding differences both for the Runx factors, usually co-recruited with Bcl11b, and for GATA3, often recruited inde pendently of Bcl11b. They also indicate a likely role for a bZIP family member in defining ILC2-specific occupancy sites of Bcl11b, Runx factors, and GATA3 These results show sharp lineagespecific binding differences both for the Runx factors, usually co-recruited with Bcl11b, and for GATA3, often recruited inde pendently of Bcl11b. They also indicate a likely role for a bZIP family member in defining ILC2-specific occupancy sites of Bcl11b, Runx factors, and GATA3 Immunohistochemical staining These results show sharp lineagespecific binding differences both for the Runx factors, usually co-recruited with Bcl11b, and for GATA3, often recruited inde pendently of Bcl11b. They also indicate a likely role for a bZIP family member in defining ILC2-specific occupancy sites of Bcl11b, Runx factors, and GATA3 Flow cytometry,Western blot,PCR 31652979 chr8 127732500 127734500 MYC Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. human,mouse breast High+Lowthroughput PIK3CA Cooperates with KRAS to Promote MYC Activity and Tumorigenesis via the Bromodomain Protein BRD9 否 无 tumour mammary gland epithelial cell E_02_0169 Western blot Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. Enhancer MYC qRT-PCR,qPCR,ChIP,3C RNA-Seq Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. Immunohistochemical staining Gene set enrichment analysis revealed that DKI cells were enriched over single mutant cells for genes that characterize a MYC target gene signature. Western blot 31652453 chr7 148804156 148806156 EZH2 FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 human bone High+Lowthroughput Ketamine induces endoplasmic reticulum stress in rats and SV-HUC-1 human uroepithelial cells by activating NLRP3/TXNIP aix 否 无 Osteosarcoma osteosarcoma cell E_01_0199 Flow cytometry, Western blot, PCR, immunofluorescence light staining FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 Immunohistochemical staining FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 EZH2 Flow cytometry,Western blot,PCR,免疫荧光光染色 FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 31652453 chr9 94600340 94602340 FBP1 FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 human bone High+Lowthroughput Ketamine induces endoplasmic reticulum stress in rats and SV-HUC-1 human uroepithelial cells by activating NLRP3/TXNIP aix 否 无 Osteosarcoma osteosarcoma cell E_01_0199 Flow cytometry, Western blot, PCR, immunofluorescence light staining FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 Enhancer FBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 Immunohistochemical staining FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23 Flow cytometry,Western blot,PCR,免疫荧光光染色 31651209 chr2 236162410 236164410 GBX2 A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. human,mouse High+Lowthroughput GSK343 induces programmed cell death through the inhibition of EZH2 and FBP1 in osteosarcoma cells 否 无 Nerve injury Schwann cell E_02_0170 PCR, Western blot, immunofluorescence staining A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. Enhancer GBX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. Immunohistochemical staining A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. PCR,Western blot ,免疫荧光染色 31651209 chr11 114056802 114058802 ZBTB16 A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. human,mouse High+Lowthroughput GSK343 induces programmed cell death through the inhibition of EZH2 and FBP1 in osteosarcoma cells 否 无 Nerve injury Schwann cell E_02_0170 PCR, Western blot, immunofluorescence staining A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. Enhancer ZBTB16 qRT-PCR,qPCR,ChIP,3C RNA-Seq A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. Immunohistochemical staining A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. TFAP2A, a gene encoding transcription factor activating enhancer binding protein 2 alpha, was found to be critical in the regulatory network. PCR,Western blot ,免疫荧光染色 31650361 chr2 236162780 236164780 GBX2 A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. - human,mouse connective tissue High+Lowthroughput Dysregulated Transcription Factor TFAP2A After Peripheral Nerve Injury Modulated Schwann Cell Phenotype 否 无 Schwann cell E_02_0171 Western blot, PCR, gene knockdown A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. - Enhancer GBX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. - A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. - Immunohistochemical staining A total of 9 transcription factor genes, including GBX2, HIF3A, IRF8, LRRC63, SNAI3, SPIB, TBX21, TFAP2A, and ZBTB16 were identifed to be commonly diferentially expressed at 1, 4, 7, and 14 days after nerve injury. - Western blot,PCR,基因敲降 31649847 chr11 70018598 70020598 Mgl2 Kin increased the expression of M2-related genes Mgl1, Mgl2,Pgc1-β, Arg-1, Il-10 and Cd206 (Fig. 3A). human,mouse connective tissue High+Lowthroughput Kinsenoside attenuates osteoarthritis by repolarizing macrophages through inactivating NF-κB/MAPK signaling and protecting chondrocytes 否 无 Osteoarthritis macrophage E_02_0172 PCR, Western blot, flow cytometry, gene knockdown Kin increased the expression of M2-related genes Mgl1, Mgl2,Pgc1-β, Arg-1, Il-10 and Cd206 (Fig. 3A). Enhancer Mgl2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Kin increased the expression of M2-related genes Mgl1, Mgl2,Pgc1-β, Arg-1, Il-10 and Cd206 (Fig. 3A). Kin increased the expression of M2-related genes Mgl1, Mgl2,Pgc1-β, Arg-1, Il-10 and Cd206 (Fig. 3A). Immunohistochemical staining Kin increased the expression of M2-related genes Mgl1, Mgl2,Pgc1-β, Arg-1, Il-10 and Cd206 (Fig. 3A). PCR,Western blot,Flow cytometry,基因敲降 31649059 chr1 8001795 8003795 ERRFI1 "As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. " human blood High+Lowthroughput Identification and dynamic quantification of regulatory elements using total RNA 否 无 leukemia myelogenous leukemia cell E_01_0200 Flow cytometry "As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. " Enhancer ERRFI1 qRT-PCR,qPCR,ChIP,3C RNA-Seq "As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. " "As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. " Immunohistochemical staining "As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. " Flow cytometry 31649055 chr2 47342302 47344302 EPCAM "The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. " human connective tissue High+Lowthroughput FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples 是 无 leukemia stromal macrophage cell E_01_0201 Flow cytometry "The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. " Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq "The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. " Immunohistochemical staining "The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. " EPCAM Flow cytometry "The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. " 31649032 chr3 66876146 66878146 Shox2 Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. human connective tissue High+Lowthroughput Shox2 regulates osteogenic differentiation and pattern formation during hard palate development in mice 否 无 mesenchymal cell E_01_0202 Flow cytometry, PCR, immunofluorescence staining Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. Enhancer Shox2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. Immunohistochemical staining Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. Flow cytometry,PCR,免疫荧光染色 31644911 chr8 101489945 101491945 GRHL2 Motif enrichment analysis of sequences within the ‘‘gained’’ DHSs in TAMR indicated that the transcription factors most likely to be interacting at these genomic loci include those that bind bZip motifs, GRHL2, AP2 factors, ER, and FOXA family members (Figure 1B). human,mouse breast High+Lowthroughput The Lineage Determining Factor GRHL2 Collaborates with FOXA1 to Establish a Targetable Pathway in Endocrine Therapy-Resistant Breast Cancer 否 无 mammary cancer breast cancer cell E_02_0173 PCR,Western blot,Flow cytometry Motif enrichment analysis of sequences within the ‘‘gained’’ DHSs in TAMR indicated that the transcription factors most likely to be interacting at these genomic loci include those that bind bZip motifs, GRHL2, AP2 factors, ER, and FOXA family members (Figure 1B). Enhancer GRHL2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Motif enrichment analysis of sequences within the ‘‘gained’’ DHSs in TAMR indicated that the transcription factors most likely to be interacting at these genomic loci include those that bind bZip motifs, GRHL2, AP2 factors, ER, and FOXA family members (Figure 1B). Motif enrichment analysis of sequences within the ‘‘gained’’ DHSs in TAMR indicated that the transcription factors most likely to be interacting at these genomic loci include those that bind bZip motifs, GRHL2, AP2 factors, ER, and FOXA family members (Figure 1B). Immunohistochemical staining Motif enrichment analysis of sequences within the ‘‘gained’’ DHSs in TAMR indicated that the transcription factors most likely to be interacting at these genomic loci include those that bind bZip motifs, GRHL2, AP2 factors, ER, and FOXA family members (Figure 1B). PCR,Western blot,Flow cytometry 31644352 chr16 28929347 28931347 CD19 "Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). " human blood High+Lowthroughput Sepsis Induces Prolonged Epigenetic Modifications in Bone Marrow and Peripheral Macrophages Impairing Inflammation and Wound Healing 否 无 septicemia B cell E_01_0203 PCR, flow cytometry, immunofluorescence staining "Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). " Enhancer CD19 qRT-PCR,qPCR,ChIP,3C RNA-Seq "Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). " "Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). " Immunohistochemical staining "Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). " PCR,Flow cytometry,免疫荧光染色 31642979 chr4 184382613 184384613 IRF2 Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b). human colon High+Lowthroughput Three functional variants were identified to affect RPS24 expression and significantly associated with risk of colorectal cancer 是 rs7071351 Colon cancer Human colorectal carcinoma cell E_01_0204 PCR,Flow cytometry Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b). Immunohistochemical staining Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b). IRF2 PCR,Flow cytometry Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b). 31642979 chr10 79066184 79068184 ZMIZ1 However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation. human colon High+Lowthroughput Three functional variants were identified to affect RPS24 expression and significantly associated with risk of colorectal cancer 是 rs704017 Colon cancer Human colorectal carcinoma cell E_01_0204 PCR,Flow cytometry However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation. Immunohistochemical staining However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation. ZMIZ1 PCR,Flow cytometry However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation. 31642363 chr7 148804489 148806489 EZH2 Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2 human connective tissue High+Lowthroughput Sepsis Induces Prolonged Epigenetic Modifications in Bone Marrow and Peripheral Macrophages Impairing Inflammation and Wound Healing 否 无 mesenchymal stem cell E_01_0205 PCR,Western blot Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2 Immunohistochemical staining Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2 EZH2 PCR,Western blot Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2 31641208 chr16 68734197 68736197 CDH1 Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis. human blood High+Lowthroughput Enhancer of zeste homolog 2 enhances the migration and chemotaxis of dental mesenchymal stem cells 是 rs7198799, tumour E_01_0206 PCR,Western blot Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis. Immunohistochemical staining Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis. CDH1 PCR,Western blot Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis. 31636473 chr10 67881712 67883712 SIRT1 Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing human Epithelial tissues High+Lowthroughput Sirtuin 1 alleviates endoplasmic reticulum stress-mediated apoptosis of intestinal epithelial cells in ulcerative colitis 否 无 epithelial cell E_01_0207 Flow cytometry,PCR,Western blot Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing Immunohistochemical staining Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing SIRT1 Flow cytometry,PCR,Western blot Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing 31636429 chr5 70046788 70048788 SMN2 The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a). human Epithelial tissues High+Lowthroughput Structural basis of a small molecule targeting RNA for a specific splicing correction 否 无 Spinal muscular atrophy HEK293T E_01_0208 Western blot The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a). Enhancer SMN2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a). The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a). Immunohistochemical staining The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a). Western blot 31636200 chr4 110614447 110616447 PITX2 Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2. human connective tissue High+Lowthroughput Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation 是 rs2595104 Atrial fibrillation embryonic stem cell E_01_0209 Flow cytometry,PCR,Western blot Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2. Immunohistochemical staining Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2. PITX2 Flow cytometry,PCR,Western blot Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2. 31634421 chr16 92395428 92397428 Runx1 Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies. human blood High+Lowthroughput Gata3 targets Runx1 in the embryonic haematopoietic stem cell niche 否 无 Hematologic disorders hematopoietic stem cell E_01_0210 Flow cytometry,PCR,Western blot Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies. Enhancer Runx1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies. Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies. Immunohistochemical staining Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies. Flow cytometry,PCR,Western blot 31633376 chr6 84684753 84686753 TBX18 Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head. human Musculature High+Lowthroughput Transcription Factor TBX18 Reprograms Vascular Smooth Muscle Cells of Ascending Aorta to Pacemaker-Like Cells 否 无 smooth muscle cell E_01_0211 Flow cytometry, PCR, immunofluorescence staining Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head. Immunohistochemical staining Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head. TBX18 Flow cytometry,PCR,免疫荧光染色 Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head. 31632241 chr20 50885804 50887804 ADNP Activity-dependent neuroprotective protein (ADNP) has been initially discovered through its eight amino acid sequence NAPVSIPQ (Bassan et al., 1999), which shares SIP motif with SALLRSIPA – a peptide derived from activity-dependent neurotrophic factor (ADNF) (Brenneman and Gozes, 1996; Zamostiano et al., 1999). human,mouse High+Lowthroughput A Novel Microtubule-Tau Association Enhancer and Neuroprotective Drug Candidate: Ac-SKIP 否 无 Alzheimer E_02_0174 Flow cytometry,PCR,Western blot Activity-dependent neuroprotective protein (ADNP) has been initially discovered through its eight amino acid sequence NAPVSIPQ (Bassan et al., 1999), which shares SIP motif with SALLRSIPA – a peptide derived from activity-dependent neurotrophic factor (ADNF) (Brenneman and Gozes, 1996; Zamostiano et al., 1999). Enhancer ADNP qRT-PCR,qPCR,ChIP,3C RNA-Seq Activity-dependent neuroprotective protein (ADNP) has been initially discovered through its eight amino acid sequence NAPVSIPQ (Bassan et al., 1999), which shares SIP motif with SALLRSIPA – a peptide derived from activity-dependent neurotrophic factor (ADNF) (Brenneman and Gozes, 1996; Zamostiano et al., 1999). Activity-dependent neuroprotective protein (ADNP) has been initially discovered through its eight amino acid sequence NAPVSIPQ (Bassan et al., 1999), which shares SIP motif with SALLRSIPA – a peptide derived from activity-dependent neurotrophic factor (ADNF) (Brenneman and Gozes, 1996; Zamostiano et al., 1999). Immunohistochemical staining Activity-dependent neuroprotective protein (ADNP) has been initially discovered through its eight amino acid sequence NAPVSIPQ (Bassan et al., 1999), which shares SIP motif with SALLRSIPA – a peptide derived from activity-dependent neurotrophic factor (ADNF) (Brenneman and Gozes, 1996; Zamostiano et al., 1999). Flow cytometry,PCR,Western blot 31631036 chr7 148804245 148806245 EZH2 To ascertain whether EZH2 expression was correlated with CEP degeneration, immunohistochemical analysis of human CEP tissue was used to compare the level of EZH2 in normal and degenerated human CEP. It was found that the expression of EZH2 increased in degenerated human CEP (Fig. 1D and 1E). human,mouse connective tissue High+Lowthroughput Inhibition of EZH2 ameliorates cartilage endplate degeneration and attenuates the progression of intervertebral disc degeneration via demethylation of Sox-9 否 无 Disc degeneration stem cell E_02_0175 PCR,Western blot To ascertain whether EZH2 expression was correlated with CEP degeneration, immunohistochemical analysis of human CEP tissue was used to compare the level of EZH2 in normal and degenerated human CEP. It was found that the expression of EZH2 increased in degenerated human CEP (Fig. 1D and 1E). Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq To ascertain whether EZH2 expression was correlated with CEP degeneration, immunohistochemical analysis of human CEP tissue was used to compare the level of EZH2 in normal and degenerated human CEP. It was found that the expression of EZH2 increased in degenerated human CEP (Fig. 1D and 1E). To ascertain whether EZH2 expression was correlated with CEP degeneration, immunohistochemical analysis of human CEP tissue was used to compare the level of EZH2 in normal and degenerated human CEP. It was found that the expression of EZH2 increased in degenerated human CEP (Fig. 1D and 1E). Immunohistochemical staining To ascertain whether EZH2 expression was correlated with CEP degeneration, immunohistochemical analysis of human CEP tissue was used to compare the level of EZH2 in normal and degenerated human CEP. It was found that the expression of EZH2 increased in degenerated human CEP (Fig. 1D and 1E). PCR,Western blot 31631026 chr1 23017098 23019098 KDM1A We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. human connective tissue High+Lowthroughput Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG 否 无 Desmosomas melanoma cells E_01_0212 Western blot,PCR,Flow cytometry We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. Immunohistochemical staining We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. KDM1A Western blot,PCR,Flow cytometry We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts. 31631012 chr2 209421458 209423458 MAP2 Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). human connective tissue High+Lowthroughput Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction 是 rs2176546 pluripotent stem cell E_01_0213 Flow cytometry,PCR Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Enhancer MAP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Immunohistochemical staining Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Flow cytometry,PCR 31631012 chr9 91560120 91562120 ROR2 Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). human connective tissue High+Lowthroughput Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction 是 rs2176546 pluripotent stem cell E_01_0213 Flow cytometry,PCR Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). Immunohistochemical staining Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). ROR2 Flow cytometry,PCR Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B). 31631012 chr12 7784977 7786977 NANOG Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. human Nervous tissue High+Lowthroughput Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction 是 rs6545663 neural progenitor cell E_01_0213 Flow cytometry,PCR Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Enhancer NANOG qRT-PCR,qPCR,ChIP,3C RNA-Seq Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Immunohistochemical staining Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Flow cytometry,PCR 31631012 chr6 31161576 31163576 POU5F1 Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. human Nervous tissue High+Lowthroughput Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction 是 rs6545663 neural progenitor cell E_01_0213 Flow cytometry,PCR Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Immunohistochemical staining Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. POU5F1 Flow cytometry,PCR Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. 31631012 chr1 212563135 212565135 ATF3 Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. human connective tissue High+Lowthroughput Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction 是 rs6545664 stem cell E_01_0213 Flow cytometry,PCR Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Enhancer ATF3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Immunohistochemical staining Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli. Flow cytometry,PCR 31629814 chrX 47632617 47634617 ELK1 Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40 human liver High+Lowthroughput The Dynamic Chromatin Architecture of the Regenerating Liver 否 无 Obesity hepatocyte E_01_0214 Flow cytometry,PCR Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40 Immunohistochemical staining Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40 KCNH4 Flow cytometry,PCR Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40 31629687 chr1 35867480 35869480 AGO1 A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells human liver High+Lowthroughput Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells 否 无 cancer HepG2 cell E_01_0215 Western blot,Flow cytometry,PCR A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells Enhancer AGO1 qRT-PCR,qPCR,ChIP,3C RNA-Seq A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells Immunohistochemical staining A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells Western blot,Flow cytometry,PCR 31628347 chr5 147234799 147236799 Cdx2 We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. human connective tissue High+Lowthroughput Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells 否 无 Trophoblast stem cell E_01_0216 Flow cytometry We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Enhancer Cdx2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Immunohistochemical staining We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Flow cytometry 31628347 chr6 128198651 128200651 Tead4 We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. human connective tissue High+Lowthroughput Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells 否 无 Trophoblast stem cell E_01_0216 Flow cytometry We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Enhancer Tead4 qRT-PCR,qPCR,ChIP,3C RNA-Seq We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Immunohistochemical staining We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Flow cytometry 31628324 chr16 72780389 72782389 ZFHX3 A third locus we examined is 16q22. The most highly AF_x0002_associated risk SNPs in this locus are found in the first intron of ZFHX3, which codes for a TF that plays key roles in development and in adult tissues56,57. human,mouse Musculature High+Lowthroughput Identification of atrial fibrillation associated genes and functional non-coding variants 是 rs281766 Arrhythmia muscle cell E_02_0176 Flow cytometry,PCR A third locus we examined is 16q22. The most highly AF_x0002_associated risk SNPs in this locus are found in the first intron of ZFHX3, which codes for a TF that plays key roles in development and in adult tissues56,57. Enhancer ZFHX3 qRT-PCR,qPCR,ChIP,3C RNA-Seq A third locus we examined is 16q22. The most highly AF_x0002_associated risk SNPs in this locus are found in the first intron of ZFHX3, which codes for a TF that plays key roles in development and in adult tissues56,57. A third locus we examined is 16q22. The most highly AF_x0002_associated risk SNPs in this locus are found in the first intron of ZFHX3, which codes for a TF that plays key roles in development and in adult tissues56,57. Immunohistochemical staining A third locus we examined is 16q22. The most highly AF_x0002_associated risk SNPs in this locus are found in the first intron of ZFHX3, which codes for a TF that plays key roles in development and in adult tissues56,57. Flow cytometry,PCR 31626715 chr4 108044853 108046853 LEF1 Here we identify the EMT transcription factor LEF1 as a critical regulator of glutathione (GSH) metabolism aside from its well-known role as EMT inducer. human,mouse breast High+Lowthroughput LEF1 supports metastatic brain colonization by regulating glutathione metabolism and increasing ROS resistance in breast cancer 否 无 mammary cancer breast cancer cell E_02_0177 Western blot,PCR,Flow cytometry Here we identify the EMT transcription factor LEF1 as a critical regulator of glutathione (GSH) metabolism aside from its well-known role as EMT inducer. Enhancer LEF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we identify the EMT transcription factor LEF1 as a critical regulator of glutathione (GSH) metabolism aside from its well-known role as EMT inducer. Here we identify the EMT transcription factor LEF1 as a critical regulator of glutathione (GSH) metabolism aside from its well-known role as EMT inducer. Immunohistochemical staining Here we identify the EMT transcription factor LEF1 as a critical regulator of glutathione (GSH) metabolism aside from its well-known role as EMT inducer. Western blot,PCR,Flow cytometry 31624269 chr14 95707296 95709296 TCL1A Wright et al.identified a total of 19 loci associated with mLOY9, including TCL1A and other genes involved in cell cycle regulation and DNA damage response. human,mouse blood High+Lowthroughput GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation 是 rs17758695 hematopoietic stem cell E_02_0178 Flow cytometry Wright et al.identified a total of 19 loci associated with mLOY9, including TCL1A and other genes involved in cell cycle regulation and DNA damage response. Enhancer TCL1A qRT-PCR,qPCR,ChIP,3C RNA-Seq Wright et al.identified a total of 19 loci associated with mLOY9, including TCL1A and other genes involved in cell cycle regulation and DNA damage response. Wright et al.identified a total of 19 loci associated with mLOY9, including TCL1A and other genes involved in cell cycle regulation and DNA damage response. Immunohistochemical staining Wright et al.identified a total of 19 loci associated with mLOY9, including TCL1A and other genes involved in cell cycle regulation and DNA damage response. Flow cytometry 31624086 chr6 45325657 45327657 RUNX2 RUNX2 is a mammalian RUNT-related transcription factor (TF) required during embryogenesis for skeletal development and for the morphogenesis of many organs such as breast and thy_x0002_roid (13, 14). human,mouse connective tissue High+Lowthroughput RAIN Is a Novel Enhancer-Associated lncRNA That Controls RUNX2 Expression and Promotes Breast and Thyroid Cancer 否 无 cancer cancer cell E_02_0179 Flow cytometry,PCR RUNX2 is a mammalian RUNT-related transcription factor (TF) required during embryogenesis for skeletal development and for the morphogenesis of many organs such as breast and thy_x0002_roid (13, 14). Enhancer RUNX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq RUNX2 is a mammalian RUNT-related transcription factor (TF) required during embryogenesis for skeletal development and for the morphogenesis of many organs such as breast and thy_x0002_roid (13, 14). RUNX2 is a mammalian RUNT-related transcription factor (TF) required during embryogenesis for skeletal development and for the morphogenesis of many organs such as breast and thy_x0002_roid (13, 14). Immunohistochemical staining RUNX2 is a mammalian RUNT-related transcription factor (TF) required during embryogenesis for skeletal development and for the morphogenesis of many organs such as breast and thy_x0002_roid (13, 14). Flow cytometry,PCR 31623059 chr1 998360 1000360 ISG15 However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b). human blood High+Lowthroughput Identification of an Interferon-Stimulated Long Noncoding RNA (LncRNA ISR) Involved in Regulation of Influenza A Virus Replication 否 无 influenza B cell E_01_0217 PCR,Western blot However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b). Enhancer ISG15 qRT-PCR,qPCR,ChIP,3C RNA-Seq However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b). However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b). Immunohistochemical staining However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b). PCR,Western blot 31622687 chr3 101825749 101827749 NFKBIZ No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B). human blood High+Lowthroughput IκBζ is a key player in the antipsoriatic effects of secukinumab 否 无 Psoriasis B cell E_01_0218 PCR,Western blot No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B). Enhancer NFKBIZ qRT-PCR,qPCR,ChIP,3C RNA-Seq No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B). No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B). Immunohistochemical staining No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B). PCR,Western blot 31621893 chr12 6531600 6533600 GAPDH The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . human liver High+Lowthroughput Costunolide represses hepatic fibrosis through WW domain-containing protein 2-mediated Notch3 degradation 否 无 hepatic stellate cell E_01_0219 PCR, Western blot, immunofluorescence staining The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . Immunohistochemical staining The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . GAPDH PCR,Western blot,免疫荧光染色 The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . 31621893 chr6 125135892 125137892 Gapdh The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . human kidney High+Lowthroughput Costunolide represses hepatic fibrosis through WW domain-containing protein 2-mediated Notch3 degradation 否 无 HEK293T E_01_0219 PCR, Western blot, immunofluorescence staining The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . Enhancer Gapdh qRT-PCR,qPCR,ChIP,3C RNA-Seq The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . Immunohistochemical staining The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt . PCR,Western blot,免疫荧光染色 31621133 chr17 42310525 42312525 STAT3 Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX. human liver High+Lowthroughput Interleukin-34 mediated by hepatitis B virus X protein via CCAAT/enhancer-binding protein α contributes to the proliferation and migration of hepatoma cells 否 无 liver cancer HCC cell E_01_0220 PCR, gene knockdown, Western blot Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX. Immunohistochemical staining Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX. STAT3 PCR,基因敲降,Western blot Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX. 31620967 chr12 6531445 6533445 GAPDH Membranes were incubated with primary antibody solution diluted 1:1000 in 5% (w/v) nonfat dry milk in TBS-T (mouse anti-ATP synthase subunit beta, ab14730, Abcam; rabbit anti-GAPDH, ab9485, Abcam; rabbit anti-ETFDH, ab91508, Abcam; mouse heart High+Lowthroughput One year of exercise training promotes distinct adaptations in right and left ventricle of female Sprague-Dawley rats 否 无 Cardiac progenitor cell E_02_0180 PCR,Western blot Membranes were incubated with primary antibody solution diluted 1:1000 in 5% (w/v) nonfat dry milk in TBS-T (mouse anti-ATP synthase subunit beta, ab14730, Abcam; rabbit anti-GAPDH, ab9485, Abcam; rabbit anti-ETFDH, ab91508, Abcam; Enhancer GAPDH qRT-PCR,qPCR,ChIP,3C RNA-Seq Membranes were incubated with primary antibody solution diluted 1:1000 in 5% (w/v) nonfat dry milk in TBS-T (mouse anti-ATP synthase subunit beta, ab14730, Abcam; rabbit anti-GAPDH, ab9485, Abcam; rabbit anti-ETFDH, ab91508, Abcam; Membranes were incubated with primary antibody solution diluted 1:1000 in 5% (w/v) nonfat dry milk in TBS-T (mouse anti-ATP synthase subunit beta, ab14730, Abcam; rabbit anti-GAPDH, ab9485, Abcam; rabbit anti-ETFDH, ab91508, Abcam; Immunohistochemical staining Membranes were incubated with primary antibody solution diluted 1:1000 in 5% (w/v) nonfat dry milk in TBS-T (mouse anti-ATP synthase subunit beta, ab14730, Abcam; rabbit anti-GAPDH, ab9485, Abcam; rabbit anti-ETFDH, ab91508, Abcam; PCR,Western blot 31619507 chr4 147635062 147637062 PRMT9 Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. human lung High+Lowthroughput PRMT6 Promotes Lung Tumor Progression via the Alternate Activation of Tumor-Associated Macrophages 否 无 tumour NSCLC cell E_01_0221 PCR, gene knockdown, Western blot Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. Enhancer PRMT9 qRT-PCR,qPCR,ChIP,3C RNA-Seq Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. Immunohistochemical staining Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. PCR,基因敲降,Western blot 31619182 chr7 148804718 148806718 EZH2 In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. human blood High+Lowthroughput Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings 否 无 leukemia leukemic cell E_01_0222 PCR, Western blot, immunofluorescence staining In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. Immunohistochemical staining In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. EZH2 PCR,Western blot,免疫荧光染色 In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported. 31618980 chr10 67881914 67883914 SIRT1 SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40]. human Musculature High+Lowthroughput Gynostemma Pentaphyllum Extract Ameliorates High-Fat Diet-Induced Obesity in C57BL/6N Mice by Upregulating SIRT1 否 无 Obesity mouse cell of skeletal muscle E_01_0223 PCR,Western blot SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40]. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40]. Immunohistochemical staining SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40]. SIRT1 PCR,Western blot SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40]. 31618627 chr12 2956471 2958471 TEAD4 Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. human connective tissue High+Lowthroughput Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51 否 无 cancer E_01_0224 PCR,Flow cytometry Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. Immunohistochemical staining Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. TEAD4 PCR,Flow cytometry Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway. 31616042 chr16 54280654 54282654 IRX3 "The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19]." human connective tissue High+Lowthroughput Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks 是 rs75059851 tumour tumor cell E_01_0225 Flow cytometry "The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19]." Enhancer IRX3 qRT-PCR,qPCR,ChIP,3C RNA-Seq "The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19]." "The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19]." Immunohistochemical staining "The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19]." Flow cytometry 31616042 chr2 57904994 57906994 VRK2 A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants. human Nervous tissue High+Lowthroughput Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks 是 rs10791097 Schizophrenia neural cell E_01_0225 Flow cytometry A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants. Enhancer VRK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants. A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants. Immunohistochemical staining A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants. Flow cytometry 31615896 chr17 39401537 39403537 MED1 In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models. human connective tissue High+Lowthroughput The transcription factor NKX1-2 promotes adipogenesis and may contribute to a balance between adipocyte and osteoblast differentiation 否 无 Thyroid cancer ear mesenchymal stem cell E_01_0226 Western blot,PCR In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models. Immunohistochemical staining In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models. MED1 Western blot,PCR In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models. 31615655 chr17 39458277 39460277 CDK12 CDK12 is a transcription-related CDK that complexes with cyclinK to regulate gene transcription [6]. CDK12 has been demonstrated to be essential for DNA damage response (DDR), mRNA processing, and differentiation [7e9]. Several recent studies also implicated CDK12 in cancer pathology [10,11]. human,mouse thyroid High+Lowthroughput Targeting CDK12-mediated transcription regulation in anaplastic thyroid carcinoma 否 无 Anaplastic thyroid cancer Anaplastic thyroid carcinoma cell E_02_0181 PCR, Western blot, flow cytometry, immunofluorescence staining CDK12 is a transcription-related CDK that complexes with cyclinK to regulate gene transcription [6]. CDK12 has been demonstrated to be essential for DNA damage response (DDR), mRNA processing, and differentiation [7e9]. Several recent studies also implicated CDK12 in cancer pathology [10,11]. Enhancer CDK12 qRT-PCR,qPCR,ChIP,3C RNA-Seq CDK12 is a transcription-related CDK that complexes with cyclinK to regulate gene transcription [6]. CDK12 has been demonstrated to be essential for DNA damage response (DDR), mRNA processing, and differentiation [7e9]. Several recent studies also implicated CDK12 in cancer pathology [10,11]. CDK12 is a transcription-related CDK that complexes with cyclinK to regulate gene transcription [6]. CDK12 has been demonstrated to be essential for DNA damage response (DDR), mRNA processing, and differentiation [7e9]. Several recent studies also implicated CDK12 in cancer pathology [10,11]. Immunohistochemical staining CDK12 is a transcription-related CDK that complexes with cyclinK to regulate gene transcription [6]. CDK12 has been demonstrated to be essential for DNA damage response (DDR), mRNA processing, and differentiation [7e9]. Several recent studies also implicated CDK12 in cancer pathology [10,11]. PCR,Western blot,Flow cytometry,免疫荧光染色 31615341 chr1 204393890 204395890 PPP1R15B However, levels of TGFβR1 did not show any change and therefore is possibly not a direct target of miR-98-5p. miR-98-5p also significantly decreased the mRNA levels of PPP1R15B (Figure 3(b)) further suggesting that this gene is targeted by miR-98-5p. human,mouse Epithelial tissues High+Lowthroughput Circulatory miR-98-5p levels are deregulated during diabetes and it inhibits proliferation and promotes apoptosis by targeting PPP1R15B in keratinocytes 否 无 diabetes HaCaT cell E_02_0182 Flow cytometry,PCR,Western blot However, levels of TGFβR1 did not show any change and therefore is possibly not a direct target of miR-98-5p. miR-98-5p also significantly decreased the mRNA levels of PPP1R15B (Figure 3(b)) further suggesting that this gene is targeted by miR-98-5p. Enhancer PPP1R15B qRT-PCR,qPCR,ChIP,3C RNA-Seq However, levels of TGFβR1 did not show any change and therefore is possibly not a direct target of miR-98-5p. miR-98-5p also significantly decreased the mRNA levels of PPP1R15B (Figure 3(b)) further suggesting that this gene is targeted by miR-98-5p. However, levels of TGFβR1 did not show any change and therefore is possibly not a direct target of miR-98-5p. miR-98-5p also significantly decreased the mRNA levels of PPP1R15B (Figure 3(b)) further suggesting that this gene is targeted by miR-98-5p. Immunohistochemical staining However, levels of TGFβR1 did not show any change and therefore is possibly not a direct target of miR-98-5p. miR-98-5p also significantly decreased the mRNA levels of PPP1R15B (Figure 3(b)) further suggesting that this gene is targeted by miR-98-5p. Flow cytometry,PCR,Western blot 31614133 chr5 88713906 88715906 MEF2C Additionally, chromatin immunoprecipitation experiments and luciferase assays confirmed MEF2C interaction and direct binding of the CAIII promoter between -416 to -200 base pair. human,mouse Musculature High+Lowthroughput CAIII expression in skeletal muscle is regulated by Ca(2+)-CaMKII-MEF2C signaling 否 无 mouse cell of skeletal muscle E_02_0183 PCR,Western blot Additionally, chromatin immunoprecipitation experiments and luciferase assays confirmed MEF2C interaction and direct binding of the CAIII promoter between -416 to -200 base pair. Enhancer MEF2C qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, chromatin immunoprecipitation experiments and luciferase assays confirmed MEF2C interaction and direct binding of the CAIII promoter between -416 to -200 base pair. Additionally, chromatin immunoprecipitation experiments and luciferase assays confirmed MEF2C interaction and direct binding of the CAIII promoter between -416 to -200 base pair. Immunohistochemical staining Additionally, chromatin immunoprecipitation experiments and luciferase assays confirmed MEF2C interaction and direct binding of the CAIII promoter between -416 to -200 base pair. PCR,Western blot 31614133 chr15 99563007 99565007 MEF2A Therefore, we evaluated the role of different MEF2 homologs in CAIII expression. Plasmids containing RNAi sequences targeting MEF2A, MEF2C, and MEF2D were transfected into C2C12 cells, and CAIII expression was evaluated. human,mouse Musculature High+Lowthroughput CAIII expression in skeletal muscle is regulated by Ca(2+)-CaMKII-MEF2C signaling 否 无 C2C12 cell E_02_0183 PCR,Western blot Therefore, we evaluated the role of different MEF2 homologs in CAIII expression. Plasmids containing RNAi sequences targeting MEF2A, MEF2C, and MEF2D were transfected into C2C12 cells, and CAIII expression was evaluated. Enhancer MEF2A qRT-PCR,qPCR,ChIP,3C RNA-Seq Therefore, we evaluated the role of different MEF2 homologs in CAIII expression. Plasmids containing RNAi sequences targeting MEF2A, MEF2C, and MEF2D were transfected into C2C12 cells, and CAIII expression was evaluated. Therefore, we evaluated the role of different MEF2 homologs in CAIII expression. Plasmids containing RNAi sequences targeting MEF2A, MEF2C, and MEF2D were transfected into C2C12 cells, and CAIII expression was evaluated. Immunohistochemical staining Therefore, we evaluated the role of different MEF2 homologs in CAIII expression. Plasmids containing RNAi sequences targeting MEF2A, MEF2C, and MEF2D were transfected into C2C12 cells, and CAIII expression was evaluated. PCR,Western blot 31610176 chr6 131945597 131947597 CCN2 Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. human connective tissue High+Lowthroughput Insights into Fibroblast Plasticity: Cellular Communication Network 2 Is Required for Activation of Cancer-Associated Fibroblasts in a Murine Model of Melanoma 否 无 tumour melanoma cells E_01_0227 Flow cytometry,PCR,Western blot Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Immunohistochemical staining Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. CCN2 Flow cytometry,PCR,Western blot Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. 31610176 chr3 34702118 34704118 Sox2 Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. human connective tissue High+Lowthroughput Insights into Fibroblast Plasticity: Cellular Communication Network 2 Is Required for Activation of Cancer-Associated Fibroblasts in a Murine Model of Melanoma 否 无 tumour stem cell E_01_0227 Flow cytometry,PCR,Western blot Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Enhancer Sox2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Immunohistochemical staining Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2. Flow cytometry,PCR,Western blot 31610176 chr7 140716436 140718436 BRAF Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens. human connective tissue High+Lowthroughput Insights into Fibroblast Plasticity: Cellular Communication Network 2 Is Required for Activation of Cancer-Associated Fibroblasts in a Murine Model of Melanoma 否 无 tumour tumor cell E_01_0227 Flow cytometry,PCR,Western blot Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens. Immunohistochemical staining Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens. BRAF Flow cytometry,PCR,Western blot Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens. 31610176 chr8 76678526 76680526 ZFHX4 This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship. human connective tissue High+Lowthroughput Insights into Fibroblast Plasticity: Cellular Communication Network 2 Is Required for Activation of Cancer-Associated Fibroblasts in a Murine Model of Melanoma 否 无 tumour dermal progenitor cell E_01_0227 Flow cytometry,PCR,Western blot This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship. Enhancer ZFHX4 qRT-PCR,qPCR,ChIP,3C RNA-Seq This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship. This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship. Immunohistochemical staining This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship. Flow cytometry,PCR,Western blot 31608710 chr1 173855753 173857753 GAS5 The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. human eye High+Lowthroughput Silencing of GAS5 Alleviates Glaucoma in Rat Models by Reducing Retinal Ganglion Cell Apoptosis 否 无 glaucoma retinal ganglion cell E_01_0228 PCR, Western blot, immunofluorescence light staining, flow cytometry The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. Immunohistochemical staining The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. GAS5 PCR,Western blot,免疫荧光光染色,Flow cytometry The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. 31608710 chr7 148804386 148806386 EZH2 The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. human kidney High+Lowthroughput Silencing of GAS5 Alleviates Glaucoma in Rat Models by Reducing Retinal Ganglion Cell Apoptosis 否 无 glaucoma HEK293 cell E_01_0228 PCR, Western blot, immunofluorescence light staining, flow cytometry The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. Immunohistochemical staining The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. EZH2 PCR,Western blot,免疫荧光光染色,Flow cytometry The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis. 31608710 chr9 104778194 104780194 ABCA1 In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis. human connective tissue High+Lowthroughput Silencing of GAS5 Alleviates Glaucoma in Rat Models by Reducing Retinal Ganglion Cell Apoptosis 否 无 glaucoma neuroblastoma cell E_01_0228 PCR, Western blot, immunofluorescence light staining, flow cytometry In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis. Enhancer ABCA1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis. In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis. Immunohistochemical staining In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis. PCR,Western blot,免疫荧光光染色,Flow cytometry 31608546 chr6 88136910 88138910 CNR1 Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response. human connective tissue High+Lowthroughput Disease-associated polymorphisms within the conserved ECR1 enhancer differentially regulate the tissue-specific activity of the cannabinoid-1 receptor gene promoter; implications for cannabinoid pharmacogenetics 是 rs2023239 Obesity SH-SY5Y (human neuroblastoma cell) E_01_0229 PCR immunofluorescence staining Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response. Enhancer CNR1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response. Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response. Immunohistochemical staining Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response. PCR免疫荧光染色 31606392 chr1 247413593 247415593 NLRP3 Several experiments have confirmed that changes in intracellular ion concentration and the content of reactive oxygen species (ROS) play an important role in the activation of the NLRP3 inflammasome, while inhibition of Ca2+ inflow/K+ outflow and decreased ROS production can block the activation of NLRP3 to a certain extent [18-21]. human,mouse blood High+Lowthroughput Nickel-refining fumes induce NLRP3 activation dependent on mitochondrial damage and ROS production in Beas-2B cells 否 无 inflammation B cell E_02_0184 PCR, Western blot, immunofluorescence staining Several experiments have confirmed that changes in intracellular ion concentration and the content of reactive oxygen species (ROS) play an important role in the activation of the NLRP3 inflammasome, while inhibition of Ca2+ inflow/K+ outflow and decreased ROS production can block the activation of NLRP3 to a certain extent [18-21]. Enhancer NLRP3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Several experiments have confirmed that changes in intracellular ion concentration and the content of reactive oxygen species (ROS) play an important role in the activation of the NLRP3 inflammasome, while inhibition of Ca2+ inflow/K+ outflow and decreased ROS production can block the activation of NLRP3 to a certain extent [18-21]. Several experiments have confirmed that changes in intracellular ion concentration and the content of reactive oxygen species (ROS) play an important role in the activation of the NLRP3 inflammasome, while inhibition of Ca2+ inflow/K+ outflow and decreased ROS production can block the activation of NLRP3 to a certain extent [18-21]. Immunohistochemical staining Several experiments have confirmed that changes in intracellular ion concentration and the content of reactive oxygen species (ROS) play an important role in the activation of the NLRP3 inflammasome, while inhibition of Ca2+ inflow/K+ outflow and decreased ROS production can block the activation of NLRP3 to a certain extent [18-21]. PCR,Western blot,免疫荧光染色 31606247 chr16 30955158 30957158 SETD1A Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions. human Nervous tissue High+Lowthroughput Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice 是 无 Schizophrenia neural progenitor cell E_01_0230 Flow cytometry, PCR, immunofluorescence staining, Western blot Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions. Enhancer SETD1A qRT-PCR,qPCR,ChIP,3C RNA-Seq Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions. Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions. Immunohistochemical staining Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions. Flow cytometry,PCR,免疫荧光染色,Western blot 31605138 chr9 21964977 21966977 CDKN2A The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7). human blood High+Lowthroughput Neural crest-derived tumor neuroblastoma and melanoma share 1p13.2 as susceptibility locus that shows a long-range interaction with the SLC16A1 gene 是 rs2153977 cancer E_01_0231 Flow cytometry,PCR,Western blot The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7). Immunohistochemical staining The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7). CDKN2A Flow cytometry,PCR,Western blot The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7). 31601918 chr7 44101861 44103861 AEBP1 We had observed earlier that adipocyte enhancer binding protein 1 (AEBP1) expression to be up-regulated in primary GBMs as opposed to progressive secondary GBMs through transcriptome analysis1 . human,mouse Nervous tissue High+Lowthroughput AEBP1 down regulation induced cell death pathway depends on PTEN status of glioma cells 否 无 tumour glioma cell E_02_0185 PCR, Western blot, immunofluorescence light staining, flow cytometry We had observed earlier that adipocyte enhancer binding protein 1 (AEBP1) expression to be up-regulated in primary GBMs as opposed to progressive secondary GBMs through transcriptome analysis1 . Enhancer AEBP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We had observed earlier that adipocyte enhancer binding protein 1 (AEBP1) expression to be up-regulated in primary GBMs as opposed to progressive secondary GBMs through transcriptome analysis1 . We had observed earlier that adipocyte enhancer binding protein 1 (AEBP1) expression to be up-regulated in primary GBMs as opposed to progressive secondary GBMs through transcriptome analysis1 . Immunohistochemical staining We had observed earlier that adipocyte enhancer binding protein 1 (AEBP1) expression to be up-regulated in primary GBMs as opposed to progressive secondary GBMs through transcriptome analysis1 . PCR,Western blot,免疫荧光光染色,Flow cytometry 31601151 chr11 35136538 35138538 CD44 The expression levels of ASCs markers CD44, SMA, and Vimentin were decreased dur_x0002_ing the differentiation process (Figure 2(Ea–c)). human,mouse connective tissue High+Lowthroughput Cl- channels regulate lipid droplet formation via Rab8a expression during adipocyte differentiation 否 无 stem cell E_02_0186 PCR, flow cytometry, Western blot, immunofluorescence staining The expression levels of ASCs markers CD44, SMA, and Vimentin were decreased dur_x0002_ing the differentiation process (Figure 2(Ea–c)). Enhancer CD44 qRT-PCR,qPCR,ChIP,3C RNA-Seq The expression levels of ASCs markers CD44, SMA, and Vimentin were decreased dur_x0002_ing the differentiation process (Figure 2(Ea–c)). The expression levels of ASCs markers CD44, SMA, and Vimentin were decreased dur_x0002_ing the differentiation process (Figure 2(Ea–c)). Immunohistochemical staining The expression levels of ASCs markers CD44, SMA, and Vimentin were decreased dur_x0002_ing the differentiation process (Figure 2(Ea–c)). PCR,Flow cytometry,Western blot,免疫荧光染色 31601151 chr1 11854664 11856664 NPPB The morphology of the differentiated cells treated with NPPB was similar to that of those untreated with NPPB (Figure 3(Aa and b)). human,mouse connective tissue High+Lowthroughput Cl- channels regulate lipid droplet formation via Rab8a expression during adipocyte differentiation 否 无 3T3-L1 cell E_02_0186 PCR, flow cytometry, Western blot, immunofluorescence staining The morphology of the differentiated cells treated with NPPB was similar to that of those untreated with NPPB (Figure 3(Aa and b)). Enhancer NPPB qRT-PCR,qPCR,ChIP,3C RNA-Seq The morphology of the differentiated cells treated with NPPB was similar to that of those untreated with NPPB (Figure 3(Aa and b)). The morphology of the differentiated cells treated with NPPB was similar to that of those untreated with NPPB (Figure 3(Aa and b)). Immunohistochemical staining The morphology of the differentiated cells treated with NPPB was similar to that of those untreated with NPPB (Figure 3(Aa and b)). PCR,Flow cytometry,Western blot,免疫荧光染色 31599948 chr12 4365800 4367800 FGF23 Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2). human Epithelial tissues High+Lowthroughput A Control Region Near the Fibroblast Growth Factor 23 Gene Mediates Response to Phosphate, 1,25(OH)2D3, and LPS In Vivo 否 无 cancer epithelial cell E_01_0232 PCR Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2). Enhancer FGF23 qRT-PCR,qPCR,ChIP,3C RNA-Seq Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2). Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2). Immunohistochemical staining Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2). PCR 31599948 chr20 54150645 54152645 CYP24A1 Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3. human blood High+Lowthroughput A Control Region Near the Fibroblast Growth Factor 23 Gene Mediates Response to Phosphate, 1,25(OH)2D3, and LPS In Vivo 否 无 cancer T cell E_01_0232 PCR Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3. Enhancer CYP24A1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3. Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3. Immunohistochemical staining Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3. PCR 31599948 chr10 126881570 126883570 Cyp27b1 Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously. human bone High+Lowthroughput A Control Region Near the Fibroblast Growth Factor 23 Gene Mediates Response to Phosphate, 1,25(OH)2D3, and LPS In Vivo 否 无 cancer osteocyte E_01_0232 PCR Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously. Enhancer Cyp27b1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously. Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously. Immunohistochemical staining Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously. PCR 31598701 chr7 55016371 55018371 EGFR Other relevant genes such as EGFR and BCL-X, also known to be regulated by pro_x0002_gestins (56,64) exhibited a similar transcriptional activity in response to R5020 in both cell lines (Supplementary Figure S4B), pointing to a gene-specific GR-PR modulation. human,mouse breast High+Lowthroughput Exogenous pyruvate represses histone gene expression and inhibits cancer cell proliferation via the NAMPT-NAD+-SIRT1 pathway 否 无 mammary cancer breast cancer cell E_02_0187 PCR,Flow cytometry,Western blot Other relevant genes such as EGFR and BCL-X, also known to be regulated by pro_x0002_gestins (56,64) exhibited a similar transcriptional activity in response to R5020 in both cell lines (Supplementary Figure S4B), pointing to a gene-specific GR-PR modulation. Enhancer EGFR qRT-PCR,qPCR,ChIP,3C RNA-Seq Other relevant genes such as EGFR and BCL-X, also known to be regulated by pro_x0002_gestins (56,64) exhibited a similar transcriptional activity in response to R5020 in both cell lines (Supplementary Figure S4B), pointing to a gene-specific GR-PR modulation. Other relevant genes such as EGFR and BCL-X, also known to be regulated by pro_x0002_gestins (56,64) exhibited a similar transcriptional activity in response to R5020 in both cell lines (Supplementary Figure S4B), pointing to a gene-specific GR-PR modulation. Immunohistochemical staining Other relevant genes such as EGFR and BCL-X, also known to be regulated by pro_x0002_gestins (56,64) exhibited a similar transcriptional activity in response to R5020 in both cell lines (Supplementary Figure S4B), pointing to a gene-specific GR-PR modulation. PCR,Flow cytometry,Western blot 31595632 chr12 6531857 6533857 GAPDH The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR. human connective tissue High+Lowthroughput The Role of miR-326 in Adipogenic Differentiation of Human Adipose-Derived Stem Cells by Targeting C/EBPα in vitro 否 无 Obesity mesenchymal stem cell E_01_0233 PCR, Western blot The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR. Immunohistochemical staining The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR. GAPDH PCR, Western blot The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR. 31592235 chr12 57744934 57746934 CDK4 Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. mouse Musculature High+Lowthroughput P21 and P27 promote tumorigenesis and progression via cell cycle acceleration in seminal vesicles of TRAMP mice 否 无 prostatic cancer smooth muscle cell E_02_0188 Western blot Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. Enhancer CDK4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. Immunohistochemical staining Not only cyclin-dependent kinase (CDK) 1 and phosphorylated forkhead box protein (FOX) O1 but also CDK4, CDK6 and phosphorylated retinoblastoma-associated protein (RB) had similar increase trends, so did epidermal growth factor receptor (EGFR), AKT serine/threonine kinase (AKT), and their respective phosphorylation levels. Western blot 31592235 chr7 55016191 55018191 EGFR The results indicated that EGFR, AKT, STAT3, and EZH2 all play a crucial role in promoting cell proliferation and tumor growth in seminal vesicles of TRAMP mice. mouse connective tissue High+Lowthroughput P21 and P27 promote tumorigenesis and progression via cell cycle acceleration in seminal vesicles of TRAMP mice 否 无 tumour tumor cell E_02_0188 Western blot The results indicated that EGFR, AKT, STAT3, and EZH2 all play a crucial role in promoting cell proliferation and tumor growth in seminal vesicles of TRAMP mice. Enhancer EGFR qRT-PCR,qPCR,ChIP,3C RNA-Seq The results indicated that EGFR, AKT, STAT3, and EZH2 all play a crucial role in promoting cell proliferation and tumor growth in seminal vesicles of TRAMP mice. The results indicated that EGFR, AKT, STAT3, and EZH2 all play a crucial role in promoting cell proliferation and tumor growth in seminal vesicles of TRAMP mice. Immunohistochemical staining The results indicated that EGFR, AKT, STAT3, and EZH2 all play a crucial role in promoting cell proliferation and tumor growth in seminal vesicles of TRAMP mice. Western blot 31592229 chr7 148804549 148806549 EZH2 In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). human,Pig intestine High+Lowthroughput Circular RNA CircEZH2 Suppresses Transmissible Gastroenteritis Coronavirus-induced Opening of Mitochondrial Permeability Transition Pore via Targeting MiR-22 in IPEC-J2 否 无 Infectious gastroenteritis porcine intestinal epthelial cell E_02_0189 Western blot, flow cytometry, PCR, immunofluorescence staining In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). Immunohistochemical staining In our previous study, we have demonstrated that circular RNA circEZH2 was down-regulated during TGEV infection and promoted the activation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) via targeting miR-22 in porcine intestinal epithelial cell line (IPEC-J2). Western blot,Flow cytometry,PCR,免疫荧光染色 31592229 chr10 74821853 74823853 KAT6B miR-22 has a strong correlation with NF-κB pathway and mitochondrial damage. Recently, it was reported that miR-22 inhibited PI3K/Akt/NF-κB signaling in tongue squamous cell carcinoma (TSCC) cells via targeting KAT6B[22]. human,Pig kidney High+Lowthroughput Circular RNA CircEZH2 Suppresses Transmissible Gastroenteritis Coronavirus-induced Opening of Mitochondrial Permeability Transition Pore via Targeting MiR-22 in IPEC-J2 否 无 cancer PK-15 cell E_02_0189 Western blot, flow cytometry, PCR, immunofluorescence staining miR-22 has a strong correlation with NF-κB pathway and mitochondrial damage. Recently, it was reported that miR-22 inhibited PI3K/Akt/NF-κB signaling in tongue squamous cell carcinoma (TSCC) cells via targeting KAT6B[22]. Enhancer KAT6B qRT-PCR,qPCR,ChIP,3C RNA-Seq miR-22 has a strong correlation with NF-κB pathway and mitochondrial damage. Recently, it was reported that miR-22 inhibited PI3K/Akt/NF-κB signaling in tongue squamous cell carcinoma (TSCC) cells via targeting KAT6B[22]. miR-22 has a strong correlation with NF-κB pathway and mitochondrial damage. Recently, it was reported that miR-22 inhibited PI3K/Akt/NF-κB signaling in tongue squamous cell carcinoma (TSCC) cells via targeting KAT6B[22]. Immunohistochemical staining miR-22 has a strong correlation with NF-κB pathway and mitochondrial damage. Recently, it was reported that miR-22 inhibited PI3K/Akt/NF-κB signaling in tongue squamous cell carcinoma (TSCC) cells via targeting KAT6B[22]. Western blot,Flow cytometry,PCR,免疫荧光染色 31592229 chr2 74831204 74833204 HK2 However, HK2 does not regulate NK-κB activation. Not only HK2, IL-6 was also identified as the target of miR-22 and suppressed TGEV-induced mPTP opening via activating NF-κB pathway, suggesting that miR-22 regulates TGEV-induced mPTP opening via at least two pathways. human,Pig blood High+Lowthroughput Circular RNA CircEZH2 Suppresses Transmissible Gastroenteritis Coronavirus-induced Opening of Mitochondrial Permeability Transition Pore via Targeting MiR-22 in IPEC-J2 否 无 cancer B cell E_02_0189 Western blot, flow cytometry, PCR, immunofluorescence staining However, HK2 does not regulate NK-κB activation. Not only HK2, IL-6 was also identified as the target of miR-22 and suppressed TGEV-induced mPTP opening via activating NF-κB pathway, suggesting that miR-22 regulates TGEV-induced mPTP opening via at least two pathways. Enhancer HK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq However, HK2 does not regulate NK-κB activation. Not only HK2, IL-6 was also identified as the target of miR-22 and suppressed TGEV-induced mPTP opening via activating NF-κB pathway, suggesting that miR-22 regulates TGEV-induced mPTP opening via at least two pathways. However, HK2 does not regulate NK-κB activation. Not only HK2, IL-6 was also identified as the target of miR-22 and suppressed TGEV-induced mPTP opening via activating NF-κB pathway, suggesting that miR-22 regulates TGEV-induced mPTP opening via at least two pathways. Immunohistochemical staining However, HK2 does not regulate NK-κB activation. Not only HK2, IL-6 was also identified as the target of miR-22 and suppressed TGEV-induced mPTP opening via activating NF-κB pathway, suggesting that miR-22 regulates TGEV-induced mPTP opening via at least two pathways. Western blot,Flow cytometry,PCR,免疫荧光染色 31592021 chr10 100370073 100372073 OLMALINC maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery. human liver High+Lowthroughput Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA 否 无 liver cancer HepG2 cell E_01_0234 Flow cytometry,Western blot maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery. Enhancer OLMALINC qRT-PCR,qPCR,ChIP,3C RNA-Seq maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery. maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery. Immunohistochemical staining maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery. Flow cytometry,Western blot 31591447 chr4 53777000 53779000 Tal2 We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes human,mouse Epithelial tissues High+Lowthroughput Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development 否 无 anterior epiblast cell E_02_0190 Flow cytometry,PCR We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Enhancer Tal2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Immunohistochemical staining We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Flow cytometry,PCR 31591447 chr5 120566993 120568993 Lhx5 We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes human,mouse blood High+Lowthroughput Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development 否 无 E_02_0190 Flow cytometry,PCR We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Enhancer Lhx5 qRT-PCR,qPCR,ChIP,3C RNA-Seq We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Immunohistochemical staining We first analyzed gene expression dynamics during the development of each lineage (Fig. 1b–e; Supplementary informa_x0002_tion, Table S2) and found that expression of ectodermal genes (e.g., Tal2 and Lhx5), mesendodermal genes Flow cytometry,PCR 31591447 chr3 34701896 34703896 Sox2 These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). human,mouse connective tissue High+Lowthroughput Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development 否 无 EpiSC细胞 E_02_0190 Flow cytometry,PCR These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Enhancer Sox2 qRT-PCR,qPCR,ChIP,3C RNA-Seq These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Immunohistochemical staining These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Flow cytometry,PCR 31591447 chr7 79439406 79441406 Mesp1 These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). human,mouse Musculature High+Lowthroughput Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development 否 无 muscle cell E_02_0190 Flow cytometry,PCR These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Enhancer Mesp1 qRT-PCR,qPCR,ChIP,3C RNA-Seq These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Immunohistochemical staining These gastrula-specific enhancer bins were enriched near genes that are related to embryonic pattern formation, gastrulation and primary germ layer specification, and are highly expressed at the gastrulation stage, such as Sox2, Eomes and Mesp1 (Fig. 5b–e). Flow cytometry,PCR 31590652 chr12 7785003 7787003 NANOG We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples. human connective tissue High+Lowthroughput AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU 否 无 cancer embryonic stem cell E_01_0235 PCR We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples. Enhancer NANOG qRT-PCR,qPCR,ChIP,3C RNA-Seq We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples. We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples. Immunohistochemical staining We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples. PCR 31589602 chr12 80713954 80715954 MYF5 We also compared motifs within H3K27ac or ATAC-seq peaks and found similar representations of jun proto-oncogene (JUN), myogenic factor 5 (MYF5), MEF2, specificity protein 1 (SP1), nuclear transcription fac_x0002_tor Y (NFY), and E-twenty-six family transcription factor (ETS) elements in MT and Quad, whereas factors critical for progenitor functions including runt-related transcription factor (RUNX), paired box (PAX), and TEA domain transcription factor 1 (TEAD) were more con_x0002_centrated in MT (Fig 4G). human,mouse blood High+Lowthroughput Dynamic enhancers control skeletal muscle identity and reprogramming 否 无 cancer T cell E_02_0191 Flow cytometry,PCR We also compared motifs within H3K27ac or ATAC-seq peaks and found similar representations of jun proto-oncogene (JUN), myogenic factor 5 (MYF5), MEF2, specificity protein 1 (SP1), nuclear transcription fac_x0002_tor Y (NFY), and E-twenty-six family transcription factor (ETS) elements in MT and Quad, whereas factors critical for progenitor functions including runt-related transcription factor (RUNX), paired box (PAX), and TEA domain transcription factor 1 (TEAD) were more con_x0002_centrated in MT (Fig 4G). Enhancer MYF5 qRT-PCR,qPCR,ChIP,3C RNA-Seq We also compared motifs within H3K27ac or ATAC-seq peaks and found similar representations of jun proto-oncogene (JUN), myogenic factor 5 (MYF5), MEF2, specificity protein 1 (SP1), nuclear transcription fac_x0002_tor Y (NFY), and E-twenty-six family transcription factor (ETS) elements in MT and Quad, whereas factors critical for progenitor functions including runt-related transcription factor (RUNX), paired box (PAX), and TEA domain transcription factor 1 (TEAD) were more con_x0002_centrated in MT (Fig 4G). We also compared motifs within H3K27ac or ATAC-seq peaks and found similar representations of jun proto-oncogene (JUN), myogenic factor 5 (MYF5), MEF2, specificity protein 1 (SP1), nuclear transcription fac_x0002_tor Y (NFY), and E-twenty-six family transcription factor (ETS) elements in MT and Quad, whereas factors critical for progenitor functions including runt-related transcription factor (RUNX), paired box (PAX), and TEA domain transcription factor 1 (TEAD) were more con_x0002_centrated in MT (Fig 4G). Immunohistochemical staining We also compared motifs within H3K27ac or ATAC-seq peaks and found similar representations of jun proto-oncogene (JUN), myogenic factor 5 (MYF5), MEF2, specificity protein 1 (SP1), nuclear transcription fac_x0002_tor Y (NFY), and E-twenty-six family transcription factor (ETS) elements in MT and Quad, whereas factors critical for progenitor functions including runt-related transcription factor (RUNX), paired box (PAX), and TEA domain transcription factor 1 (TEAD) were more con_x0002_centrated in MT (Fig 4G). Flow cytometry,PCR 31589096 chr17 42697169 42699169 EZH1 Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels. human nasopharynx High+Lowthroughput Glycyrrhiza glabra suppresses nasopharyngeal carcinoma cell proliferation through inhibiting the expression of lncRNA, AK027294 否 无 Nasopharyngeal carcinoma nasopharyngeal carcinoma cell E_01_0236 Western blot,Flow cytometry,PCR Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels. Enhancer EZH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels. Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels. Immunohistochemical staining Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels. Western blot,Flow cytometry,PCR 31588347 chr5 113018862 113020862 MCC Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport. human Epithelial tissues High+Lowthroughput Benzisothiazolinone upregulates the MUC5AC expression via ERK1/2, p38, and NF-κB pathways in airway epithelial cells 否 无 asthma epithelial cell E_01_0237 PCR,Western blot Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport. Enhancer MCC qRT-PCR,qPCR,ChIP,3C RNA-Seq Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport. Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport. Immunohistochemical staining Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport. PCR,Western blot 31588046 chr12 7785776 7787776 NANOG After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A) human connective tissue High+Lowthroughput The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis 否 无 cancer cancer cell E_01_0238 Flow cytometry, PCR, immunofluorescence staining After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A) Enhancer NANOG qRT-PCR,qPCR,ChIP,3C RNA-Seq After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A) After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A) Immunohistochemical staining After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A) Flow cytometry,PCR,免疫荧光染色 31588023 chr1 170660059 170662059 PRRX1 Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D) human connective tissue High+Lowthroughput Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State 否 无 Malignancy immune cell E_01_0239 Flow cytometry, PCR, immunofluorescence staining Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D) Enhancer PRRX1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D) Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D) Immunohistochemical staining Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D) Flow cytometry,PCR,免疫荧光染色 31588020 chr17 39685586 39687586 ERBB2 However, the National Comprehensive Can_x0002_cer Network guidelines for non-small cell lung cancer (NSCLC) recommend that newly diagnosed patients undergo broad mo_x0002_lecular profiling to detect ERBB2 mutations (Ettinger et al., 2018). mouse blood High+Lowthroughput Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity 否 无 cancer Ba/F3 cell E_02_0192 PCR,Western blot However, the National Comprehensive Can_x0002_cer Network guidelines for non-small cell lung cancer (NSCLC) recommend that newly diagnosed patients undergo broad mo_x0002_lecular profiling to detect ERBB2 mutations (Ettinger et al., 2018). Enhancer ERBB2 qRT-PCR,qPCR,ChIP,3C RNA-Seq However, the National Comprehensive Can_x0002_cer Network guidelines for non-small cell lung cancer (NSCLC) recommend that newly diagnosed patients undergo broad mo_x0002_lecular profiling to detect ERBB2 mutations (Ettinger et al., 2018). However, the National Comprehensive Can_x0002_cer Network guidelines for non-small cell lung cancer (NSCLC) recommend that newly diagnosed patients undergo broad mo_x0002_lecular profiling to detect ERBB2 mutations (Ettinger et al., 2018). Immunohistochemical staining However, the National Comprehensive Can_x0002_cer Network guidelines for non-small cell lung cancer (NSCLC) recommend that newly diagnosed patients undergo broad mo_x0002_lecular profiling to detect ERBB2 mutations (Ettinger et al., 2018). PCR,Western blot 31586130 chr3 194133931 194135931 HES1 Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f). human blood High+Lowthroughput NRARP displays either pro- or anti-tumoral roles in T-cell acute lymphoblastic leukemia depending on Notch and Wnt signaling 否 无 Acute lymphoblastic leukemia T cell E_01_0240 PCR,Western blot Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f). Immunohistochemical staining Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f). HES1 PCR,Western blot Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f). 31586130 chr4 108044223 108046223 LEF1 Thus, we next dissected the impact of LEF1 downstream from NRARP by silencing LEF1 in DND4.1 and Loucy cells with and without NRARP overexpression (Supplementary Fig. S4A, B). mouse Nervous tissue High+Lowthroughput NRARP displays either pro- or anti-tumoral roles in T-cell acute lymphoblastic leukemia depending on Notch and Wnt signaling 否 无 Acute lymphoblastic leukemia neural crest cell E_01_0240 PCR,Western blot Thus, we next dissected the impact of LEF1 downstream from NRARP by silencing LEF1 in DND4.1 and Loucy cells with and without NRARP overexpression (Supplementary Fig. S4A, B). Enhancer LEF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Thus, we next dissected the impact of LEF1 downstream from NRARP by silencing LEF1 in DND4.1 and Loucy cells with and without NRARP overexpression (Supplementary Fig. S4A, B). Thus, we next dissected the impact of LEF1 downstream from NRARP by silencing LEF1 in DND4.1 and Loucy cells with and without NRARP overexpression (Supplementary Fig. S4A, B). Immunohistochemical staining Thus, we next dissected the impact of LEF1 downstream from NRARP by silencing LEF1 in DND4.1 and Loucy cells with and without NRARP overexpression (Supplementary Fig. S4A, B). PCR,Western blot 31586043 chr5 1389936 1391936 SLC6A3 Many environmental factors can regulate dopaminergic (DAergic) activity including SLC6A3, the gene encoding the dopamine transporter (DAT)1–7 . human,mouse Nervous tissue High+Lowthroughput Identification of HIVEP2 as a dopaminergic transcription factor related to substance use disorders in rats and humans 是 rs67175440 Immunodeficiencies SH-SH5Y cell E_02_0193 PCR,Western blot Many environmental factors can regulate dopaminergic (DAergic) activity including SLC6A3, the gene encoding the dopamine transporter (DAT)1–7 . Enhancer SLC6A3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Many environmental factors can regulate dopaminergic (DAergic) activity including SLC6A3, the gene encoding the dopamine transporter (DAT)1–7 . Many environmental factors can regulate dopaminergic (DAergic) activity including SLC6A3, the gene encoding the dopamine transporter (DAT)1–7 . Immunohistochemical staining Many environmental factors can regulate dopaminergic (DAergic) activity including SLC6A3, the gene encoding the dopamine transporter (DAT)1–7 . PCR,Western blot 31586043 chr10 102227203 102229203 PITX3 Recently, several TFs for SLC6A3 have been cloned, including Nurr1 (NR4A2), paired-like homeobox 3 pro_x0002_tein (PITX3), HEY1, SP1, SP3, AZI23′UTR, SRP54, and Nfe2l18–13. human,mouse Nervous tissue High+Lowthroughput Identification of HIVEP2 as a dopaminergic transcription factor related to substance use disorders in rats and humans 是 rs748209 Immunodeficiencies SK-N-AS cell E_02_0193 PCR,Western blot Recently, several TFs for SLC6A3 have been cloned, including Nurr1 (NR4A2), paired-like homeobox 3 pro_x0002_tein (PITX3), HEY1, SP1, SP3, AZI23′UTR, SRP54, and Nfe2l18–13. Enhancer PITX3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Recently, several TFs for SLC6A3 have been cloned, including Nurr1 (NR4A2), paired-like homeobox 3 pro_x0002_tein (PITX3), HEY1, SP1, SP3, AZI23′UTR, SRP54, and Nfe2l18–13. Recently, several TFs for SLC6A3 have been cloned, including Nurr1 (NR4A2), paired-like homeobox 3 pro_x0002_tein (PITX3), HEY1, SP1, SP3, AZI23′UTR, SRP54, and Nfe2l18–13. Immunohistochemical staining Recently, several TFs for SLC6A3 have been cloned, including Nurr1 (NR4A2), paired-like homeobox 3 pro_x0002_tein (PITX3), HEY1, SP1, SP3, AZI23′UTR, SRP54, and Nfe2l18–13. PCR,Western blot 31586032 chr16 67559931 67561931 CTCF Since enhancer-promoter looping is mediated by various transcription factors (69) and chromatin remodelers such as Mediator, Cohesin (70), CTCF proteins (71) and YY1(72), it is possible that the acidic and PEST domains interact with different factors to establish enhancer_x0002_promoter interactions in a gene and cell type_x0002_specific manner. mouse tumour High+Lowthroughput The transcription factor PU.1 mediates enhancer-promoter looping that is required for IL-1β eRNA and mRNA transcription in mouse melanoma and macrophage cell lines 否 无 tumour melanoma cells E_02_0194 PCR,Western blot,Flow cytometry Since enhancer-promoter looping is mediated by various transcription factors (69) and chromatin remodelers such as Mediator, Cohesin (70), CTCF proteins (71) and YY1(72), it is possible that the acidic and PEST domains interact with different factors to establish enhancer_x0002_promoter interactions in a gene and cell type_x0002_specific manner. Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq Since enhancer-promoter looping is mediated by various transcription factors (69) and chromatin remodelers such as Mediator, Cohesin (70), CTCF proteins (71) and YY1(72), it is possible that the acidic and PEST domains interact with different factors to establish enhancer_x0002_promoter interactions in a gene and cell type_x0002_specific manner. Since enhancer-promoter looping is mediated by various transcription factors (69) and chromatin remodelers such as Mediator, Cohesin (70), CTCF proteins (71) and YY1(72), it is possible that the acidic and PEST domains interact with different factors to establish enhancer_x0002_promoter interactions in a gene and cell type_x0002_specific manner. Immunohistochemical staining Since enhancer-promoter looping is mediated by various transcription factors (69) and chromatin remodelers such as Mediator, Cohesin (70), CTCF proteins (71) and YY1(72), it is possible that the acidic and PEST domains interact with different factors to establish enhancer_x0002_promoter interactions in a gene and cell type_x0002_specific manner. PCR,Western blot,Flow cytometry 31585804 chrX 100840244 100842244 NOX1 Endo_x0002_thelial cells express 4 ROS-generating NOX isoforms (eg, NOX1, NOX2, NOX4, and NOX5). mouse Epithelial tissues High+Lowthroughput Sildenafil Protects Endothelial Cells From Radiation-Induced Oxidative Stress 否 无 atherosclerosis endothelial cell E_02_0195 PCR Endo_x0002_thelial cells express 4 ROS-generating NOX isoforms (eg, NOX1, NOX2, NOX4, and NOX5). Enhancer NOX1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Endo_x0002_thelial cells express 4 ROS-generating NOX isoforms (eg, NOX1, NOX2, NOX4, and NOX5). Endo_x0002_thelial cells express 4 ROS-generating NOX isoforms (eg, NOX1, NOX2, NOX4, and NOX5). Immunohistochemical staining Endo_x0002_thelial cells express 4 ROS-generating NOX isoforms (eg, NOX1, NOX2, NOX4, and NOX5). PCR 31585741 chrX 48506512 48508512 PORCN To explore kidney_x0002_specific functions of PORCN in UUO pathogenesis, we first confirmed that expression of Wnt pathway components were induced in the obstructed kidney mouse bone High+Lowthroughput Opposing actions of renal tubular- and myeloid-derived porcupine in obstruction-induced?kidney fibrosis 否 无 infiltrating myeloid cell E_02_0196 PCR,Western blot To explore kidney_x0002_specific functions of PORCN in UUO pathogenesis, we first confirmed that expression of Wnt pathway components were induced in the obstructed kidney Enhancer PORCN qRT-PCR,qPCR,ChIP,3C RNA-Seq To explore kidney_x0002_specific functions of PORCN in UUO pathogenesis, we first confirmed that expression of Wnt pathway components were induced in the obstructed kidney To explore kidney_x0002_specific functions of PORCN in UUO pathogenesis, we first confirmed that expression of Wnt pathway components were induced in the obstructed kidney Immunohistochemical staining To explore kidney_x0002_specific functions of PORCN in UUO pathogenesis, we first confirmed that expression of Wnt pathway components were induced in the obstructed kidney PCR,Western blot 31585741 chr11 108808537 108810537 Axin2 Accordingly, ablation of PORCN in the obstructed KKO kidneys led not only to reduced expression of Wnt target genes, Axin2 and Nkd1, but also several Wnt ligands including Wnt3, Wnt4, Wnt7a, and Wnt9b. mouse Epithelial tissues High+Lowthroughput Opposing actions of renal tubular- and myeloid-derived porcupine in obstruction-induced?kidney fibrosis 否 无 Renal fibrosis epithelial cell E_02_0196 PCR,Western blot Accordingly, ablation of PORCN in the obstructed KKO kidneys led not only to reduced expression of Wnt target genes, Axin2 and Nkd1, but also several Wnt ligands including Wnt3, Wnt4, Wnt7a, and Wnt9b. Enhancer Axin2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Accordingly, ablation of PORCN in the obstructed KKO kidneys led not only to reduced expression of Wnt target genes, Axin2 and Nkd1, but also several Wnt ligands including Wnt3, Wnt4, Wnt7a, and Wnt9b. Accordingly, ablation of PORCN in the obstructed KKO kidneys led not only to reduced expression of Wnt target genes, Axin2 and Nkd1, but also several Wnt ligands including Wnt3, Wnt4, Wnt7a, and Wnt9b. Immunohistochemical staining Accordingly, ablation of PORCN in the obstructed KKO kidneys led not only to reduced expression of Wnt target genes, Axin2 and Nkd1, but also several Wnt ligands including Wnt3, Wnt4, Wnt7a, and Wnt9b. PCR,Western blot 31584754 chr3 41191952 41193952 CTNNB1 It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1 human tumour High+Lowthroughput The usefulness of lymphoid enhancer-binding factor 1 and androgen receptor in diagnosing solid pseudopapillary neoplasm of the pancreas on cytopathology 否 无 tumour tumor cell E_01_0241 Immunohistochemistry It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1 Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1 Immunohistochemical staining It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1 CTNNB1 免疫组化 It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1 31583122 chr11 35136216 35138216 CD44 It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11. human lung High+Lowthroughput Targeting Wnt/EZH2/microRNA-708 signaling pathway inhibits neuroendocrine differentiation in prostate cancer 否 无 Lung adenocarcinoma adenocarcinoma cell E_01_0242 PCR,Western blot It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11. Enhancer CD44 qRT-PCR,qPCR,ChIP,3C RNA-Seq It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11. It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11. Immunohistochemical staining It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11. PCR,Western blot 31582835 chr7 148804794 148806794 EZH2 Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression. human tumour High+Lowthroughput EZH2 targeting reduces medulloblastoma growth through epigenetic reactivation of the BAI1/p53 tumor suppressor pathway 否 无 Medulloblastoma Medulloblastoma cell E_01_0243 PCR,Western blot Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression. Immunohistochemical staining Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression. EZH2 PCR,Western blot Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression. 31581708 chr17 39726151 39728151 MIEN1 Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed. human prostate High+Lowthroughput Migration and Invasion Enhancer 1 Is an NF-?B-Inducing Gene Enhancing the Cell Proliferation and Invasion Ability of Human Prostate Carcinoma Cells In Vitro and In Vivo 否 无 prostatic cancer prostate cancer cell E_01_0244 PCR,Western blot,Flow cytometry Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed. Enhancer MIEN1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed. Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed. Immunohistochemical staining Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed. PCR,Western blot,Flow cytometry 31581708 chr8 133234553 133236553 NDRG1 Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19]. human Epithelial tissues High+Lowthroughput Migration and Invasion Enhancer 1 Is an NF-?B-Inducing Gene Enhancing the Cell Proliferation and Invasion Ability of Human Prostate Carcinoma Cells In Vitro and In Vivo 否 无 prostatic cancer epithelial cell E_01_0244 PCR,Western blot,Flow cytometry Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19]. Enhancer NDRG1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19]. Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19]. Immunohistochemical staining Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19]. PCR,Western blot,Flow cytometry 31581661 chr8 127733019 127735019 MYC Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines. human prostate High+Lowthroughput Curcumin-Gene Expression Response in Hormone Dependent and Independent Metastatic Prostate Cancer Cells 否 无 prostatic cancer prostate cancer cell E_01_0245 PCR Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines. Immunohistochemical staining Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines. MYC PCR Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines. 31579944 chr7 148804427 148806427 EZH2 Dysregulation of histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the pathogenesis of many cancers. human,mouse Epithelial tissues High+Lowthroughput Genetic or pharmacologic blockade of enhancer of zeste homolog 2 inhibits the progression of peritoneal fibrosis 否 无 cancer peritoneal mesothelial cell E_02_0197 PCR, Western blot, immunofluorescence staining Dysregulation of histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the pathogenesis of many cancers. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Dysregulation of histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the pathogenesis of many cancers. Dysregulation of histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the pathogenesis of many cancers. Immunohistochemical staining Dysregulation of histone methyltransferase enhancer of zeste homolog 2 (EZH2) has been implicated in the pathogenesis of many cancers. PCR,Western blot,免疫荧光染色 31579944 chr17 78850292 78852292 TIMP2 Moreover, delayed administration of 3-DZNeP inhibited peritoneal fibrosis progression, reversed established peritoneal fibrosis and reduced expression of tissue inhibitor of metalloproteinase 2 (TIMP2), and matrix metalloproteinase-2 and -9. human,mouse connective tissue High+Lowthroughput Genetic or pharmacologic blockade of enhancer of zeste homolog 2 inhibits the progression of peritoneal fibrosis 否 无 inflammation Inflammatory cell E_02_0197 PCR, Western blot, immunofluorescence staining Moreover, delayed administration of 3-DZNeP inhibited peritoneal fibrosis progression, reversed established peritoneal fibrosis and reduced expression of tissue inhibitor of metalloproteinase 2 (TIMP2), and matrix metalloproteinase-2 and -9. Enhancer TIMP2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, delayed administration of 3-DZNeP inhibited peritoneal fibrosis progression, reversed established peritoneal fibrosis and reduced expression of tissue inhibitor of metalloproteinase 2 (TIMP2), and matrix metalloproteinase-2 and -9. Moreover, delayed administration of 3-DZNeP inhibited peritoneal fibrosis progression, reversed established peritoneal fibrosis and reduced expression of tissue inhibitor of metalloproteinase 2 (TIMP2), and matrix metalloproteinase-2 and -9. Immunohistochemical staining Moreover, delayed administration of 3-DZNeP inhibited peritoneal fibrosis progression, reversed established peritoneal fibrosis and reduced expression of tissue inhibitor of metalloproteinase 2 (TIMP2), and matrix metalloproteinase-2 and -9. PCR,Western blot,免疫荧光染色 31579944 chr17 42310753 42312753 STAT3 Therefore, we speculated that EZH2 blockade suppressed the MMP2 by inhibiting the EZH2- STAT3 signaling axis. In addition, genome wide approaches suggest that EZH2 targets Fosl1 and Klf5, two activators of MMP9 [40]. human,mouse pancreas High+Lowthroughput Genetic or pharmacologic blockade of enhancer of zeste homolog 2 inhibits the progression of peritoneal fibrosis 否 无 pancreatic cancer pancreatic cancer cell E_02_0197 PCR, Western blot, immunofluorescence staining Therefore, we speculated that EZH2 blockade suppressed the MMP2 by inhibiting the EZH2- STAT3 signaling axis. In addition, genome wide approaches suggest that EZH2 targets Fosl1 and Klf5, two activators of MMP9 [40]. Enhancer STAT3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Therefore, we speculated that EZH2 blockade suppressed the MMP2 by inhibiting the EZH2- STAT3 signaling axis. In addition, genome wide approaches suggest that EZH2 targets Fosl1 and Klf5, two activators of MMP9 [40]. Therefore, we speculated that EZH2 blockade suppressed the MMP2 by inhibiting the EZH2- STAT3 signaling axis. In addition, genome wide approaches suggest that EZH2 targets Fosl1 and Klf5, two activators of MMP9 [40]. Immunohistochemical staining Therefore, we speculated that EZH2 blockade suppressed the MMP2 by inhibiting the EZH2- STAT3 signaling axis. In addition, genome wide approaches suggest that EZH2 targets Fosl1 and Klf5, two activators of MMP9 [40]. PCR,Western blot,免疫荧光染色 31579913 chr20 63192571 63194571 YTHDF1 After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and human colon High+Lowthroughput Genetic variants in m6A modification genes are associated with colorectal cancer risk 是 rs118049207 Colon cancer Human colorectal carcinoma cell E_01_0246 PCR After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Enhancer YTHDF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Immunohistochemical staining After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and PCR 31579913 chr8 63165861 63167861 YTHDF3 After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and human colon High+Lowthroughput Genetic variants in m6A modification genes are associated with colorectal cancer risk 是 rs118049207 Colon cancer Human colorectal carcinoma cell E_01_0246 PCR After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Enhancer YTHDF3 qRT-PCR,qPCR,ChIP,3C RNA-Seq After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Immunohistochemical staining After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and PCR 31579913 chr1 28734326 28736326 YTHDF2 After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and human colon High+Lowthroughput Genetic variants in m6A modification genes are associated with colorectal cancer risk 是 rs118049207 Colon cancer Human colorectal carcinoma cell E_01_0246 PCR After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Enhancer YTHDF2 qRT-PCR,qPCR,ChIP,3C RNA-Seq After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Immunohistochemical staining After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and PCR 31579913 chr10 119031225 119033225 EIF3A After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and human colon High+Lowthroughput Genetic variants in m6A modification genes are associated with colorectal cancer risk 是 rs118049207 Colon cancer Human colorectal carcinoma cell E_01_0246 PCR After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Enhancer EIF3A qRT-PCR,qPCR,ChIP,3C RNA-Seq After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and Immunohistochemical staining After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and PCR 31579098 chr7 148804077 148806077 EZH2 The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees. human tumour High+Lowthroughput DZNep inhibits Hif-1α and Wnt signalling molecules to attenuate the proliferation and invasion of BGC-823 gastric cancer cells 否 无 tumour tumor cell E_01_0247 PCR,Western blot,Flow cytometry The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees. Immunohistochemical staining The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees. EZH2 PCR,Western blot,Flow cytometry The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees. 31575636 chr22 41830453 41832453 SREBF2 Among the cholesterol biosynthetic genes,we observed upregulation during mid-regeneration (4-7 dpi) of SREBF2, a known cholesterol master-regulatory transcription factor (Madison 2016; Smith et al. 2018). human,mouse High+Lowthroughput Regeneration Rosetta: An Interactive Web Application To Explore Regeneration-Associated Gene Expression and Chromatin Accessibility 否 无 E_02_0198 RNA-seq Among the cholesterol biosynthetic genes,we observed upregulation during mid-regeneration (4-7 dpi) of SREBF2, a known cholesterol master-regulatory transcription factor (Madison 2016; Smith et al. 2018). Enhancer SREBF2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Among the cholesterol biosynthetic genes,we observed upregulation during mid-regeneration (4-7 dpi) of SREBF2, a known cholesterol master-regulatory transcription factor (Madison 2016; Smith et al. 2018). Among the cholesterol biosynthetic genes,we observed upregulation during mid-regeneration (4-7 dpi) of SREBF2, a known cholesterol master-regulatory transcription factor (Madison 2016; Smith et al. 2018). Immunohistochemical staining Among the cholesterol biosynthetic genes,we observed upregulation during mid-regeneration (4-7 dpi) of SREBF2, a known cholesterol master-regulatory transcription factor (Madison 2016; Smith et al. 2018). RNA-seq 31573688 chr12 16545165 16547165 LMO3 LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013). human connective tissue High+Lowthroughput Resveratrol Inhibits Human Visceral Preadipocyte Proliferation and Differentiation in vitro 否 无 diabetes 3T3-L1 cell E_01_0248 PCR,Western blot LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013). Enhancer LMO3 qRT-PCR,qPCR,ChIP,3C RNA-Seq LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013). LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013). Immunohistochemical staining LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013). PCR,Western blot 31572429 chr22 41558440 41560440 CSDC2 Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells. human breast High+Lowthroughput Purification and Identification of miRNA Target Sites in Genome Using DNA Affinity Precipitation 否 无 mammary cancer MCF-7 cell E_01_0249 Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells. Enhancer CSDC2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells. Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells. Immunohistochemical staining Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells. 31571902 chr22 15781801 15783801 DUXAP8 Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes. human liver High+Lowthroughput Up-regulated long non-coding RNA DUXAP8 promotes cell growth through repressing Krüppel-like factor 2 expression in human hepatocellular carcinoma 否 无 liver cancer hepatocellular carcinoma cell E_01_0250 PCR Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes. Enhancer DUXAP8 qRT-PCR,qPCR,ChIP,3C RNA-Seq Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes. Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes. Immunohistochemical staining Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes. PCR 31570750 chr1 10633990 10635990 CASZ1 This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease. human kidney High+Lowthroughput A variant of the castor zinc finger 1 (CASZ1) gene is differentially associated with the clinical classification of chronic venous disease 是 rs11121615 Chronic venous disease HEK293 cell E_01_0251 PCR,Flow cytometry This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease. Enhancer CASZ1 qRT-PCR,qPCR,ChIP,3C RNA-Seq This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease. This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease. Immunohistochemical staining This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease. PCR,Flow cytometry 31570746 chr13 40553093 40555093 FOXO1 Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated human connective tissue High+Lowthroughput Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder 否 无 cancer cancer cell E_01_0252 PCR Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated Immunohistochemical staining Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated FOXO1 PCR Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated 31570000 chr19 10651535 10653535 ILF3 The presence of multiple additional ILF3 binding interac_x0002_tions with introns, coding exons, noncoding non-AS exons, and SINEs on the transcribed strand probably reflects the extensive functional diversity of the ILF3 gene in addition to an incomplete annotation of the transcriptome. human,mouse High+Lowthroughput The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs 否 无 liver cancer DH5a cells E_02_0199 Western blot,Flow cytometry,PCR The presence of multiple additional ILF3 binding interac_x0002_tions with introns, coding exons, noncoding non-AS exons, and SINEs on the transcribed strand probably reflects the extensive functional diversity of the ILF3 gene in addition to an incomplete annotation of the transcriptome. Enhancer ILF3 qRT-PCR,qPCR,ChIP,3C RNA-Seq The presence of multiple additional ILF3 binding interac_x0002_tions with introns, coding exons, noncoding non-AS exons, and SINEs on the transcribed strand probably reflects the extensive functional diversity of the ILF3 gene in addition to an incomplete annotation of the transcriptome. The presence of multiple additional ILF3 binding interac_x0002_tions with introns, coding exons, noncoding non-AS exons, and SINEs on the transcribed strand probably reflects the extensive functional diversity of the ILF3 gene in addition to an incomplete annotation of the transcriptome. Immunohistochemical staining The presence of multiple additional ILF3 binding interac_x0002_tions with introns, coding exons, noncoding non-AS exons, and SINEs on the transcribed strand probably reflects the extensive functional diversity of the ILF3 gene in addition to an incomplete annotation of the transcriptome. Western blot,Flow cytometry,PCR 31563853 chr3 186840138 186842138 ADIPOQ Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b) human Fat High+Lowthroughput CIDEA Transcriptionally Regulates UCP1 for Britening and Thermogenesis in Human Fat Cells 否 无 fat cell E_01_0253 Western blot, flow cytometry, PCR, immunofluorescence staining Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b) Enhancer ADIPOQ qRT-PCR,qPCR,ChIP,3C RNA-Seq Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b) Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b) Immunohistochemical staining Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b) Western blot,Flow cytometry,PCR,免疫荧光染色 31563432 chr4 154747879 154749879 Actrt2 Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B). human colon High+Lowthroughput Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes 否 无 Colon cancer HCT116 cells E_01_0254 Immunofluorescence light staining, flow cytometry, PCR Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B). Enhancer Actrt2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B). Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B). Immunohistochemical staining Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B). 免疫荧光光染色,Flow cytometry,PCR 31563432 chr17 42310179 42312179 STAT3 Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015). human kidney High+Lowthroughput Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes 否 无 HEK293T E_01_0254 Immunofluorescence light staining, flow cytometry, PCR Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015). Immunohistochemical staining Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015). STAT3 免疫荧光光染色,Flow cytometry,PCR Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015). 31562697 chr3 69736600 69738600 MITF MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, en_x0002_codes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. human,mouse connective tissue High+Lowthroughput Delineating the role of MITF isoforms in pigmentation and tissue homeostasis 否 无 Melanoma Pigment Cell E_02_0200 PCR, Western blot, immunofluorescence staining MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, en_x0002_codes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. Enhancer MITF qRT-PCR,qPCR,ChIP,3C RNA-Seq MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, en_x0002_codes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, en_x0002_codes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. Immunohistochemical staining MITF, a gene that is mutated in familial melanoma and Waardenburg syndrome, en_x0002_codes multiple isoforms expressed from alternative promoters that share common coding exons but have unique amino termini. PCR,Western blot,免疫荧光染色 31562697 chr11 89175705 89177705 TYR We previously showed that 9‐cis retinoic acid upregulates MITF and TYR expression in cultured melanocytes, stimulating pigment production in melano_x0002_cyte and melanoma cell lines (Paterson, Ho, Kapadia, & Ganesan, 2013). human,mouse breast High+Lowthroughput Delineating the role of MITF isoforms in pigmentation and tissue homeostasis 否 无 mammary cancer breast cancer stem cell E_02_0200 PCR, Western blot, immunofluorescence staining We previously showed that 9‐cis retinoic acid upregulates MITF and TYR expression in cultured melanocytes, stimulating pigment production in melano_x0002_cyte and melanoma cell lines (Paterson, Ho, Kapadia, & Ganesan, 2013). Enhancer TYR qRT-PCR,qPCR,ChIP,3C RNA-Seq We previously showed that 9‐cis retinoic acid upregulates MITF and TYR expression in cultured melanocytes, stimulating pigment production in melano_x0002_cyte and melanoma cell lines (Paterson, Ho, Kapadia, & Ganesan, 2013). We previously showed that 9‐cis retinoic acid upregulates MITF and TYR expression in cultured melanocytes, stimulating pigment production in melano_x0002_cyte and melanoma cell lines (Paterson, Ho, Kapadia, & Ganesan, 2013). Immunohistochemical staining We previously showed that 9‐cis retinoic acid upregulates MITF and TYR expression in cultured melanocytes, stimulating pigment production in melano_x0002_cyte and melanoma cell lines (Paterson, Ho, Kapadia, & Ganesan, 2013). PCR,Western blot,免疫荧光染色 31561451 chr7 55016281 55018281 EGFR In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs. human connective tissue High+Lowthroughput Fluorescein- and EGFR-Antibody Conjugated Silica Nanoparticles for Enhancement of Real-time Tumor Border Definition Using Confocal Laser Endomicroscopy in Squamous Cell Carcinoma of the Head and Neck 否 无 tumour squamous cell E_01_0255 PCR, Western blot, immunofluorescence staining In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs. Immunohistochemical staining In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs. EGFR PCR,Western blot,免疫荧光染色 In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs. 31561366 chr11 47463063 47465063 CELF1 The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133. human blood High+Lowthroughput Fluorescein- and EGFR-Antibody Conjugated Silica Nanoparticles for Enhancement of Real-time Tumor Border Definition Using Confocal Laser Endomicroscopy in Squamous Cell Carcinoma of the Head and Neck 是 rs8093731 Chronic myeloid leukemia K562 cells E_01_0256 PCR,Flow cytometry The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133. Enhancer CELF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133. The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133. Immunohistochemical staining The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133. PCR,Flow cytometry 31561366 chr14 52854332 52856332 FERMT2 Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2). human connective tissue High+Lowthroughput Inferring the Molecular Mechanisms of Noncoding Alzheimer's Disease-Associated Genetic Variants 是 rs4543938 Chronic myeloid leukemia monocyte cells E_01_0256 PCR,Flow cytometry Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2). Enhancer FERMT2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2). Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2). Immunohistochemical staining Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2). PCR,Flow cytometry 31560287 chr11 116832779 116834779 APOA1 Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7]. human Fat High+Lowthroughput New Insights into Apolipoprotein A5 and the Modulation of Human Adipose-derived Mesenchymal Stem Cells Adipogenesis 是 无 Obesity adipose-derived mesenchymal stem cells E_01_0257 PCR,Western blot Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7]. Enhancer APOA1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7]. Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7]. Immunohistochemical staining Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7]. PCR,Western blot 31558567 chrX 47579564 47581564 TIMP1 Among the 40 chemo_x0002_kines/cytokines we analyzed, nine were consistently up_x0002_regulated in Lats1/2 CKO sham hearts, including TIMP1, CXCL1, CXCL12, and CSF1. human,mouse bone High+Lowthroughput Hippo pathway deletion in adult resting cardiac fibroblasts initiates a cell state transition with spontaneous and self-sustaining fibrosis 否 无 miocardial infarction myeloid cell E_02_0201 PCR, flow cytometry, gene knockdown Among the 40 chemo_x0002_kines/cytokines we analyzed, nine were consistently up_x0002_regulated in Lats1/2 CKO sham hearts, including TIMP1, CXCL1, CXCL12, and CSF1. Enhancer TIMP1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Among the 40 chemo_x0002_kines/cytokines we analyzed, nine were consistently up_x0002_regulated in Lats1/2 CKO sham hearts, including TIMP1, CXCL1, CXCL12, and CSF1. Among the 40 chemo_x0002_kines/cytokines we analyzed, nine were consistently up_x0002_regulated in Lats1/2 CKO sham hearts, including TIMP1, CXCL1, CXCL12, and CSF1. Immunohistochemical staining Among the 40 chemo_x0002_kines/cytokines we analyzed, nine were consistently up_x0002_regulated in Lats1/2 CKO sham hearts, including TIMP1, CXCL1, CXCL12, and CSF1. PCR,Flow cytometry,基因敲降 31557715 chr7 25947403 25949403 MIR148A Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes human connective tissue High+Lowthroughput Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation 是 rs1055144 liver cancer mesenchymal stem cell E_01_0258 PCR, flow cytometry, immunofluorescence staining Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes Enhancer MIR148A qRT-PCR,qPCR,ChIP,3C RNA-Seq Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes Immunohistochemical staining Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes PCR,Flow cytometry,免疫荧光染色 31557715 chr7 26288944 26290944 SNX10 The region is delimited by the distal gene NPVF and the proximal gene SNX10. human Fat High+Lowthroughput Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation 是 rs7798002 liver cancer SGBS cells E_01_0258 PCR, flow cytometry, immunofluorescence staining The region is delimited by the distal gene NPVF and the proximal gene SNX10. Enhancer SNX10 qRT-PCR,qPCR,ChIP,3C RNA-Seq The region is delimited by the distal gene NPVF and the proximal gene SNX10. The region is delimited by the distal gene NPVF and the proximal gene SNX10. Immunohistochemical staining The region is delimited by the distal gene NPVF and the proximal gene SNX10. PCR,Flow cytometry,免疫荧光染色 31557715 chr1 203176161 203178161 CHI3L1 RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets. human liver cancer High+Lowthroughput Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation 是 rs1451385 liver cancer HepG2 cell E_01_0258 PCR, flow cytometry, immunofluorescence staining RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets. Enhancer CHI3L1 qRT-PCR,qPCR,ChIP,3C RNA-Seq RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets. RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets. Immunohistochemical staining RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets. PCR,Flow cytometry,免疫荧光染色 31554806 chr1 37806934 37808934 MTF1 PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome human breast High+Lowthroughput Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers 否 无 mammary cancer breast cancer cell E_01_0259 Flow cytometry PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome Enhancer MTF1 qRT-PCR,qPCR,ChIP,3C RNA-Seq PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome Immunohistochemical staining PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome Flow cytometry 31551362 chr3 181709186 181711186 SOX2 We proposed SOX2 as a lineage_x0002_survival oncogene in squamous cell cancers for its essential role during the development in the specification of the squamous cell lineages by opposing the role of Nkx2-1 in the dividing foregut and its essentiality for LUSC cell survival (9). human,mouse lung High+Lowthroughput Epigenomic Profiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma 是 无 Lung squamous cell carcinoma Lung squamous cell E_02_0202 PCR, Western blot, flow cytometry, immunofluorescence staining We proposed SOX2 as a lineage_x0002_survival oncogene in squamous cell cancers for its essential role during the development in the specification of the squamous cell lineages by opposing the role of Nkx2-1 in the dividing foregut and its essentiality for LUSC cell survival (9). Enhancer SOX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We proposed SOX2 as a lineage_x0002_survival oncogene in squamous cell cancers for its essential role during the development in the specification of the squamous cell lineages by opposing the role of Nkx2-1 in the dividing foregut and its essentiality for LUSC cell survival (9). We proposed SOX2 as a lineage_x0002_survival oncogene in squamous cell cancers for its essential role during the development in the specification of the squamous cell lineages by opposing the role of Nkx2-1 in the dividing foregut and its essentiality for LUSC cell survival (9). Immunohistochemical staining We proposed SOX2 as a lineage_x0002_survival oncogene in squamous cell cancers for its essential role during the development in the specification of the squamous cell lineages by opposing the role of Nkx2-1 in the dividing foregut and its essentiality for LUSC cell survival (9). PCR,Western blot,Flow cytometry,免疫荧光染色 31551362 chr6 98831871 98833871 POU3F2 For the TCGA-LUSC RNA-seq data, the 501 LUSC tumor tissues were classified on the basis of the expression level of TP63, SOX2, and POU3F2. human,mouse kidney High+Lowthroughput Epigenomic Profiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma 是 无 HEK293T E_02_0202 PCR, Western blot, flow cytometry, immunofluorescence staining For the TCGA-LUSC RNA-seq data, the 501 LUSC tumor tissues were classified on the basis of the expression level of TP63, SOX2, and POU3F2. Enhancer POU3F2 qRT-PCR,qPCR,ChIP,3C RNA-Seq For the TCGA-LUSC RNA-seq data, the 501 LUSC tumor tissues were classified on the basis of the expression level of TP63, SOX2, and POU3F2. For the TCGA-LUSC RNA-seq data, the 501 LUSC tumor tissues were classified on the basis of the expression level of TP63, SOX2, and POU3F2. Immunohistochemical staining For the TCGA-LUSC RNA-seq data, the 501 LUSC tumor tissues were classified on the basis of the expression level of TP63, SOX2, and POU3F2. PCR,Western blot,Flow cytometry,免疫荧光染色 31551335 chr12 55963742 55965742 CDK2 HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression. human blood High+Lowthroughput The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter 否 无 AIDS blood mononuclear cells E_01_0260 Western blot,PCR HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression. Enhancer CDK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression. HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression. Immunohistochemical staining HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression. Western blot,PCR 31551335 chr11 65419837 65421837 NEAT1 The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs human blood High+Lowthroughput The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter 否 无 AIDS T cell E_01_0260 Western blot,PCR The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs Enhancer NEAT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs Immunohistochemical staining The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs Western blot,PCR 31551256 chr9 134027777 134029777 BRD3 BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers. human breast High+Lowthroughput Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells 否 无 mammary cancer breast cancer cell E_01_0261 Western blot,PCR,Flow cytometry BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers. Enhancer BRD3 qRT-PCR,qPCR,ChIP,3C RNA-Seq BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers. BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers. Immunohistochemical staining BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers. Western blot,PCR,Flow cytometry 31551012 chr7 148804569 148806569 EZH2 Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells human stomach High+Lowthroughput HOXD-AS1 confers cisplatin resistance in gastric cancer through epigenetically silencing PDCD4 via recruiting EZH2 否 无 gastric cancer gastric cancer cell E_01_0262 Western blot,PCR Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Immunohistochemical staining Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells EZH2 Western blot,PCR Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells 31551012 chr10 110869187 110871187 PDCD4 Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells human stomach High+Lowthroughput HOXD-AS1 confers cisplatin resistance in gastric cancer through epigenetically silencing PDCD4 via recruiting EZH2 否 无 gastric cancer gastric cancer cell E_01_0262 Western blot,PCR Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Enhancer PDCD4 qRT-PCR,qPCR,ChIP,3C RNA-Seq Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Immunohistochemical staining Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells Western blot,PCR 31550664 chr17 13222491 13224491 Sod2 Specifically, we used Mn2+-superoxide dismutase (Sod2) deficient mice, in which oxidative stress is significantly increased even in a heterozygous state [6]. human,mouse pancreas High+Lowthroughput Gestational oxidative stress protects against adult obesity and insulin resistance 否 无 Pancreatic β - cell dysfunction Beta cell E_02_0203 PCR Specifically, we used Mn2+-superoxide dismutase (Sod2) deficient mice, in which oxidative stress is significantly increased even in a heterozygous state [6]. Enhancer Sod2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Specifically, we used Mn2+-superoxide dismutase (Sod2) deficient mice, in which oxidative stress is significantly increased even in a heterozygous state [6]. Specifically, we used Mn2+-superoxide dismutase (Sod2) deficient mice, in which oxidative stress is significantly increased even in a heterozygous state [6]. Immunohistochemical staining Specifically, we used Mn2+-superoxide dismutase (Sod2) deficient mice, in which oxidative stress is significantly increased even in a heterozygous state [6]. PCR 31548608 chr9 107481891 107483891 KLF4 The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 human,mouse connective tissue High+Lowthroughput KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks 否 无 pluripotent stem cell E_02_0204 Western blot,PCR,Flow cytometry The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Enhancer KLF4 qRT-PCR,qPCR,ChIP,3C RNA-Seq The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Immunohistochemical staining The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Western blot,PCR,Flow cytometry 31548608 chr17 35814159 35816159 Pou5f1 The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 human,mouse connective tissue High+Lowthroughput KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks 否 无 pluripotent stem cell E_02_0204 Western blot,PCR,Flow cytometry The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Enhancer Pou5f1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Immunohistochemical staining The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Western blot,PCR,Flow cytometry 31548608 chr4 56645505 56647505 HOPX The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 human,mouse connective tissue High+Lowthroughput KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks 否 无 pluripotent stem cell E_02_0204 Western blot,PCR,Flow cytometry The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Enhancer HOPX qRT-PCR,qPCR,ChIP,3C RNA-Seq The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Immunohistochemical staining The architectural function of KLF4 is further supported by the observations that KLF4 depletion abrogates long-range chromatin contacts at specific genomic loci, such as the Pou5f1 (Oct4) locus in mouse PSCs18 and the HOPX gene in human epidermal keratinocytes22 Western blot,PCR,Flow cytometry 31547883 chr16 67559930 67561930 CTCF In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig.  2b). human kidney High+Lowthroughput CGGBP1 regulates CTCF occupancy at repeats 否 无 HEK293T E_01_0263 Flow cytometry,PCR In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig.  2b). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig.  2b). Immunohistochemical staining In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig.  2b). CTCF Flow cytometry,PCR In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig.  2b). 31547433 chr13 40553074 40555074 FOXO1 The forkhead box protein class O type 1 (FOXO1) also participates in adipogenesis, by preventing adipose tissue differentiation through the inhibition of PPAR-γ transcription. human,mouse connective tissue High+Lowthroughput Transcriptional Analysis of FOXO1, C/EBP-α and PPAR-γ2 Genes and Their Association with Obesity-Related Insulin Resistance 否 无 Obesity NIH-3T3 fibroblastic cell E_02_0205 Western blot,PCR The forkhead box protein class O type 1 (FOXO1) also participates in adipogenesis, by preventing adipose tissue differentiation through the inhibition of PPAR-γ transcription. Enhancer FOXO1 qRT-PCR,qPCR,ChIP,3C RNA-Seq The forkhead box protein class O type 1 (FOXO1) also participates in adipogenesis, by preventing adipose tissue differentiation through the inhibition of PPAR-γ transcription. The forkhead box protein class O type 1 (FOXO1) also participates in adipogenesis, by preventing adipose tissue differentiation through the inhibition of PPAR-γ transcription. Immunohistochemical staining The forkhead box protein class O type 1 (FOXO1) also participates in adipogenesis, by preventing adipose tissue differentiation through the inhibition of PPAR-γ transcription. Western blot,PCR 31546863 chr11 36480909 36482909 TRAF6 sion of the proteins involved in osteoclastogenesis including TRAF6, c-Fos, NFATc1, and cathepsin K. Western blotting indicated that RANKL significantly increased the expression of TRAF6, NFATc1, and cathepsin K. Pre-treatm mouse blood High+Lowthroughput Egg White Ovotransferrin Attenuates RANKL-Induced Osteoclastogenesis and Bone Resorption 否 无 osteoporosis B cell E_02_0206 Western blot,PCR sion of the proteins involved in osteoclastogenesis including TRAF6, c-Fos, NFATc1, and cathepsin K. Western blotting indicated that RANKL significantly increased the expression of TRAF6, NFATc1, and cathepsin K. Pre-treatm Enhancer TRAF6 qRT-PCR,qPCR,ChIP,3C RNA-Seq sion of the proteins involved in osteoclastogenesis including TRAF6, c-Fos, NFATc1, and cathepsin K. Western blotting indicated that RANKL significantly increased the expression of TRAF6, NFATc1, and cathepsin K. Pre-treatm sion of the proteins involved in osteoclastogenesis including TRAF6, c-Fos, NFATc1, and cathepsin K. Western blotting indicated that RANKL significantly increased the expression of TRAF6, NFATc1, and cathepsin K. Pre-treatm Immunohistochemical staining sion of the proteins involved in osteoclastogenesis including TRAF6, c-Fos, NFATc1, and cathepsin K. Western blotting indicated that RANKL significantly increased the expression of TRAF6, NFATc1, and cathepsin K. Pre-treatm Western blot,PCR 31546763 chr4 77508709 77510709 CXCL13 During the disease state, this subset of mDCs displayed heightened toll-like receptors 7 and 9 (TLR 7/9) responses with increased interleukin 10 (IL-10) and C-X-C motif chemokine ligand 13 (CXCL13) expressions. human,mouse blood High+Lowthroughput Heightened TLR7/9-Induced IL-10 and CXCL13 Production with Dysregulated NF-?B Activation in CD11c(hi)CD11b(+) Dendritic Cells in NZB/W F1 Mice 否 无 Systemic lupus erythematosus T cell E_02_0207 Western blot,PCR,Flow cytometry During the disease state, this subset of mDCs displayed heightened toll-like receptors 7 and 9 (TLR 7/9) responses with increased interleukin 10 (IL-10) and C-X-C motif chemokine ligand 13 (CXCL13) expressions. Enhancer CXCL13 qRT-PCR,qPCR,ChIP,3C RNA-Seq During the disease state, this subset of mDCs displayed heightened toll-like receptors 7 and 9 (TLR 7/9) responses with increased interleukin 10 (IL-10) and C-X-C motif chemokine ligand 13 (CXCL13) expressions. During the disease state, this subset of mDCs displayed heightened toll-like receptors 7 and 9 (TLR 7/9) responses with increased interleukin 10 (IL-10) and C-X-C motif chemokine ligand 13 (CXCL13) expressions. Immunohistochemical staining During the disease state, this subset of mDCs displayed heightened toll-like receptors 7 and 9 (TLR 7/9) responses with increased interleukin 10 (IL-10) and C-X-C motif chemokine ligand 13 (CXCL13) expressions. Western blot,PCR,Flow cytometry 31546150 chr16 68734373 68736373 CDH1 EMT is a process in which epithelial cells lose their cell junctions and polarity characterized by E-cadherin (CDH1) downregulation to gain a motile mesenchymal phenotype, in_x0002_duction of a series of mesenchymal-specific transcription factors, such as Snail1, Snail2, ZEB1, ZEB2 and Twist1. human,mouse pancreas High+Lowthroughput Menin Coordinates C/EBPβ-Mediated TGF-β Signaling for Epithelial-Mesenchymal Transition and Growth Inhibition in Pancreatic Cancer 否 无 Pancreatic ductal adenocarcinoma PANC1 cells E_02_0208 Western blot,PCR,Flow cytometry EMT is a process in which epithelial cells lose their cell junctions and polarity characterized by E-cadherin (CDH1) downregulation to gain a motile mesenchymal phenotype, in_x0002_duction of a series of mesenchymal-specific transcription factors, such as Snail1, Snail2, ZEB1, ZEB2 and Twist1. Enhancer CDH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq EMT is a process in which epithelial cells lose their cell junctions and polarity characterized by E-cadherin (CDH1) downregulation to gain a motile mesenchymal phenotype, in_x0002_duction of a series of mesenchymal-specific transcription factors, such as Snail1, Snail2, ZEB1, ZEB2 and Twist1. EMT is a process in which epithelial cells lose their cell junctions and polarity characterized by E-cadherin (CDH1) downregulation to gain a motile mesenchymal phenotype, in_x0002_duction of a series of mesenchymal-specific transcription factors, such as Snail1, Snail2, ZEB1, ZEB2 and Twist1. Immunohistochemical staining EMT is a process in which epithelial cells lose their cell junctions and polarity characterized by E-cadherin (CDH1) downregulation to gain a motile mesenchymal phenotype, in_x0002_duction of a series of mesenchymal-specific transcription factors, such as Snail1, Snail2, ZEB1, ZEB2 and Twist1. Western blot,PCR,Flow cytometry 31546122 chr11 120694060 120696060 Fasn We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). mouse connective tissue High+Lowthroughput Promoting differentiation and lipid metabolism are the primary effects for DINP exposure on 3T3-L1 preadipocytes 否 无 3T3-L1 cell E_02_0209 PCR,Western blot,Flow cytometry We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). Enhancer Fasn qRT-PCR,qPCR,ChIP,3C RNA-Seq We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). Immunohistochemical staining We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). PCR,Western blot,Flow cytometry 31546122 chr16 22962769 22964769 Adipoq We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). mouse kidney High+Lowthroughput Promoting differentiation and lipid metabolism are the primary effects for DINP exposure on 3T3-L1 preadipocytes 否 无 HEK-293T cells E_02_0209 PCR,Western blot,Flow cytometry We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). Enhancer Adipoq qRT-PCR,qPCR,ChIP,3C RNA-Seq We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). Immunohistochemical staining We also measured the expression of adiponectin (Adipoq), li_x0002_poprotein lipase (Lpl), and fatty acid synthase (Fasn), which were reported to be used as adipogenesis markers, and the results showed that the DINP exposure induced the upregulation of Adipoq and Lpl, however, unlike Rosi, the Fasn was not significantly affected with DINP exposure (Fig. S4). PCR,Western blot,Flow cytometry 31545422 chr7 148804556 148806556 EZH2 In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo. human neck High+Lowthroughput Targeting of EZH2 inhibits epithelial?mesenchymal transition in head and neck squamous cell carcinoma via regulating the STAT3/VEGFR2 axis 否 无 cancer neck squamous cell E_01_0264 PCR, Western blot, immunofluorescence staining In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo. Immunohistochemical staining In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo. EZH2 PCR,Western blot,免疫荧光染色 In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo. 31545422 chr17 42310472 42312472 STAT3 We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC. human Head, neck High+Lowthroughput Targeting of EZH2 inhibits epithelial?mesenchymal transition in head and neck squamous cell carcinoma via regulating the STAT3/VEGFR2 axis 否 无 cancer HNSCC cells E_01_0264 PCR, Western blot, immunofluorescence staining We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC. Immunohistochemical staining We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC. STAT3 PCR,Western blot,免疫荧光染色 We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC. 31544892 chr13 30453885 30455885 HMGB1 In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. human,Hamster ovary High+Lowthroughput Enhancers Improve the AID-Induced Hypermutation in Episomal Vector for Antibody Affinity Maturation in Mammalian Cell Display 否 无 cancer CHO cells E_02_0210 Flow cytometry In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. Enhancer HMGB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. Immunohistochemical staining In this study, we examined the role of Ig and Ek enhancers in enhancing SHM in the episomal vector pCEP4 that expresses an anti-high mobility group box 1 (HMGB1) full-length antibody. Flow cytometry 31542774 chr19 29809345 29811345 CCNE1 By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1. human blood High+Lowthroughput Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma 否 无 gastric cancer B cell E_01_0265 PCR,Flow cytometry By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1. Immunohistochemical staining By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1. CCNE1 PCR,Flow cytometry By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1. 31541592 chr6 35570844 35572844 FKBP5 We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level. human bone High+Lowthroughput Amyloid precursor protein, an androgen-regulated gene, is targeted by RNA-binding protein PSF/SFPQ in neuronal cells 否 无 Osteoma SH‐SY5Y cells E_01_0266 PCR,Western blot We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level. Enhancer FKBP5 qRT-PCR,qPCR,ChIP,3C RNA-Seq We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level. We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level. Immunohistochemical staining We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level. PCR,Western blot 31538139 chr3 186839743 186841743 ADIPOQ The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro. human Fat High+Lowthroughput Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans 是 rs10788522 fat cell E_01_0267 PCR,Flow cytometry The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro. Enhancer ADIPOQ qRT-PCR,qPCR,ChIP,3C RNA-Seq The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro. The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro. Immunohistochemical staining The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro. PCR,Flow cytometry 31536603 chr22 43148768 43150768 TSPO The 18- kDa translocator protein TSPO is used as an imaging target in positron emission tomogra_x0002_phy to detect neuroinflammation, and its expression is correlated with microglial activation human,mouse Nervous tissue High+Lowthroughput Lipopolysaccharide induces mouse translocator protein (18 kDa) expression via the AP-1 complex in the microglial cell line, BV-2 否 无 Neuroinflammation microglial cell E_02_0211 PCR, Western blot, immunofluorescence staining The 18- kDa translocator protein TSPO is used as an imaging target in positron emission tomogra_x0002_phy to detect neuroinflammation, and its expression is correlated with microglial activation Enhancer TSPO qRT-PCR,qPCR,ChIP,3C RNA-Seq The 18- kDa translocator protein TSPO is used as an imaging target in positron emission tomogra_x0002_phy to detect neuroinflammation, and its expression is correlated with microglial activation The 18- kDa translocator protein TSPO is used as an imaging target in positron emission tomogra_x0002_phy to detect neuroinflammation, and its expression is correlated with microglial activation Immunohistochemical staining The 18- kDa translocator protein TSPO is used as an imaging target in positron emission tomogra_x0002_phy to detect neuroinflammation, and its expression is correlated with microglial activation PCR,Western blot,免疫荧光染色 31536603 chr1 32289598 32291598 HDAC1 In addition, the binding of histone deacetylase 1 (HDAC1) to the enhancer region, which contains the AP-1 site, was decreased by LPS treatment, but there were no significant differences in HDAC1 binding to the proximal promoter region with or without LPS. human,mouse connective tissue High+Lowthroughput Lipopolysaccharide induces mouse translocator protein (18 kDa) expression via the AP-1 complex in the microglial cell line, BV-2 否 无 Neuroinflammation immune cell E_02_0211 PCR, Western blot, immunofluorescence staining In addition, the binding of histone deacetylase 1 (HDAC1) to the enhancer region, which contains the AP-1 site, was decreased by LPS treatment, but there were no significant differences in HDAC1 binding to the proximal promoter region with or without LPS. Enhancer HDAC1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, the binding of histone deacetylase 1 (HDAC1) to the enhancer region, which contains the AP-1 site, was decreased by LPS treatment, but there were no significant differences in HDAC1 binding to the proximal promoter region with or without LPS. In addition, the binding of histone deacetylase 1 (HDAC1) to the enhancer region, which contains the AP-1 site, was decreased by LPS treatment, but there were no significant differences in HDAC1 binding to the proximal promoter region with or without LPS. Immunohistochemical staining In addition, the binding of histone deacetylase 1 (HDAC1) to the enhancer region, which contains the AP-1 site, was decreased by LPS treatment, but there were no significant differences in HDAC1 binding to the proximal promoter region with or without LPS. PCR,Western blot,免疫荧光染色 31535083 chr6 90460328 90462328 Aldh1l1 We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). human,mouse Epithelial tissues High+Lowthroughput Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation 是 rs11804091 Obesity endothelial cell E_02_0212 Immunofluorescence staining, chip, flow cytometry We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). Enhancer Aldh1l1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). Immunohistochemical staining We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). 免疫荧光染色,CHIP,Flow cytometry 31535083 chr9 119727541 119729541 Cx3cr1 We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). human,mouse tumour High+Lowthroughput Genomic and epigenomic mapping of leptin-responsive neuronal populations involved in body weight regulation 是 rs11804091 Obesity tumor cell E_02_0212 Immunofluorescence staining, chip, flow cytometry We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). Enhancer Cx3cr1 qRT-PCR,qPCR,ChIP,3C RNA-Seq We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). Immunohistochemical staining We performed RNA-seq both on GFP+ and GFP− sorted nuclei in all physiological conditions tested. The specificity of our nuclei isolation protocol was validated by the high level of enrichment of Lepr and by the strong depletion of genes spe_x0002_cifically expressed in oligodendrocytes (Mag), microglia (Cx3cr1) and astrocytes (Aldh1l1) (Fig. 2a). 免疫荧光染色,CHIP,Flow cytometry 31534142 chr16 67559649 67561649 CTCF To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e). human kidney High+Lowthroughput Epigenome editing strategies for the functional annotation of CTCF insulators 否 无 tumour HEK293 cell E_01_0268 PCR,Flow cytometry To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e). Immunohistochemical staining To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e). CTCF PCR,Flow cytometry To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e). 31534142 chr4 54096948 54098948 GSX2 We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. human High+Lowthroughput Epigenome editing strategies for the functional annotation of CTCF insulators 否 无 tumour E_01_0268 PCR,Flow cytometry We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. Enhancer GSX2 qRT-PCR,qPCR,ChIP,3C RNA-Seq We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. Immunohistochemical staining We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. PCR,Flow cytometry 31534142 chr4 54226570 54228570 PDGFRA We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. human High+Lowthroughput Epigenome editing strategies for the functional annotation of CTCF insulators 否 无 tumour E_01_0268 PCR,Flow cytometry We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. Immunohistochemical staining We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. PDGFRA PCR,Flow cytometry We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint. 31533028 chr21 34785012 34787012 RUNX1 The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1. human blood High+Lowthroughput RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction 否 无 leukemia hematopoietic stem cell E_01_0269 PCR,Flow cytometry The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1. Immunohistochemical staining The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1. RUNX1 PCR,Flow cytometry The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1. 31533028 chr12 4266618 4268618 CCND2 Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red). human blood High+Lowthroughput RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction 否 无 leukemia Kasumi-1 cells E_01_0269 PCR,Flow cytometry Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red). Enhancer CCND2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red). Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red). Immunohistochemical staining Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red). PCR,Flow cytometry 31531679 chr16 86564387 86566387 FOXC2 FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker. human Epithelial tissues High+Lowthroughput Evidence for miR-548c-5p regulation of FOXC2 transcription through a distal genomic target site in human podocytes 否 无 epithelial cell E_01_0270 PCR, Western blot, immunofluorescence staining FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker. Immunohistochemical staining FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker. FOXC2 PCR,Western blot,免疫荧光染色 FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker. 31531679 chr1 179548051 179550051 NPHS2 As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22]. human Epithelial tissues High+Lowthroughput Evidence for miR-548c-5p regulation of FOXC2 transcription through a distal genomic target site in human podocytes 否 无 epithelial cell E_01_0270 PCR, Western blot, immunofluorescence staining As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22]. Enhancer NPHS2 qRT-PCR,qPCR,ChIP,3C RNA-Seq As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22]. As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22]. Immunohistochemical staining As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22]. PCR,Western blot,免疫荧光染色 31531679 chr16 86527297 86529297 MTHFSD Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16. human Epithelial tissues High+Lowthroughput Evidence for miR-548c-5p regulation of FOXC2 transcription through a distal genomic target site in human podocytes 否 无 epithelial cell E_01_0270 PCR, Western blot, immunofluorescence staining Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16. Enhancer MTHFSD qRT-PCR,qPCR,ChIP,3C RNA-Seq Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16. Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16. Immunohistochemical staining Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16. PCR,Western blot,免疫荧光染色 31530818 chr8 127732403 127734403 MYC FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. human blood High+Lowthroughput Identification of significant chromatin contacts from HiChIP data by FitHiChIP 否 无 leukemia T cell E_01_0271 Flow cytometry FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. Immunohistochemical staining FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. MYC Flow cytometry FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. 31530818 chr17 7659021 7661021 TP53 FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. human blood High+Lowthroughput Identification of significant chromatin contacts from HiChIP data by FitHiChIP 否 无 leukemia K562 cell E_01_0271 Flow cytometry FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. Immunohistochemical staining FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. TP53 Flow cytometry FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU. 31530812 chr2 24200308 24202308 ITSN2 In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g). human Nervous tissue High+Lowthroughput Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants 是 无 neuronal cell E_01_0272 Flow cytometry,Western blot In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g). Enhancer ITSN2 qRT-PCR,qPCR,ChIP,3C RNA-Seq In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g). In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g). Immunohistochemical staining In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g). Flow cytometry,Western blot 31530812 chr6 11180134 11182134 NEDD9 Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression human connective tissue High+Lowthroughput Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants 是 无 male germ cells E_01_0272 Flow cytometry,Western blot Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression Enhancer NEDD9 qRT-PCR,qPCR,ChIP,3C RNA-Seq Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression Immunohistochemical staining Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression Flow cytometry,Western blot 31530225 chr16 53698982 53700982 FTO FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids human connective tissue High+Lowthroughput Functional genomic characterization of the FTO locus in African Americans 是 rs9927317 Obesity mesenchymal stem cell E_01_0273 Flow cytometry FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids Enhancer FTO qRT-PCR,qPCR,ChIP,3C RNA-Seq FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids Immunohistochemical staining FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids Flow cytometry 31530225 chr16 53595395 53597395 RPGRIP1L The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction. human connective tissue High+Lowthroughput Functional genomic characterization of the FTO locus in African Americans 是 rs62033405 Obesity mesenchymal stem cell E_01_0273 Flow cytometry The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction. Enhancer RPGRIP1L qRT-PCR,qPCR,ChIP,3C RNA-Seq The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction. The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction. Immunohistochemical staining The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction. Flow cytometry 31530225 chr7 101813374 101815374 CUX1 We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44). human Fat High+Lowthroughput Functional genomic characterization of the FTO locus in African Americans 是 rs9939609 Obesity white adipocytes E_01_0273 Flow cytometry We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44). Immunohistochemical staining We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44). CUX1 Flow cytometry We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44). 31530225 chr16 54280685 54282685 IRX3 Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. human Fat High+Lowthroughput Functional genomic characterization of the FTO locus in African Americans 是 rs8050136 Obesity white adipocytes E_01_0273 Flow cytometry Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Enhancer IRX3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Immunohistochemical staining Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Flow cytometry 31530225 chr16 54928124 54930124 IRX5 Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. human Fat High+Lowthroughput Functional genomic characterization of the FTO locus in African Americans 是 rs9930506 Obesity white adipocytes E_01_0273 Flow cytometry Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Enhancer IRX5 qRT-PCR,qPCR,ChIP,3C RNA-Seq Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Immunohistochemical staining Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L. Flow cytometry 31530015 chr16 23577727 23579727 NDUFAB1 A dramatic decrease of NDUFAB1 protein was detected in the skeletal muscle of both db/db diabetic mice (Fig. 2A) and HFD-induced insulin resistance mice (Fig. 2B), amid myriads of other changes, such as elevated serum glucose levels, and altered insulin signaling and gene expression (22, 23). human,mouse connective tissue High+Lowthroughput NDUFAB1 protects against obesity and insulin resistance by enhancing mitochondrial metabolism 否 无 insulin resistance murine embryonic stem (ES) cell E_02_0213 PCR,Western blot A dramatic decrease of NDUFAB1 protein was detected in the skeletal muscle of both db/db diabetic mice (Fig. 2A) and HFD-induced insulin resistance mice (Fig. 2B), amid myriads of other changes, such as elevated serum glucose levels, and altered insulin signaling and gene expression (22, 23). Enhancer NDUFAB1 qRT-PCR,qPCR,ChIP,3C RNA-Seq A dramatic decrease of NDUFAB1 protein was detected in the skeletal muscle of both db/db diabetic mice (Fig. 2A) and HFD-induced insulin resistance mice (Fig. 2B), amid myriads of other changes, such as elevated serum glucose levels, and altered insulin signaling and gene expression (22, 23). A dramatic decrease of NDUFAB1 protein was detected in the skeletal muscle of both db/db diabetic mice (Fig. 2A) and HFD-induced insulin resistance mice (Fig. 2B), amid myriads of other changes, such as elevated serum glucose levels, and altered insulin signaling and gene expression (22, 23). Immunohistochemical staining A dramatic decrease of NDUFAB1 protein was detected in the skeletal muscle of both db/db diabetic mice (Fig. 2A) and HFD-induced insulin resistance mice (Fig. 2B), amid myriads of other changes, such as elevated serum glucose levels, and altered insulin signaling and gene expression (22, 23). PCR,Western blot 31529763 chr17 43041465 43043465 BRCA1 Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1. human High+Lowthroughput (19) F?NMR Spectroscopy Tagging and Paramagnetic Relaxation Enhancement-Based Conformation Analysis of Intrinsically Disordered Protein Complexes 否 无 tumour E-coli cell E_01_0274 Flow cytometry Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1. Immunohistochemical staining Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1. BRCA1 Flow cytometry Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1. 31525599 chr11 10302280 10304280 ADM ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature. human High+Lowthroughput Tracing upconversion nanoparticle penetration in human skin 否 无 E_01_0275 PCR, immunofluorescence staining ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature. Enhancer ADM qRT-PCR,qPCR,ChIP,3C RNA-Seq ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature. ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature. Immunohistochemical staining ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature. PCR,免疫荧光染色 31521883 chr18 63120882 63122882 BCL2 In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed. human blood High+Lowthroughput Trehalose supplementation during porcine oocytes in?vitro maturation improves the developmental capacity of parthenotes 否 无 B cell E_01_0276 PCR, immunofluorescence staining In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed. Immunohistochemical staining In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed. BCL2 PCR,免疫荧光染色 In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed. 31521109 chr11 58037956 58039956 VN2R9P For the human genome, cluster34 (chr11:54591480– 59,749,574) is the richest cluster of the olfactome 1 Mb cutoff list; it harbors a single VR pseudogene (VN2R9P) in between OR genes. Cluster15 (chr6:131700469–132, 646,003) of the same list is the TAAR locus, which starts with a single, otherwise remarkably isolated (39 Mb) OR gene: OR2A4 [25] human,mouse blood High+Lowthroughput A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers 否 无 T cell E_02_0214 PCR For the human genome, cluster34 (chr11:54591480– 59,749,574) is the richest cluster of the olfactome 1 Mb cutoff list; it harbors a single VR pseudogene (VN2R9P) in between OR genes. Cluster15 (chr6:131700469–132, 646,003) of the same list is the TAAR locus, which starts with a single, otherwise remarkably isolated (39 Mb) OR gene: OR2A4 [25] Enhancer VN2R9P qRT-PCR,qPCR,ChIP,3C RNA-Seq For the human genome, cluster34 (chr11:54591480– 59,749,574) is the richest cluster of the olfactome 1 Mb cutoff list; it harbors a single VR pseudogene (VN2R9P) in between OR genes. Cluster15 (chr6:131700469–132, 646,003) of the same list is the TAAR locus, which starts with a single, otherwise remarkably isolated (39 Mb) OR gene: OR2A4 [25] For the human genome, cluster34 (chr11:54591480– 59,749,574) is the richest cluster of the olfactome 1 Mb cutoff list; it harbors a single VR pseudogene (VN2R9P) in between OR genes. Cluster15 (chr6:131700469–132, 646,003) of the same list is the TAAR locus, which starts with a single, otherwise remarkably isolated (39 Mb) OR gene: OR2A4 [25] Immunohistochemical staining For the human genome, cluster34 (chr11:54591480– 59,749,574) is the richest cluster of the olfactome 1 Mb cutoff list; it harbors a single VR pseudogene (VN2R9P) in between OR genes. Cluster15 (chr6:131700469–132, 646,003) of the same list is the TAAR locus, which starts with a single, otherwise remarkably isolated (39 Mb) OR gene: OR2A4 [25] PCR 31520529 chr1 156461014 156463014 MEF2D Mt2Ddn bound strongly to the ND6-MEF2 site and disrupted the function of normal mitochondrial MEF2D without affecting the expression of the nuclear MEF2 reporter (She et al. 2011). mouse Nervous tissue High+Lowthroughput Salidroside protects dopaminergic neurons by regulating the mitochondrial MEF2D-ND6 pathway in the MPTP/MPP(+) -induced model of Parkinson's disease 是 无 Parkinson SN4741 cells E_02_0215 PCR, immunofluorescence staining, Western blot Mt2Ddn bound strongly to the ND6-MEF2 site and disrupted the function of normal mitochondrial MEF2D without affecting the expression of the nuclear MEF2 reporter (She et al. 2011). Enhancer MEF2D qRT-PCR,qPCR,ChIP,3C RNA-Seq Mt2Ddn bound strongly to the ND6-MEF2 site and disrupted the function of normal mitochondrial MEF2D without affecting the expression of the nuclear MEF2 reporter (She et al. 2011). Mt2Ddn bound strongly to the ND6-MEF2 site and disrupted the function of normal mitochondrial MEF2D without affecting the expression of the nuclear MEF2 reporter (She et al. 2011). Immunohistochemical staining Mt2Ddn bound strongly to the ND6-MEF2 site and disrupted the function of normal mitochondrial MEF2D without affecting the expression of the nuclear MEF2 reporter (She et al. 2011). PCR,免疫荧光染色,Western blot 31519749 chr3 142303842 142305842 XRN1 Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs. human High+Lowthroughput Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection 否 无 Villous carcinoma choriocarcinoma cells E_01_0277 PCR,Western blot Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs. Enhancer XRN1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs. Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs. Immunohistochemical staining Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs. PCR,Western blot 31519704 chr9 136491964 136493964 NOTCH1 MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. human,mouse blood High+Lowthroughput GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia 否 无 leukemia T cell E_02_0216 PCR,Flow cytometry MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. Enhancer NOTCH1 qRT-PCR,qPCR,ChIP,3C RNA-Seq MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. Immunohistochemical staining MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. PCR,Flow cytometry 31519704 chr8 127732540 127734540 MYC MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. human,mouse blood High+Lowthroughput GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia 否 无 leukemia T cell E_02_0216 PCR,Flow cytometry MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. Enhancer MYC qRT-PCR,qPCR,ChIP,3C RNA-Seq MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. Immunohistochemical staining MYC is a major effector of NOTCH1 oncogenic programs in T-ALL. PCR,Flow cytometry 31519520 chr16 67560000 67562000 CTCF Sequence constraint was even higher when considering DI bins either bound by CTCF (DI_CTCF) or MYOD (DI_MYOD) or co-bound by these two TFs (DI_MYOD_CTCF) (Figure S5A). human,mouse connective tissue High+Lowthroughput Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation 否 无 somatic cell E_02_0217 PCR, Western blot, flow cytometry, immunofluorescence staining Sequence constraint was even higher when considering DI bins either bound by CTCF (DI_CTCF) or MYOD (DI_MYOD) or co-bound by these two TFs (DI_MYOD_CTCF) (Figure S5A). Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq Sequence constraint was even higher when considering DI bins either bound by CTCF (DI_CTCF) or MYOD (DI_MYOD) or co-bound by these two TFs (DI_MYOD_CTCF) (Figure S5A). Sequence constraint was even higher when considering DI bins either bound by CTCF (DI_CTCF) or MYOD (DI_MYOD) or co-bound by these two TFs (DI_MYOD_CTCF) (Figure S5A). Immunohistochemical staining Sequence constraint was even higher when considering DI bins either bound by CTCF (DI_CTCF) or MYOD (DI_MYOD) or co-bound by these two TFs (DI_MYOD_CTCF) (Figure S5A). PCR,Western blot,Flow cytometry,免疫荧光染色 31519520 chr12 55681811 55683811 ITGA7 Upon ectopic expression, MYOD bound the promoter of ITGA7 and RDH5 at CTCF-bound elements in IMR90 (Figure 4L) and this coincided with increased interaction between the two CTCF-bound re_x0002_gions, as measured by Hi-C (Figures 4K and 4L) and validated by 3C (Figure 4L, bottom right). Importantly, these events corre_x0002_lated with an increased expression of both ITGA7 and RDH5 (Figure 4L, bottom left). human,mouse bone High+Lowthroughput Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation 否 无 mouse cell of skeletal muscle E_02_0217 PCR, Western blot, flow cytometry, immunofluorescence staining Upon ectopic expression, MYOD bound the promoter of ITGA7 and RDH5 at CTCF-bound elements in IMR90 (Figure 4L) and this coincided with increased interaction between the two CTCF-bound re_x0002_gions, as measured by Hi-C (Figures 4K and 4L) and validated by 3C (Figure 4L, bottom right). Importantly, these events corre_x0002_lated with an increased expression of both ITGA7 and RDH5 (Figure 4L, bottom left). Enhancer ITGA7 qRT-PCR,qPCR,ChIP,3C RNA-Seq Upon ectopic expression, MYOD bound the promoter of ITGA7 and RDH5 at CTCF-bound elements in IMR90 (Figure 4L) and this coincided with increased interaction between the two CTCF-bound re_x0002_gions, as measured by Hi-C (Figures 4K and 4L) and validated by 3C (Figure 4L, bottom right). Importantly, these events corre_x0002_lated with an increased expression of both ITGA7 and RDH5 (Figure 4L, bottom left). Upon ectopic expression, MYOD bound the promoter of ITGA7 and RDH5 at CTCF-bound elements in IMR90 (Figure 4L) and this coincided with increased interaction between the two CTCF-bound re_x0002_gions, as measured by Hi-C (Figures 4K and 4L) and validated by 3C (Figure 4L, bottom right). Importantly, these events corre_x0002_lated with an increased expression of both ITGA7 and RDH5 (Figure 4L, bottom left). Immunohistochemical staining Upon ectopic expression, MYOD bound the promoter of ITGA7 and RDH5 at CTCF-bound elements in IMR90 (Figure 4L) and this coincided with increased interaction between the two CTCF-bound re_x0002_gions, as measured by Hi-C (Figures 4K and 4L) and validated by 3C (Figure 4L, bottom right). Importantly, these events corre_x0002_lated with an increased expression of both ITGA7 and RDH5 (Figure 4L, bottom left). PCR,Western blot,Flow cytometry,免疫荧光染色 31519520 chr1 201356451 201358451 TNNT2 Upon MYOD induction in fibroblasts and its binding to TNNT2 promoter, we observed an increase in TNNT2 pro_x0002_moter-enhancer interaction together with an increase in TNNT2 expression (Figures 5D–5F). human,mouse lung High+Lowthroughput Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation 否 无 IMR90 cell E_02_0217 PCR, Western blot, flow cytometry, immunofluorescence staining Upon MYOD induction in fibroblasts and its binding to TNNT2 promoter, we observed an increase in TNNT2 pro_x0002_moter-enhancer interaction together with an increase in TNNT2 expression (Figures 5D–5F). Enhancer TNNT2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Upon MYOD induction in fibroblasts and its binding to TNNT2 promoter, we observed an increase in TNNT2 pro_x0002_moter-enhancer interaction together with an increase in TNNT2 expression (Figures 5D–5F). Upon MYOD induction in fibroblasts and its binding to TNNT2 promoter, we observed an increase in TNNT2 pro_x0002_moter-enhancer interaction together with an increase in TNNT2 expression (Figures 5D–5F). Immunohistochemical staining Upon MYOD induction in fibroblasts and its binding to TNNT2 promoter, we observed an increase in TNNT2 pro_x0002_moter-enhancer interaction together with an increase in TNNT2 expression (Figures 5D–5F). PCR,Western blot,Flow cytometry,免疫荧光染色 31518916 chr7 148804819 148806819 EZH2 The function of histone methyltransferase enhancer of zeste homolog 2 (EZH2) in sepsis remains unknown. human,mouse connective tissue High+Lowthroughput Novel pharmacological inhibition of EZH2 attenuates septic shock by altering innate inflammatory responses to sepsis 否 无 Sepsis Inflammatory cell E_02_0218 PCR, Western blot, flow cytometry, immunofluorescence staining The function of histone methyltransferase enhancer of zeste homolog 2 (EZH2) in sepsis remains unknown. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq The function of histone methyltransferase enhancer of zeste homolog 2 (EZH2) in sepsis remains unknown. The function of histone methyltransferase enhancer of zeste homolog 2 (EZH2) in sepsis remains unknown. Immunohistochemical staining The function of histone methyltransferase enhancer of zeste homolog 2 (EZH2) in sepsis remains unknown. PCR,Western blot,Flow cytometry,免疫荧光染色 31518916 chr17 42310415 42312415 STAT3 Blockage of EZH2 also suppressed the progression of lung injury and alleviated in_x0002_flammation by decreasing the pulmonary cell apoptosis, reducing inflammatory cells infiltration and cytokines release through inhibition of the STAT3 signaling pathway and recovery of PPARγ activation. I human,mouse lung High+Lowthroughput Novel pharmacological inhibition of EZH2 attenuates septic shock by altering innate inflammatory responses to sepsis 否 无 Sepsis pneumocyte E_02_0218 PCR, Western blot, flow cytometry, immunofluorescence staining Blockage of EZH2 also suppressed the progression of lung injury and alleviated in_x0002_flammation by decreasing the pulmonary cell apoptosis, reducing inflammatory cells infiltration and cytokines release through inhibition of the STAT3 signaling pathway and recovery of PPARγ activation. I Enhancer STAT3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Blockage of EZH2 also suppressed the progression of lung injury and alleviated in_x0002_flammation by decreasing the pulmonary cell apoptosis, reducing inflammatory cells infiltration and cytokines release through inhibition of the STAT3 signaling pathway and recovery of PPARγ activation. I Blockage of EZH2 also suppressed the progression of lung injury and alleviated in_x0002_flammation by decreasing the pulmonary cell apoptosis, reducing inflammatory cells infiltration and cytokines release through inhibition of the STAT3 signaling pathway and recovery of PPARγ activation. I Immunohistochemical staining Blockage of EZH2 also suppressed the progression of lung injury and alleviated in_x0002_flammation by decreasing the pulmonary cell apoptosis, reducing inflammatory cells infiltration and cytokines release through inhibition of the STAT3 signaling pathway and recovery of PPARγ activation. I PCR,Western blot,Flow cytometry,免疫荧光染色 31518916 chr17 78354497 78356497 SOCS3 In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. human,mouse Epithelial tissues High+Lowthroughput Novel pharmacological inhibition of EZH2 attenuates septic shock by altering innate inflammatory responses to sepsis 否 无 Sepsis epithelial cell E_02_0218 PCR, Western blot, flow cytometry, immunofluorescence staining In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. Enhancer SOCS3 qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. Immunohistochemical staining In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. PCR,Western blot,Flow cytometry,免疫荧光染色 31518916 chr2 190905505 190907505 STAT1 In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. human,mouse Epithelial tissues High+Lowthroughput Novel pharmacological inhibition of EZH2 attenuates septic shock by altering innate inflammatory responses to sepsis 否 无 Sepsis epithelial cell E_02_0218 PCR, Western blot, flow cytometry, immunofluorescence staining In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. Enhancer STAT1 qRT-PCR,qPCR,ChIP,3C RNA-Seq In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. Immunohistochemical staining In addition, EZH2 inhibitor blunted macrophage M1 polarization by SOCS3/STAT1 pathway. Overall, these data suggest that EZH2 could be a potential biomarker predicting clinical outcome and a new target for therapeutic interference in sepsis. PCR,Western blot,Flow cytometry,免疫荧光染色 31517633 chr19 2246854 2248854 AMH Hormonal disturbances, including increased level of androgens, estradiol, AMH and lower level of progesterone, also are one of etiologies related to PCOS (Patel 2018). human,mouse stomach High+Lowthroughput Ulmus minor bark hydro-alcoholic extract ameliorates histological parameters and testosterone level in an experimental model of PCOS rats 否 无 Gastric adenocarcinoma, polycystic ovary syndrome gastric adenocarcinoma cell E_02_0219 PCR Hormonal disturbances, including increased level of androgens, estradiol, AMH and lower level of progesterone, also are one of etiologies related to PCOS (Patel 2018). Enhancer AMH qRT-PCR,qPCR,ChIP,3C RNA-Seq Hormonal disturbances, including increased level of androgens, estradiol, AMH and lower level of progesterone, also are one of etiologies related to PCOS (Patel 2018). Hormonal disturbances, including increased level of androgens, estradiol, AMH and lower level of progesterone, also are one of etiologies related to PCOS (Patel 2018). Immunohistochemical staining Hormonal disturbances, including increased level of androgens, estradiol, AMH and lower level of progesterone, also are one of etiologies related to PCOS (Patel 2018). PCR 31515577 chr19 4966088 4968088 KDM4B Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. human,mouse bone High+Lowthroughput Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling 否 无 osteoporosis Bone marrow stromal cell E_02_0220 PCR,Western blot Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Enhancer KDM4B qRT-PCR,qPCR,ChIP,3C RNA-Seq Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Immunohistochemical staining Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. PCR,Western blot 31515577 chr17 7831872 7833872 KDM6B Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. human,mouse bone High+Lowthroughput Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling 否 无 osteoporosis Bone marrow stromal cell E_02_0220 PCR,Western blot Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Enhancer KDM6B qRT-PCR,qPCR,ChIP,3C RNA-Seq Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. Immunohistochemical staining Depletion of KDM4B or KDM6B favored adipogenic dif_x0002_ferentiation at the expense of osteogenic differentiation. PCR,Western blot 31515577 chr17 72118259 72120259 SOX9 KDM4B also promotes chondrogenic differentiation of human MSCs due to its recruitment to the chondrogenic gene SOX9 promoter, removing the silencing H3K9me3 marks, and thus activat_x0002_ing the transcription of SOX9 [14]. human,mouse bone High+Lowthroughput Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling 否 无 osteoporosis ST2 cell E_02_0220 PCR,Western blot KDM4B also promotes chondrogenic differentiation of human MSCs due to its recruitment to the chondrogenic gene SOX9 promoter, removing the silencing H3K9me3 marks, and thus activat_x0002_ing the transcription of SOX9 [14]. Enhancer SOX9 qRT-PCR,qPCR,ChIP,3C RNA-Seq KDM4B also promotes chondrogenic differentiation of human MSCs due to its recruitment to the chondrogenic gene SOX9 promoter, removing the silencing H3K9me3 marks, and thus activat_x0002_ing the transcription of SOX9 [14]. KDM4B also promotes chondrogenic differentiation of human MSCs due to its recruitment to the chondrogenic gene SOX9 promoter, removing the silencing H3K9me3 marks, and thus activat_x0002_ing the transcription of SOX9 [14]. Immunohistochemical staining KDM4B also promotes chondrogenic differentiation of human MSCs due to its recruitment to the chondrogenic gene SOX9 promoter, removing the silencing H3K9me3 marks, and thus activat_x0002_ing the transcription of SOX9 [14]. PCR,Western blot 31515496 chr16 67559926 67561926 CTCF By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. human prostate High+Lowthroughput A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome 是 无 prostatic cancer prostate cancer cell E_01_0278 PCR,Flow cytometry By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. Immunohistochemical staining By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. CTCF PCR,Flow cytometry By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells. 31515496 chr14 37586728 37588728 FOXA1 Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors. human prostate High+Lowthroughput A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome 是 无 prostatic cancer RWPE1 cell E_01_0278 PCR,Flow cytometry Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors. Immunohistochemical staining Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors. FOXA1 PCR,Flow cytometry Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors. 31515496 chr12 114667426 114669426 TBX3 Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. human connective tissue High+Lowthroughput A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome 是 无 prostatic cancer cancer cell E_01_0278 PCR,Flow cytometry Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. Immunohistochemical staining Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. TBX3 PCR,Flow cytometry Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. 31515496 chr1 107053881 107055881 PRMT6 Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. human connective tissue High+Lowthroughput A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome 是 无 prostatic cancer cancer cell E_01_0278 PCR,Flow cytometry Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. Enhancer PRMT6 qRT-PCR,qPCR,ChIP,3C RNA-Seq Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. Immunohistochemical staining Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24. PCR,Flow cytometry 31515496 chr15 26540728 26542728 GABRB3 Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1. human Prostate A.H High+Lowthroughput A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome 是 无 prostatic cancer 22Rv1 cell E_01_0278 PCR,Flow cytometry Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1. Enhancer GABRB3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1. Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1. Immunohistochemical staining Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1. PCR,Flow cytometry 31514731 chr16 67559877 67561877 CTCF These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. human blood High+Lowthroughput The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance 是 无 leukemia K562 cell E_01_0279 PCR These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. Immunohistochemical staining These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. CTCF PCR These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops. 31513772 chr9 21074265 21076265 IFNB1 We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). human uterus High+Lowthroughput The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers 否 无 cervical carcinoma HeLa cell E_01_0280 PCR, Western blot, flow cytometry, immunofluorescence staining We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). Immunohistochemical staining We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). IFNB1 PCR,Western blot,Flow cytometry,免疫荧光染色 We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D). 31513343 chr17 42310771 42312771 STAT3 Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. human,mouse connective tissue High+Lowthroughput Generation of Nanog reporter mice that distinguish pluripotent stem cells from unipotent primordial germ cells 否 无 pluripotent stem cell E_02_0221 PCR, flow cytometry, immunofluorescence staining Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Enhancer STAT3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. Immunohistochemical staining Nanog is also regulated by the binding of STAT3 (Suzuki et al., 2006a), T (also known as Brachyury) (Suzuki et al., 2006a), and Sall4/ Nanog complex (Wu et al., 2006) at −4.9 kb region. Although the reg_x0002_ulation of Nanog expression by these transcription factors has been elucidated using the reporter assays in vitro, in vivo tissue specificity has not been demonstrated by using the standard Nanog reporter Tg mouse lines. PCR,Flow cytometry,免疫荧光染色 31511694 chr21 45491095 45493095 SLC19A1 SLC19A1 was one of the most significant hits in both screens. SLC19A1 is a folate–organic phosphate antiporter that transports folates, structurally similar antifolates and a variety of organic phos_x0002_phates encompassing (among others) thiamine derivatives and nucle_x0002_otides15,16. human,mouse blood High+Lowthroughput SLC19A1 transports immunoreactive cyclic dinucleotides 否 无 leukemia B cell E_02_0222 Western blot,PCR,Flow cytometry SLC19A1 was one of the most significant hits in both screens. SLC19A1 is a folate–organic phosphate antiporter that transports folates, structurally similar antifolates and a variety of organic phos_x0002_phates encompassing (among others) thiamine derivatives and nucle_x0002_otides15,16. Enhancer SLC19A1 qRT-PCR,qPCR,ChIP,3C RNA-Seq SLC19A1 was one of the most significant hits in both screens. SLC19A1 is a folate–organic phosphate antiporter that transports folates, structurally similar antifolates and a variety of organic phos_x0002_phates encompassing (among others) thiamine derivatives and nucle_x0002_otides15,16. SLC19A1 was one of the most significant hits in both screens. SLC19A1 is a folate–organic phosphate antiporter that transports folates, structurally similar antifolates and a variety of organic phos_x0002_phates encompassing (among others) thiamine derivatives and nucle_x0002_otides15,16. Immunohistochemical staining SLC19A1 was one of the most significant hits in both screens. SLC19A1 is a folate–organic phosphate antiporter that transports folates, structurally similar antifolates and a variety of organic phos_x0002_phates encompassing (among others) thiamine derivatives and nucle_x0002_otides15,16. Western blot,PCR,Flow cytometry 31511694 chr17 35868537 35870537 CCL5 SLC19A1 depletion—similar to depletion of IRF3 or STING—also inhibited CDN-induced expression of direct downstream target genes in the STING pathway, including IFNB1 and the chemokine genes CCL5 and CXCL1021,22 (Fig. 2c, Extended Data Fig. 3g–i). human,mouse blood High+Lowthroughput SLC19A1 transports immunoreactive cyclic dinucleotides 否 无 leukemia THP-1 cells E_02_0222 Western blot,PCR,Flow cytometry SLC19A1 depletion—similar to depletion of IRF3 or STING—also inhibited CDN-induced expression of direct downstream target genes in the STING pathway, including IFNB1 and the chemokine genes CCL5 and CXCL1021,22 (Fig. 2c, Extended Data Fig. 3g–i). Enhancer CCL5 qRT-PCR,qPCR,ChIP,3C RNA-Seq SLC19A1 depletion—similar to depletion of IRF3 or STING—also inhibited CDN-induced expression of direct downstream target genes in the STING pathway, including IFNB1 and the chemokine genes CCL5 and CXCL1021,22 (Fig. 2c, Extended Data Fig. 3g–i). SLC19A1 depletion—similar to depletion of IRF3 or STING—also inhibited CDN-induced expression of direct downstream target genes in the STING pathway, including IFNB1 and the chemokine genes CCL5 and CXCL1021,22 (Fig. 2c, Extended Data Fig. 3g–i). Immunohistochemical staining SLC19A1 depletion—similar to depletion of IRF3 or STING—also inhibited CDN-induced expression of direct downstream target genes in the STING pathway, including IFNB1 and the chemokine genes CCL5 and CXCL1021,22 (Fig. 2c, Extended Data Fig. 3g–i). Western blot,PCR,Flow cytometry 31511694 chr19 49656530 49658530 IRF3 Protein levels of STING, TBK1 and IRF3 were unaltered in SLC19A1- depleted cells human,mouse blood High+Lowthroughput SLC19A1 transports immunoreactive cyclic dinucleotides 否 无 leukemia L1210 cell E_02_0222 Western blot,PCR,Flow cytometry Protein levels of STING, TBK1 and IRF3 were unaltered in SLC19A1- depleted cells Enhancer IRF3 qRT-PCR,qPCR,ChIP,3C RNA-Seq Protein levels of STING, TBK1 and IRF3 were unaltered in SLC19A1- depleted cells Protein levels of STING, TBK1 and IRF3 were unaltered in SLC19A1- depleted cells Immunohistochemical staining Protein levels of STING, TBK1 and IRF3 were unaltered in SLC19A1- depleted cells Western blot,PCR,Flow cytometry 31511524 chr20 43664495 43666495 MYBL2 Strikingly, targeting this GGAA-microsatellite by clustered regularly interspaced short palindromic repeats inter_x0002_ference (CRISPRi)26–28 in highly MYBL2 expressing RDES cells strongly suppressed MYBL2 transcription (Fig. 1f) and induced a potentially counter-regulatory upregulation of EWSR1-FLI1 (Sup_x0002_plementary Fig. 1i). I human,mouse connective tissue High+Lowthroughput Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes 否 无 Malignancy E_02_0223 Flow cytometry,Western blot Strikingly, targeting this GGAA-microsatellite by clustered regularly interspaced short palindromic repeats inter_x0002_ference (CRISPRi)26–28 in highly MYBL2 expressing RDES cells strongly suppressed MYBL2 transcription (Fig. 1f) and induced a potentially counter-regulatory upregulation of EWSR1-FLI1 (Sup_x0002_plementary Fig. 1i). I Enhancer MYBL2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Strikingly, targeting this GGAA-microsatellite by clustered regularly interspaced short palindromic repeats inter_x0002_ference (CRISPRi)26–28 in highly MYBL2 expressing RDES cells strongly suppressed MYBL2 transcription (Fig. 1f) and induced a potentially counter-regulatory upregulation of EWSR1-FLI1 (Sup_x0002_plementary Fig. 1i). I Strikingly, targeting this GGAA-microsatellite by clustered regularly interspaced short palindromic repeats inter_x0002_ference (CRISPRi)26–28 in highly MYBL2 expressing RDES cells strongly suppressed MYBL2 transcription (Fig. 1f) and induced a potentially counter-regulatory upregulation of EWSR1-FLI1 (Sup_x0002_plementary Fig. 1i). I Immunohistochemical staining Strikingly, targeting this GGAA-microsatellite by clustered regularly interspaced short palindromic repeats inter_x0002_ference (CRISPRi)26–28 in highly MYBL2 expressing RDES cells strongly suppressed MYBL2 transcription (Fig. 1f) and induced a potentially counter-regulatory upregulation of EWSR1-FLI1 (Sup_x0002_plementary Fig. 1i). I Flow cytometry,Western blot 31511524 chr12 55964008 55966008 CDK2 High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. human,mouse kidney High+Lowthroughput Cooperation of cancer drivers with regulatory germline variants shapes clinical outcomes 否 无 Malignancy HEK293T E_02_0223 Flow cytometry,Western blot High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Enhancer CDK2 qRT-PCR,qPCR,ChIP,3C RNA-Seq High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Immunohistochemical staining High MYBL2 levels sensitize EwS cells for inhibition of its upstream activating kinase CDK2 in vitro and in vivo, suggesting MYBL2 as a putative biomarker for anti-CDK2-therapy. Flow cytometry,Western blot 31511494 chr7 148804549 148806549 EZH2 Here we found that Pb exposure diminished H3K27me3 levels in vivo by suppressing EZH2 (enhancer of zeste homolog 2) expression at an early stage. mouse connective tissue High+Lowthroughput Interplay of miR-137 and EZH2 contributes to the genome-wide redistribution of H3K27me3 underlying the Pb-induced memory impairment 否 无 Multiple neurodegenerative diseases PC 12 cell E_02_0224 PCR, Western blot, immunofluorescence staining Here we found that Pb exposure diminished H3K27me3 levels in vivo by suppressing EZH2 (enhancer of zeste homolog 2) expression at an early stage. Enhancer EZH2 qRT-PCR,qPCR,ChIP,3C RNA-Seq Here we found that Pb exposure diminished H3K27me3 levels in vivo by suppressing EZH2 (enhancer of zeste homolog 2) expression at an early stage. Here we found that Pb exposure diminished H3K27me3 levels in vivo by suppressing EZH2 (enhancer of zeste homolog 2) expression at an early stage. Immunohistochemical staining Here we found that Pb exposure diminished H3K27me3 levels in vivo by suppressing EZH2 (enhancer of zeste homolog 2) expression at an early stage. PCR,Western blot,免疫荧光染色 31511252 chr5 29675484 29677484 Mnx1 Our data suggest that these substantial alterations in TAD structure have no readily detectable effect on Shh expression patterns or levels of Shh expression during development – except where enhancers are deleted – and result in no detectable phenotypes. Only in the case of a larger deletion at one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. mouse connective tissue High+Lowthroughput Developmentally regulated Shh expression is robust to TAD perturbations 否 无 embryonic stem cell E_02_0225 PCR,Flow cytometry Our data suggest that these substantial alterations in TAD structure have no readily detectable effect on Shh expression patterns or levels of Shh expression during development – except where enhancers are deleted – and result in no detectable phenotypes. Only in the case of a larger deletion at one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. Enhancer Mnx1 qRT-PCR,qPCR,ChIP,3C RNA-Seq Our data suggest that these substantial alterations in TAD structure have no readily detectable effect on Shh expression patterns or levels of Shh expression during development – except where enhancers are deleted – and result in no detectable phenotypes. Only in the case of a larger deletion at one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. Our data suggest that these substantial alterations in TAD structure have no readily detectable effect on Shh expression patterns or levels of Shh expression during development – except where enhancers are deleted – and result in no detectable phenotypes. Only in the case of a larger deletion at one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. Immunohistochemical staining Our data suggest that these substantial alterations in TAD structure have no readily detectable effect on Shh expression patterns or levels of Shh expression during development – except where enhancers are deleted – and result in no detectable phenotypes. Only in the case of a larger deletion at one TAD boundary could ectopic influence of the Shh limb enhancer be detected on a gene (Mnx1) in the neighbouring TAD. PCR,Flow cytometry 31511252 chr16 67559977 67561977 CTCF Interprobe distances between all three probe pairs were significantly increased in CTCF deletion cells compared with wild-type ESCs (Fig. 3E; Table S2), consistent with the reduced interactions between Shh and mouse connective tissue High+Lowthroughput Developmentally regulated Shh expression is robust to TAD perturbations 否 无 posterior limb bud cell E_02_0225 PCR,Flow cytometry Interprobe distances between all three probe pairs were significantly increased in CTCF deletion cells compared with wild-type ESCs (Fig. 3E; Table S2), consistent with the reduced interactions between Shh and Enhancer CTCF qRT-PCR,qPCR,ChIP,3C RNA-Seq Interprobe distances between all three probe pairs were significantly increased in CTCF deletion cells compared with wild-type ESCs (Fig. 3E; Table S2), consistent with the reduced interactions between Shh and Interprobe distances between all three probe pairs were significantly increased in CTCF deletion cells compared with wild-type ESCs (Fig. 3E; Table S2), consistent with the reduced interactions between Shh and Immunohistochemical staining Interprobe distances between all three probe pairs were significantly increased in CTCF deletion cells compared with wild-type ESCs (Fig. 3E; Table S2), consistent with the reduced interactions between Shh and PCR,Flow cytometry 31509720 chr10 121475640 121477640 FGFR2 Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis. human bone High+Lowthroughput Genetic Polymorphisms in FGFR2 Underlie Skeletal Malocclusion 是 rs2162540 Osteosarcoma MG-63 cell E_01_0281 Western blot,PCR,Flow cytometry Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis. Immunohistochemical staining Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis. FGFR2 Western blot,PCR,Flow cytometry Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis. 31509720 chr6 45325598 45327598 RUNX2 That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. human bone High+Lowthroughput Genetic Polymorphisms in FGFR2 Underlie Skeletal Malocclusion 是 rs11200014 Osteosarcoma cementoblast E_01_0281 Western blot,PCR,Flow cytometry That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. Immunohistochemical staining That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. RUNX2 Western blot,PCR,Flow cytometry That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. 31509720 chr18 51025518 51027518 SMAD4 That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. human lung High+Lowthroughput Genetic Polymorphisms in FGFR2 Underlie Skeletal Malocclusion 是 rs2981578 asthma NHLF cell E_01_0281 Western blot,PCR,Flow cytometry That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. Enhancer qRT-PCR,qPCR,ChIP,3C RNA-Seq That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. Immunohistochemical staining That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4. SMAD4 Western blot,PCR,Flow cytometry That is, rs2162