About Enhancer
| Enhancer ID: | E_01_270 | |
| Enhancer symbol: | CD47 SE E3.2 | |
| Species: | Human | |
| Position : | chr3:107842838-107845592   |
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| Biosample name: | MCF-7 | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer | |
| Disease: | Breast Cancer | |
| DO: | DOID:1612 | |
| Mesh: | D001943 | |
| Distance from TSS: | >2KB | |
| Pubmed ID: | 28378740 |
| Enhancer experiment: | ChIP-seq,Luciferase Reporter Assay | |
| Enhancer experiment description: | By rank-ordering of enhancer regions based on H3K27ac enrichment, we discovered that T-cell acute lymphoblastic leukemia (T-ALL (RPMI18402, Jurkat and MOLT3)) diffuse large B-cell lymphoma (DLBCL (LY4)) and breast cancer (MCF7 and HCC1954) cell lines have SEs within B200 kb of CD47 (Fig. 1a). To validate their function experimentally, we cloned each candidate CD47 enhancer (E1–9) into an EGFP reporter lentiviral construct containing the minimal (basal) promoter for the thymidine kinase (TK) gene7. We found that two of the CD47 enhancers (E5 and E3.2) had MCF7- and Jurkat-specific regulatory activity (Fig. 2a–c).First, E5, in the downstream CD47 SE seen in breast cancers (Fig. 1a,b), showed increased reporter activity specifically in the MCF7 breast cancer cell line (Fig. 2a). Further analysis of publicly available Paired-End Tag (ChIA-PET) data22,23 confirmed that E5 and the downstream CD47 SE in MCF7 are connected by a DNA loop containing RNA Polymerase II.Second, we found that E3.2, located within the upstream CD47 SE (Fig. 1a), had increased reporter expression specifically in the Jurkat cell line (Fig. 2b). We also found that a third functional enhancer, E7, located within the upstream CD47 SE (Fig. 1a), drove reporter expression in all of the cancer cell lines tested (Fig. 2d). |
About Target gene
| Target gene : | CD47(IAP,MER6,OA3) | |
| Strong evidence: | -- | |
| Less strong evidence: | ChIP-seq,Luciferase Reporter Assay | |
| Target gene experiment description: | To validate their function experimentally, we cloned each candidate CD47 enhancer (E1–9) into an EGFP reporter lentiviral construct containing the minimal (basal) promoter for the thymidine kinase (TK) gene7. We found that two of the CD47 enhancers (E5 and E3.2) had MCF7- and Jurkat-specific regulatory activity (Fig. 2a–c).First, E5, in the downstream CD47 SE seen in breast cancers (Fig. 1a,b), showed increased reporter activity specifically in the MCF7 breast cancer cell line (Fig. 2a). Further analysis of publicly available Paired-End Tag (ChIA-PET) data22,23 confirmed that E5 and the downstream CD47 SE in MCF7 are connected by a DNA loop containing RNA Polymerase II.Second, we found that E3.2, located within the upstream CD47 SE (Fig. 1a), had increased reporter expression specifically in the Jurkat cell line (Fig. 2b). We also found that a third functional enhancer, E7, located within the upstream CD47 SE (Fig. 1a), drove reporter expression in all of the cancer cell lines tested (Fig. 2d). |
About TF
| TF name : | NFKB1(CVID12,EBP-1,KBF1,NF-kB,NF-kB1,NF-kappa-B1,NF-kappaB,NFKB-p105,NFKB-p50,NFkappaB,p105,p50) | |
| TF experiment: | shRNA | |
| TF experiment description: | We observed that 72 h after shRNA transduction, expression of CD47 transcript and protein (measured by flow cytometry) was significantly reduced by NFKB1 (Fig. 3b,c) and PPARα (Fig. 3b, Supplementary Fig. 3d,e) shRNAs, when compared to control shRNA. On the other hand, shRNAs against STATs 3, 5 and 6 did not reduce CD47 expression significantly (Fig. 3b). This information demonstrates that NFKB and PPAR are involved in the regulation of CD47 in MCF7 cells and since knocking down NFKB1 had the strongest effect on CD47 gene expression, we focus this study on the regulatory role of this transcription factor. |
About Function
| Enhancer function : | -- |
| Enhancer function experiment: | -- |
| Enhancer function experiment description: |
-- |
About SNP
| SNP ID: | -- | |
| SNP position: | -- |
| SNP experiment: | -- |
Enhancer associated network
The number on yellow line represents the distance between enhancer and target gene
