Enhancer ID: | E_01_259 | |
Enhancer symbol: | GIMAP Enhancer | |
Species: | Human | |
Position : | chr7:150360500-150366500 |
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Biosample name: | T-acute lymphoblastic leukemia (T-ALL) | |
Experiment class : | Low+High throughput |
Enhancer type: | Super-Enhancer | |
Disease: | T-Cell Acute Lymphoblastic Leukemia | |
DO: | DOID:5602 | |
Mesh: | D054218 | |
Distance from TSS: | >2KB | |
Pubmed ID: | 28028313 |
Enhancer experiment: | ChIP-seq,CRISPR/Cas9,PCR | |
Enhancer experiment description: | DNA binding of the TAL1 complex was observed between the GIMAP2 and GIMAP6 genes across different TAL1-positive T-ALL cell lines (CCRF-CEM, RPMI-8402 and Jurkat) (Figures 1A and 1B, orange box). Notably, this region was also occupied by NOTCH1, which is another prevalent oncogene in T-ALL, with its binding partner RBPJ/CSL. .Importantly, there was substantial binding of RNA polymerase II (RNAP2) and mediator 1 (MED1) as well as extensive acetylation of histone H3 lysine 27 (H3K27Ac), constituting the formation of a super-enhancer in this region (Figure 1A, red box; Supplementary Figure 1C). We next examined whether the region bound by the TAL1 complex (Figures 1 and 2A, orange box) can control the expression of GIMAP genes in T-ALL cells.We designed guide RNAs (gRNAs) targeting either this locus or the whole GIMAP gene cluster (Figure 2B, bottom) and transduced a pair of gRNAs with the Cas9 endonuclease to enable removal of these genomic regions using CRISPR/Cas9 technology.PCR analysis showed successful deletions of the target locus (Supplementary Figure 2C). The chromatogram demonstrated a successful recombination after the cleavage (Supplementary Figure 2D). Importantly, compared to cells transduced with control gRNAs, gene expression of the GIMAP genes was concomitantly downregulated in samples where either the TAL1-bound region or the whole cluster was deleted (Figure 2B). These results demonstrate that the locus bound by the TAL1 complex possesses enhancer activity to induce the expression of the GIMAP genes (GIMAP enhancer). Of note, an additional TAL1 binding site was identified between the GIMAP4 and GIMAP7 genes (Figures 1A and 2A, arrowhead). |
Target gene : | GIMAP4(IAN-1,IAN1,IMAP4,MSTP062),GIMAP7(IAN7,hIAN7) | |
Strong evidence: | CRISPR/Cas9 | |
Less strong evidence: | PCR | |
Target gene experiment description: | We next examined whether the region bound by the TAL1 complex (Figures 1 and 2A, orange box) can control the expression of GIMAP genes in T-ALL cells.We designed guide RNAs (gRNAs) targeting either this locus or the whole GIMAP gene cluster (Figure 2B, bottom) and transduced a pair of gRNAs with the Cas9 endonuclease to enable removal of these genomic regions using CRISPR/Cas9 technology.PCR analysis showed successful deletions of the target locus (Supplementary Figure 2C). The chromatogram demonstrated a successful recombination after the cleavage (Supplementary Figure 2D). Importantly, compared to cells transduced with control gRNAs, gene expression of the GIMAP genes was concomitantly downregulated in samples where either the TAL1-bound region or the whole cluster was deleted (Figure 2B). These results demonstrate that the locus bound by the TAL1 complex possesses enhancer activity to induce the expression of the GIMAP genes (GIMAP enhancer). Of note, an additional TAL1 binding site was identified between the GIMAP4 and GIMAP7 genes (Figures 1A and 2A, arrowhead). |
TF name : | TAL1(SCL,TCL5,bHLHa17,tal-1) | |
TF experiment: | ChIP-seq | |
TF experiment description: | We previously identified transcriptional targets directly regulated by TAL1 and its regulatory partners by chromatin immunoprecipitation-sequencing (ChIP-Seq) and microarray analysis in TAL1 -positive T-ALL cell samples. |
Enhancer function : | -- |
Enhancer function experiment: | -- |
Enhancer function experiment description: |
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SNP ID: | -- | |
SNP position: | -- |
SNP experiment: | -- |
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