About Enhancer
| Enhancer ID: | E_02_0782 |
| Species: | human |
| Position : | chr4:55449628-55461828   |
| Biosample name: | |
| Experiment class : | low throughput |
| Enhancer type: | Enhancer |
| Disease: | -- |
| Pubmed ID: | 28982762 |
| Enhancer experiment: | Luciferase Reporter Assay,3C |
| Enhancer experiment description: | DNA fragments containing E1 and E2 specifically exhibited high transcriptional activity in na?ve state mESCs relative to primed EpiSCs as determined by transgene-driven luciferase assays, consistent with the Klf4 expression pattern in these two pluripotent cell types (Fig. 1B,C).To probe whether the putative enhancers E1 and E2 communicate with the Klf4 promoter ?55 kb away, we performed chromosome conformation capture (3C) assays to detect long-range interactions. For both E1 and E2, there was a significantly higher frequency of cross-linking to the Klf4 promoter in mESCs compared with EpiSCs (Fig. 1F), indicating that E1 and E2 spatially juxtapose the promoter in mESCs. |
About Target gene
| Target gene : | Klf4(EZF,Gklf,Zie),Klf4(EZF,Gklf,Zie) |
| Strong evidence: | CRISPR/Cas9,3C |
| Less strong evidence: | -- |
| Target gene experiment description: | Additionally, biallelic deletion of either E1 or E2 by CRISPR/Cas9-mediated genome editing reduced Klf4 expression by ?70% and 85%, respectively, without significantly affecting the expression of an adjacent gene (Rad23b) or another pluripotency gene (Pou5f1) (Fig. 1E).Nevertheless, for the remainder of this report, we primarily discuss our findings regarding E1 and E2, as these two enhancers clearly represent dominant elements that regulate Klf4 expression in na?ve state mESCs.;Additionally, biallelic deletion of either E1 or E2 by CRISPR/Cas9-mediated genome editing reduced Klf4 expression by ?70% and 85%, respectively, without significantly affecting the expression of an adjacent gene (Rad23b) or another pluripotency gene (Pou5f1) (Fig. 1E).Nevertheless, for the remainder of this report, we primarily discuss our findings regarding E1 and E2, as these two enhancers clearly represent dominant elements that regulate Klf4 expression in na?ve state mESCs. |
About TF
| TF name : | Oct4Sox2(ANOP3,MCOPS3)Stat3 (ADMIO,ADMIO1,APRF,HIES)Oct4Sox2(ANOP3,MCOPS3)Stat3 (ADMIO,ADMIO1,APRF,HIES) |
| TF experiment: | ChIP-exo,CRISPR/Cas9,ChIP-qPCR |
| TF experiment description: | To validate the direct binding of these candidate TFs to the Klf4 Enhancers, we performed genome-wide high-resolution ChIP-exo experiments for SOX2, STAT3, and ESRRB in mESCs.Here, we probed whether the binding activities of OCT4, SOX2, ESRRB, and STAT3 at E2 are interdependent through ChIP-qPCR (ChIP combined with quantitative PCR) analysis following endogenous deletion of individual TF-binding sites.Peaks identified by ChIP-exo were consistent with peaks from previous ChIP-seq (ChIP combined with high-throughput sequcing) protocols (Supplemental Fig. S2B,C). As expected, we observed significant enrichment of all three TFs at the Klf4 enhancer cluster, particularly at E2 (Fig. 2D).;To validate the direct binding of these candidate TFs to the Klf4 Enhancers, we performed genome-wide high-resolution ChIP-exo experiments for SOX2, STAT3, and ESRRB in mESCs.Here, we probed whether the binding activities of OCT4, SOX2, ESRRB, and STAT3 at E2 are interdependent through ChIP-qPCR (ChIP combined with quantitative PCR) analysis following endogenous deletion of individual TF-binding sites.Peaks identified by ChIP-exo were consistent with peaks from previous ChIP-seq (ChIP combined with high-throughput sequcing) protocols (Supplemental Fig. S2B,C). As expected, we observed significant enrichment of all three TFs at the Klf4 enhancer cluster, particularly at E2 (Fig. 2D). |
About Function
| Enhancer function : | -- |
| Enhancer function experiment: | -- |
| Enhancer function experiment description: |
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About SNP
| SNP ID: | -- |
Upstream Pathway Annotation of TF
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene