About Enhancer
| Enhancer ID: | E_02_0882 |
| Species: | mouse |
| Position : | chr3:34743178-34776096   |
| Biosample name: | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Super-Enhancer |
| Disease: | -- |
| Pubmed ID: | 25486255 |
| Enhancer experiment: | ChIP-seq,RNA-seq |
| Enhancer experiment description: | We examined ENCODE ChIP-seq data from 23 different mouse tissues or cell types focusing on the Sox2 locus. Using H3K27ac, a histone mark for active enhancers, we observed a distal SE that is only present in mouse ESC lines, which is approximately 100kb downstream from the Sox2 locus. This sequence spans a relatively large 13kb region, and corresponds to a recently defined super-enhancer or stretch enhancer. |
About Target gene
| Target gene : | Sox2(ANOP3,MCOPS3) |
| Strong evidence: | CRISPR/Cas9 |
| Less strong evidence: | PCR |
| Target gene experiment description: | We analyzed epigenomic data within the 1.5 Mb gene-desert regions around the Sox2 gene and identified a 13kb-long super-Enhancer (SE) located 100kb downstream of Sox2 in mouse ESCs. |
About TF
| TF name : | Oct4Sox2(ANOP3,MCOPS3)Nanog(NANOG) |
| TF experiment: | ChIP-seq |
| TF experiment description: | First, we observed strong H3K27ac signal at this SE in two additional mouse ES cell lines (F123 and J1), indicating that usage of this SE is conserved across different mice strains.Previously published ChIP-seq data shows that Sox2-SEdistal is occupied by Oct4,Sox2 and Nanog. |
About Function
| Enhancer function : | SE is occupied by Oct4, Sox2, Nanog,and the mediator complex, and physically interacts with the Sox2 locus via DNA looping |
| Enhancer function experiment: | RT-qPCR,ChIP-seq |
| Enhancer function experiment description: |
To test the in vivo function of Sox2-SEdistal, we sought to delete the entire Enhancer sequence from the endogenous locus. Given that the SE spans a,13kb region, deletion of this region using conventional methods would be very inefficient.Therefore, we explored whether the recently developed CRISPR technology could be utilized to delete this large non-coding sequence in mouse ESCs. |
About SNP
| SNP ID: | -- |
Upstream Pathway Annotation of TF
| GeneName | Pathway Name | Source | Gene Number |
|---|---|---|---|
| Sox2 | Deactivation of the beta-catenin transactivating complex | reactome | 42 |
| Sox2 | POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation | reactome | 13 |
| Sox2 | POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation | reactome | 10 |
| Sox2 | Transcriptional regulation of pluripotent stem cells | reactome | 28 |
| Sox2 | Hs_Endoderm_Differentiation_WP2853_88152 | wikipathways | 62 |
| Sox2 | Hs_Dopaminergic_Neurogenesis_WP2855_87239 | wikipathways | 19 |
| Sox2 | Hs_Wnt_Signaling_Pathway_and_Pluripotency_WP399_90291 | wikipathways | 12 |
| Sox2 | Hs_Mesodermal_Commitment_Pathway_WP2857_87780 | wikipathways | 47 |
| Sox2 | Hs_Ectoderm_Differentiation_WP2858_89329 | wikipathways | 56 |
| Nanog | POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation | reactome | 13 |
| Nanog | POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation | reactome | 10 |
| Nanog | Transcriptional regulation of pluripotent stem cells | reactome | 28 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene