About Enhancer

Enhancer ID: E_02_0843
Species: mouse
Position : chr2:168744572-168752225
Biosample name:
Experiment class : Low+High throughput
Enhancer type: Super-Enhancer
Disease: --
Pubmed ID:  26659182
Enhancer experiment: ChIP-seq,ATAC-seq,CRISPR/Cas9
Enhancer experiment description: To validate these observations with an independent, higher resolution method, we performed Assay of Transposase Accessible Chromatin using sequencing (ATAC-seq), which detects integration of the Tn5 transposase in open chromatin regions27 (Extended Data Fig. 7c). Consistent with the SONO-seq data, ATAC-seq analysis of early reprogramming intermediates showed a more accessible chromatin configuration at regulatory regions including ESC-specific enhancers upon suppression of Chaf1a (Fig. 5a; P value <10?15). Moreover, Chaf1a knockdown caused a significant increase in chromatin accessibility across ESC-specific super-enhancers at day 3 of iPSC formation (Supplementary Table 3 and Extended Data Fig. 7d,e; P value <5.310?16). Of note, super-enhancers linked to specialized cell types such as macrophages, lymphocytes and muscle cells were also significantly more accessible in Chaf1a depleted reprogramming intermediates compared to controls (Extended Data Fig. 7f).

About Target gene

Target gene : Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20),Sall4(5730441M18Rik,AA407717,AL022809,AW536104,C330011P20Rik,C78083,C78563,Tex20)
Strong evidence: --
Less strong evidence: ChIP-seq,ATAC-seq
Target gene experiment description: Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.;Moreover,Chaf1a knockdown caused a significant increase in Chromatin accessibility across ES-cell-specific Super-Enhancers at day 3 of iPS cell formation.

About TF

TF name : Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)Sox2(ANOP3,MCOPS3)
TF experiment: ChIP-seq,ATAC-seq
TF experiment description: Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis. ;Next,we performed ChIP-seq analysis for Sox2 at day 3 of OKSM expression in order to test our hypothesis that increased Chromatin accessibility at Enhancer lements influences reprogramming factor binding. Of the Sox2-bound super-Enhancers unique to CAF-1 knockdown cells, a subset also showed a more accessible chromatin structure by ATAC-seq analysis.

About Function

Enhancer function : --
Enhancer function experiment: --
Enhancer function
experiment description:		 --

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
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
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
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
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
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
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
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
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
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
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
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

Enhancer associated network

The number on yellow line represents the distance between enhancer and target gene

Expression of target genes for the enhancer

Enhancer associated SNPs