About Enhancer
| Enhancer ID: | E_02_0778 |
| Species: | human |
| Position : | chr3:180728712-180730712   |
| Biosample name: | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer |
| Disease: | Low-grade astrocytomas |
| Pubmed ID: | 29091765 |
| Enhancer experiment: | ChIP-seq,ChIP-qPCR,4C-seq,Hi-C |
| Enhancer experiment description: | To understand if loss of CTCF binding affects chromatin contacts at the SOX2 locus, we performed circularized chromosome conformation capture (4C-Seq) using the SOX2 promoter as bait to identify genomic interactions that may regulate its expression (Figure 6B, S6B). |
About Target gene
| Target gene : | SOX2(ANOP3,MCOPS3),SOX2(ANOP3,MCOPS3),SOX2(ANOP3,MCOPS3) |
| Strong evidence: | 4C-seq |
| Less strong evidence: | Hi-C |
| Target gene experiment description: | To understand if loss of CTCF binding affects chromatin contacts at the SOX2 locus, we performed circularized chromosome conformation capture (4C-Seq) using the SOX2 promoter as bait to identify genomic interactions that may regulate its expression (Figure 6B, S6B).To see if this same pattern of chromatin contacts is maintained in other cell types, we examined the HiC profiles of hESCs, which express high levels of SOX2 , and IMR90 lung fibroblasts, which are low for SOX2These findings suggest that in LGA SOX2 downregulation is due to aberrant chromatin looping that results in disassociation of the SOX2 promoter from a downstream enhancer.;To understand if loss of CTCF binding affects chromatin contacts at the SOX2 locus, we performed circularized chromosome conformation capture (4C-Seq) using the SOX2 promoter as bait to identify genomic interactions that may regulate its expression (Figure 6B, S6B).To see if this same pattern of chromatin contacts is maintained in other cell types, we examined the HiC profiles of hESCs, which express high levels of SOX2 , and IMR90 lung fibroblasts, which are low for SOX2These findings suggest that in LGA SOX2 downregulation is due to aberrant chromatin looping that results in disassociation of the SOX2 promoter from a downstream enhancer.;To understand if loss of CTCF binding affects chromatin contacts at the SOX2 locus, we performed circularized chromosome conformation capture (4C-Seq) using the SOX2 promoter as bait to identify genomic interactions that may regulate its expression (Figure 6B, S6B).To see if this same pattern of chromatin contacts is maintained in other cell types, we examined the HiC profiles of hESCs, which express high levels of SOX2 , and IMR90 lung fibroblasts, which are low for SOX2These findings suggest that in LGA SOX2 downregulation is due to aberrant chromatin looping that results in disassociation of the SOX2 promoter from a downstream enhancer. |
About TF
| TF name : | CTCF(MRD21)CTCF(MRD21)CTCF(MRD21) |
| TF experiment: | ChIP-qPCR |
| TF experiment description: | To assess whether CTCF occupancy at these motifs had changed, we performed ChIP-qPCR for CTCF. Every site assayed had an 2-fold decrease in CTCF occupancy, supporting the hypothesis that DNA hypermethylation in 3-hit NSCs leads to reduced CTCF occupancy around. the SOX2 locus.;To assess whether CTCF occupancy at these motifs had changed, we performed ChIP-qPCR for CTCF. Every site assayed had an 2-fold decrease in CTCF occupancy, supporting the hypothesis that DNA hypermethylation in 3-hit NSCs leads to reduced CTCF occupancy around. the SOX2 locus.;To assess whether CTCF occupancy at these motifs had changed, we performed ChIP-qPCR for CTCF. Every site assayed had an 2-fold decrease in CTCF occupancy, supporting the hypothesis that DNA hypermethylation in 3-hit NSCs leads to reduced CTCF occupancy around. the SOX2 locus. |
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 |
|---|---|---|---|
| CTCF | Activation of anterior HOX genes in hindbrain development during early embryogenesis | reactome | 120 |
| CTCF | TGF_beta_Receptor | netpath | 220 |
| CTCF | Activation of anterior HOX genes in hindbrain development during early embryogenesis | reactome | 120 |
| CTCF | TGF_beta_Receptor | netpath | 220 |
| CTCF | Activation of anterior HOX genes in hindbrain development during early embryogenesis | reactome | 120 |
| CTCF | TGF_beta_Receptor | netpath | 220 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene