CTCF

CCCTC-binding factor | CFAP108, FAP108

This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor. If the protein is bound to a transcriptional insulator element, it can block communication between enhancers and upstream promoters, thereby regulating imprinted expression. Mutations in this gene have been associated with invasive breast cancers, prostate cancers, and Wilms' tumors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

Member of: DE-11 DE-11.2

Biological processes 44 terms

DNA binding (GO:0003677)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription factor activity (GO:0003700)DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978)chromatin binding (GO:0003682)chromatin insulator sequence binding (GO:0043035)chromatin loop anchoring activity (GO:0140587)chromatin looping (GO:0140588)chromatin looping (GO:0140588)chromosome (GO:0005694)chromosome, centromeric region (GO:0000775)chromosome, centromeric region (GO:0000775)cis-regulatory region sequence-specific DNA binding (GO:0000987)condensed chromosome (GO:0000793)epigenetic regulation of gene expression (GO:0040029)epigenetic regulation of gene expression (GO:0040029)genomic imprinting (GO:0071514)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of cell population proliferation (GO:0008285)negative regulation of gene expression (GO:0010629)negative regulation of transcription by RNA polymerase II (GO:0000122)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of gene expression (GO:0010628)positive regulation of gene expression (GO:0010628)positive regulation of transcription by RNA polymerase II (GO:0045944)protein binding (GO:0005515)protein localization to chromosome, centromeric region (GO:0071459)regulation of DNA-templated transcription (GO:0006355)regulation of centromeric sister chromatid cohesion (GO:0070602)regulation of transcription by RNA polymerase II (GO:0006357)sequence-specific DNA binding (GO:0043565)sequence-specific DNA binding (GO:0043565)sequence-specific double-stranded DNA binding (GO:1990837)transcription cis-regulatory region binding (GO:0000976)transcription coregulator binding (GO:0001221)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating CTCF 0 TFs

Transcription factors with Perturb-seq knockdown data for CTCF. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CTCF upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to CTCF

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CTCF, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr16:67,262,177–67,262,869	300.0 kb	Distal (>10kb) Multiome	24
chr16:67,278,724–67,279,792	283.1 kb	Distal (>10kb) Multiome	869
chr16:67,326,413–67,327,343	235.7 kb	Distal (>10kb) Multiome	585
chr16:67,393,199–67,393,789	169.0 kb	Distal (>10kb) Multiome	377
chr16:67,396,006–67,396,718	166.1 kb	Distal (>10kb) Multiome	375
chr16:67,399,230–67,399,872	162.9 kb	Distal (>10kb) Multiome	211
chr16:67,415,996–67,416,812	146.1 kb	Distal (>10kb) Multiome	687
chr16:67,428,012–67,428,783	134.2 kb	Distal (>10kb) Multiome	382
chr16:67,430,407–67,432,610	131.4 kb	Distal (>10kb) Multiome	790
chr16:67,480,508–67,481,841	81.3 kb	Distal (>10kb) Multiome	1002
chr16:67,521,086–67,521,812	41.1 kb	Distal (>10kb) Multiome	775
chr16:67,528,470–67,529,464	33.7 kb	Distal (>10kb) Multiome	641
chr16:67,537,215–67,538,620	24.5 kb	Distal (>10kb) Multiome	560
chr16:67,561,597–67,563,672	216 bp	At TSS Multiome	1044
chr16:67,644,719–67,645,304	82.4 kb	Distal (>10kb) Multiome	638
chr16:67,649,353–67,649,999	87.2 kb	Distal (>10kb) Multiome	112
chr16:67,652,610–67,653,810	90.5 kb	Distal (>10kb) Multiome	498
chr16:67,659,631–67,661,707	98.3 kb	Distal (>10kb) Multiome	962
chr16:67,666,180–67,667,235	104.1 kb	Distal (>10kb) Multiome	713
chr16:67,667,674–67,668,349	105.6 kb	Distal (>10kb) Multiome	628
chr16:67,718,772–67,720,138	156.8 kb	Distal (>10kb) Multiome	866
chr16:67,806,066–67,807,386	244.2 kb	Distal (>10kb) Multiome	914
chr16:67,816,404–67,816,888	254.2 kb	Distal (>10kb) Multiome	690
chr16:67,833,426–67,834,269	271.4 kb	Distal (>10kb) Multiome	838
chr16:67,841,337–67,843,276	279.6 kb	Distal (>10kb) Multiome	927
chr16:67,846,090–67,847,897	284.2 kb	Distal (>10kb) Multiome	1025

Genome Browser

Genomic view of the CTCF locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.