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CTCF CCCTC-binding factor [ Homo sapiens (human) ]

Gene ID: 10664, updated on 3-Nov-2024

Summary

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Official Symbol
CTCFprovided by HGNC
Official Full Name
CCCTC-binding factorprovided by HGNC
Primary source
HGNC:HGNC:13723
See related
Ensembl:ENSG00000102974 MIM:604167; AllianceGenome:HGNC:13723
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
MRD21; FAP108; CFAP108
Summary
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]
Expression
Ubiquitous expression in lymph node (RPKM 18.3), spleen (RPKM 14.7) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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See CTCF in Genome Data Viewer
Location:
16q22.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67562526..67639185)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73357293..73433954)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67596429..67673088)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100505942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7610 Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67571987-67572608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7613 Neighboring gene Sharpr-MPRA regulatory region 14438 Neighboring gene uncharacterized LOC124903703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586099-67586600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586601-67587100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10978 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67596785-67597647 Neighboring gene CTCF divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67687361-67687893 Neighboring gene capping protein regulator and myosin 1 linker 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67693493-67694076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7618 Neighboring gene par-6 family cell polarity regulator alpha Neighboring gene ACD shelterin complex subunit and telomerase recruitment factor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding. Mujahed H, et al. Blood, 2020 Jul 16. PMID 32232485
  2. A short autonomous repression motif is located within the N-terminal domain of CTCF. Drueppel L, et al. FEBS Lett, 2004 Aug 13. PMID 15304340
  3. Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs. Do C, et al. Genome Biol, 2020 Jun 29. PMID 32594908, Free PMC Article
  4. Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures. Su QP, et al. Proc Natl Acad Sci U S A, 2020 Jun 30. PMID 32541019, Free PMC Article
  5. CTCF-mediated genome organization and leukemogenesis. Qiu Y, et al. Leukemia, 2020 Sep. PMID 32518417, Free PMC Article

See all (458) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. METTL3 aggravates cell damage induced by Streptococcus pneumoniae via the NEAT1/CTCF/MUC19 axis.
    Title: METTL3 aggravates cell damage induced by Streptococcus pneumoniae via the NEAT1/CTCF/MUC19 axis.
  2. CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer.
    Title: CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer.
  3. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
    Title: CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
  4. Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
    Title: Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
  5. CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
    Title: CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
  6. The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality.
    Title: The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality.
  7. RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter.
    Title: RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter.
  8. Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene.
    Title: Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene.
  9. CCCTC-binding factor: the specific transcription factor of beta-galactoside alpha-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
    Title: CCCTC-binding factor: the specific transcription factor of β-galactoside α-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
  10. Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping.
    Title: Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping.
Submit: New GeneRIF Correction See all GeneRIFs (328)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2021-09-22)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2021-09-22)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human CCCTC-binding factor (zinc finger protein) (CTCF) at amino acid residues 360-361 by the HIV-1 protease PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin insulator sequence binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables chromatin insulator sequence binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin loop anchoring activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA methylation-dependent heterochromatin formation IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in chromatin looping IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chromatin looping IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromosome segregation IEA
Inferred from Electronic Annotation
more info
  
involved_in epigenetic regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in epigenetic regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in genomic imprinting IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in mitochondrion organization IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cell population proliferation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of gene expression via chromosomal CpG island methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein localization to chromosome, centromeric region IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of centromeric sister chromatid cohesion NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in chromosome, centromeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in condensed chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in male germ cell nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
transcriptional repressor CTCF
Names
11 zinc finger transcriptional repressor
11-zinc finger protein
CCCTC-binding factor (zinc finger protein)
CTCFL paralog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033892.1 RefSeqGene

    Range
    5120..81771
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001191022.2 → NP_001177951.1  transcriptional repressor CTCF isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks internal two consecutive exons, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter N-terminus, as compared to isoform 1.
    Source sequence(s)
    AA814313, AB209793, DB229066
    Consensus CDS
    CCDS54029.1
    UniProtKB/Swiss-Prot
    P49711
    Related
    ENSP00000384707.1, ENST00000401394.6
    Conserved Domains (3) summary
    COG5048
    Location:38 → 172
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:25 → 45
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:181 → 206
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001363916.1 → NP_001350845.1  transcriptional repressor CTCF isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC009095, AC027682
    Consensus CDS
    CCDS86536.1
    UniProtKB/TrEMBL
    A0A2R8Y595, A0A2R8YFL0
    Related
    ENSP00000495218.1, ENST00000645306.1
    Conserved Domains (4) summary
    COG5048
    Location:366 → 500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268 → 288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:280 → 305
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:351 → 375
    zf-H2C2_5; C2H2-type zinc-finger domain

  3. NM_006565.4 → NP_006556.1  transcriptional repressor CTCF isoform 1

    See identical proteins and their annotated locations for NP_006556.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA814313, BC014267, DB229066
    Consensus CDS
    CCDS10841.1
    UniProtKB/Swiss-Prot
    B5MC38, P49711, Q53XI7, Q59EL8
    UniProtKB/TrEMBL
    A0A2R8Y595
    Related
    ENSP00000264010.4, ENST00000264010.10
    Conserved Domains (4) summary
    COG5048
    Location:366 → 500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268 → 288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:280 → 305
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:351 → 375
    zf-H2C2_5; C2H2-type zinc-finger domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    67562526..67639185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005255775.4 → XP_005255832.1  transcriptional repressor CTCF isoform X2

    See identical proteins and their annotated locations for XP_005255832.1

    UniProtKB/TrEMBL
    A0A2R8Y595, A0A2R8YFL0
    Related
    ENSP00000494443.1, ENST00000646771.1
    Conserved Domains (4) summary
    COG5048
    Location:366 → 500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268 → 288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:280 → 305
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:351 → 375
    zf-H2C2_5; C2H2-type zinc-finger domain

  2. XM_017022868.2 → XP_016878357.1  transcriptional repressor CTCF isoform X1

    UniProtKB/Swiss-Prot
    B5MC38, P49711, Q53XI7, Q59EL8
    UniProtKB/TrEMBL
    A0A2R8Y595
    Related
    ENSP00000493495.1, ENST00000644753.1
    Conserved Domains (4) summary
    COG5048
    Location:366 → 500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268 → 288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:280 → 305
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:351 → 375
    zf-H2C2_5; C2H2-type zinc-finger domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73357293..73433954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379399.1 → XP_054235374.1  transcriptional repressor CTCF isoform X2

    UniProtKB/TrEMBL
    A0A2R8YFL0

  2. XM_054379398.1 → XP_054235373.1  transcriptional repressor CTCF isoform X1

    UniProtKB/Swiss-Prot
    B5MC38, P49711, Q53XI7, Q59EL8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P49711.1 GenPept UniProtKB/Swiss-Prot:P49711

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