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CTCF (CCCTC-binding factor (zinc finger protein))

Written2011-04Jacques Piette
Institut de Genetique Moleculaire de Montpellier (CNRS-Universite de Montpellier I-II UMR5535), 1919 Route de Mende, 34293, Montpellier-Cedex 5, France
Updated2013-05Jacques Piette
Institut de Genetique Moleculaire de Montpellier (CNRS-Universite de Montpellier I-II UMR5535), 1919 Route de Mende, 34293, Montpellier-Cedex 5, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesCCCTC-binding factor (zinc finger protein)
Other alias
HGNC (Hugo) CTCF
LocusID (NCBI) 10664
Atlas_Id 40187
Location 16q22.1  [Link to chromosome band 16q22]
Location_base_pair Starts at 67562407 and ends at 67639185 bp from pter ( according to hg19-Feb_2009)  [Mapping CTCF.png]
Local_order AGRP, FAM65A, CTCF, RLTPR, ACD, PARD6A.
 
  Figure 1. Schematic representation of CTCF location on chromosome 16, gene structure and transcripts. Chromosome 16 is represented with the characteristic banding pattern. The region surrounding the CTCF gene is enlarged. Genes are represented by arrows pointing in the direction of transcription. Transcripts are represented with exons as vertical bars and introns as lines. Distances are in kilo bases (NCBI Map Viewer).
Fusion genes
(updated 2016)
CTCF (16q22.1) / ARF1 (1q42.13)CTCF (16q22.1) / CES2 (16q22.1)CTCF (16q22.1) / CTCF (16q22.1)
CTCF (16q22.1) / PARD6A (16q22.1)

DNA/RNA

Note See figure 1.
Description 76776 bp gene (Ensembl).
Transcription Ubiquitously highly expressed gene (GeneCards), 12 exons, 11 introns with at least 5 differentially spliced transcripts (Ensembl).
Pseudogene No.

Protein

 
  Figure 2. Schematic representation of the CTCF protein. Protein sequences encoded by exons are boxed. 11 ring fingers are indicated by green boxes as also putative AT-hooks by blue boxes (Ensembl). The interaction domain with the SA2 subunit of cohesin is underlined in red (Xiao et al., 2011). Phosphorylated residues are in black (PhosphoSitePlus), those sensitive to rapamycin are indicated by R (Chen et al., 2009) and those phosphorylated by CKII by CKII (El-Kady and Klenova, 2005; Klenova et al., 2001), sumoylated residues are in red (Kitchen and Schoenherr, 2010; MacPherson et al., 2009), acetylated residue is indicated by Ac (Choudhary et al., 2009). The domain containing poly(ADPribosyl)ation sites (PAR) is boxed in red (Farrar et al., 2010), the NTP-binding site in blue and the NLS in purple. Residues mutated in tumors are indicated (see further), BT = breast tumor, PT = prostate tumor and WT = Wilms tumor.
Description CTCF was originally described as a c-myc activator (Klenova et al., 1993). It is a 727 aa protein with a MW of 82.8 kD, a charge of 8.5 and an iso electric point of 6.95 (Ensembl). The central domain with 11 zinc fingers of the C2H2 type is highly conserved.
Expression CTCF is an abundant and ubiquitously expressed protein, yet absent in primary spermatocytes (Loukinov et al., 2002). It is downregulated during differentiation of human myeloid leukemia cells (Delgado et al., 1999; Torrano et al., 2005). Post-traductional modifications include acetylation (Choudhary et al., 2009), sumoylation (Kitchen and Schoenherr, 2010; MacPherson et al., 2009), which is regulated by hypoxic stress (Wang et al., 2012a), phosphorylation, in particular ser604-612 by CKII (El-Kady and Klenova, 2005; Klenova et al., 2001), and poly(ADPribo)sylation (see figure 2). The latter modification is lost or decreased in proliferating cells and in BT (Docquier et al., 2009) (for sites and role see Farrar et al., 2010; Yu et al., 2004; Guastafierro et al., 2013). CTCF is a downstream target protein of growth factor-induced pathways and is regulated by EGF and insulin through activation of ERK and AKT signaling cascades (Gao et al., 2007). It was recently shown to be regulated by NF-kB (Lu et al., 2010).
Localisation CTCF is localized in the nucleoplasm of proliferating cells with exclusion from the nucleolus. It was detected at the centrosomes and midbody during mitosis (Zhang et al., 2004). It is associated with the nuclear matrix (Dunn et al., 2003; Yusufzai and Felsenfeld, 2004) and the Lamina (Guelen et al., 2008; Ottaviani et al., 2009). Nucleolar translocation after growth arrest is accompanied by inhibition of nucleolar transcription (Torrano et al., 2006). Cytoplasmic expression was described in sporadic breast tumors (Rakha et al., 2004).
Function CTCF is an essential protein, since KO mice die before ED 9.5 (Heath et al., 2008) (reviewed in Filippova, 2008; Phillips and Corces, 2009). It interacts with numerous ubiquitous and cell-type specific genomic sites (Chen et al., 2008; Bao et al., 2008; Barski et al., 2007; Kim et al., 2007; Chen et al., 2012). The 11 Zn fingers would provide flexibility in DNA recognition (Filippova et al., 1996), the central 4 bind to a consensus DNA sequence (Filippova et al., 1998; Renda et al., 2007). Multiple interacting proteins were described including RNA polymerase II (Chernukhin et al., 2007), cohesin (Parelho et al., 2008; Rubio et al., 2008; Wendt et al., 2008; Xiao et al., 2011), Suz12 (Li et al., 2008), CHD8 (Ishihara et al., 2006), YY1 (Donohoe et al., 2007), nucleophosmin (Yusufzai et al., 2004), Kaiso (Defossez et al., 2005) and Sin3A (Lutz et al., 2000). XPG endonuclease promotes DNA breaks and DNA demethylation at promoters allowing the recruitment of CTCF and gene looping, which is further stabilized by XPF (Le May et al., 2012). By mediating intra and interchromosomal contacts through its interaction with cohesin, CTCF plays a central role in organization of topological domains inside the nucleus. Cell-type specific binding sites lead to specific interactomes and transcriptional programs (Hou et al., 2010; Handoko et al., 2011; Dixon et al., 2012; Botta et al., 2010; reviewed by Merkenschlager and Odom, 2013). The plasticity in binding sites occupancy is linked to DNA methylation (Wang et al., 2012b) and could depend also on CTCF interaction with other factors (see concept of modular insulators in Weth et al., 2010). One thoroughly studied factor is the thyroid receptor (Awad et al., 1999; Lutz et al., 2003). Its peculiar chromosomal environment could explain the multiple (not necessarily exclusive) functions that were described for CTCF, including chromatin barrier (Cuddapah et al., 2009; Witcher and Emerson, 2009), promoter insulation from enhancer (Bell et al., 1999) or silencer (Hou et al., 2008), transcriptional activation (Gombert and Krumm, 2009) (for instance of the tumour suppressor genes INK4A/ARF (Rodriguez et al., 2010) and p53 (Soto-Reyes and Recillas-Targa, 2010)), repression (for instance hTERT (Renaud et al., 2005)), nucleosome positioning (Fu et al., 2008b), protection from DNA methylation (Mukhopadhyay et al., 2004; Schoenherr et al., 2003; Guastafierro et al., 2008), preservation of triplet-repeat stability (Cho et al., 2005; Filippova et al., 2001; Libby et al., 2008), imprinting (Fedoriw et al., 2004; Fitzpatrick et al., 2007), X chromosome inactivation (Chao et al., 2002), chromosome "kissing" (Ling et al., 2006), transvection (Liu et al., 2008), death signaling (Docquier et al., 2005; Gomes and Espinosa, 2010; Li and Lu, 2007), replication timing (Bergstrom et al., 2007), mitotic bookmarking (Burke et al., 2005), MHC class II gene expression (Majumder et al., 2008), V(D)J recombination (Guo et al., 2011; reviewed by Chaumeil and Skok, 2012), miRNA expression (Saito and Saito, 2012), telomere end protection (Deng et al., 2012), neuronal diversity (Monahan et al., 2012), myogenesis (Delgado-Olguin et al., 2011), splicing (Shukla et al., 2011) and angiogenesis (Tang et al., 2011). Considering the central role of CTCF in transcriptional regulation, it is likely to play a role in adaptive evolution in Drosophila (Ni et al., 2012), and in the evolutionary succes of bilateria (Heger et al., 2012). Remodeling of CTCF binding sites and the accompanying interactome during evolution could be driven by retrotransposon expansion (Schmidt et al., 2012).
Homology 49 orthologues were described including D. melanogaster (Smith et al., 2009) and C. elegans proteins (Moon et al., 2005), 3 paralogues: CTCFL or BORIS, originating from a gene duplication in reptiles (Hore et al., 2008; Loukinov et al., 2002), and possibly ZFP64 (Mack et al., 1997) and the Histone H4 transcription factor HINF-P (van Wijnen et al., 1991).

Mutations

Note SNP at AA 630 /K /E 90 /D /G 447 fR (NCBI).
Germinal Non-coding mutations only.
Somatic Mutations are rare and include point mutations of Zn-fingers in breast (BT) (Aulmann et al., 2003), prostate (PT) and Wilms tumor (WT) (Filippova et al., 2002; Tiffen et al., 2013), insertion in BT (Aulmann et al., 2003) (see figure 2), and indels in AML (Dolnik et al., 2012).

Implicated in

Note
  
Entity Various cancers
Note There is evidence for a tumor-suppressor role of CTCF (reviewed in Fiorentino and Giordano, 2012). LOH of CTCF was described in many cancers together with potential tumor suppressor genes (TSG), including E-Cad, since it is part of a larger deletion (Cancer Chromosomes; Sanger institute). In addition to WT (Yeh et al., 2002; Mummert et al., 2005), BT (Rakha et al., 2004), PT (Filippova et al., 1998), LOH was found in laryngeal squamous cell carcinoma (Grbesa et al., 2008), however, there is no evidence that CTCF is the TSG at 16q22.1 (Rakha et al., 2005), except possibly in lobular carcinoma in situ of the breast (Green et al., 2009). CTCF was also described to be overexpressed in BT (Docquier et al., 2005). An indirect role of CTCF in tumor progression is mainly suggested by mutation or aberrant methylation of its bindings sites (reviewed by Recillas-Targa et al., 2006). Interestingly, a causal link between LOH of CTCF and hypermethylation was proposed by Mummert et al. in 2005, although no real correlation was found by Yeh et al. in 2002. Methylation of CTCF sites was first described in the IGF2 imprinting control region in WT (Cui et al., 2001). Aberrant methylation of this region was also found in PT (Fu et al., 2008a; Paradowska et al., 2009), HNSCC (De Castro Valente Esteves et al., 2006; Esteves et al., 2005), colorectal cancer (Nakagawa et al., 2001), osteosarcoma (Ulaner et al., 2003), ovarian carcinoma (Dammann et al., 2010) and laryngeal squamous cell carcinoma (Grbesa et al., 2008). Hypomethylation was described in bladder cancer (Takai et al., 2001). YY1 binds with CTCF to a hypomethylated form of the macrosatellite DXZ4 on the inactive X chromosome in some male carcinomas (Moseley et al., 2012). Microdeletions were described in Beckwith-Wiedemann syndrome and WT (Prawitt et al., 2005; Sparago et al., 2007; Beygo et al., 2013). Other methylated CTCF targets were found in the genes AWT1 or WT1-AS in WT (Hancock et al., 2007), Bcl6 in B cell lymphomas (Lai et al., 2010), the miR125b locus in breast cancer (Soto-Reyes et al., 2012), p53, pRb (De La Rosa-Velazquez et al., 2007; Davalos-Salas et al., 2011), ARF (Tam et al., 2003; Rodriguez et al., 2010), INK4B, BRCA1 (Butcher et al., 2004; Butcher and Rodenhiser, 2007; Xu et al., 2010) and Rasgrf1 (Yoon et al., 2005). CTCF and its paralogue BORIS regulate pRb in lung cancer (Fiorentino et al., 2011), and CTCF could regulate the response to oestrogen in breast cancer (Zhang et al., 2010).
We describe below the rare cases of point mutations affecting the CTCF protein.
  
  
Entity Invasive ductal breast carcinoma, grade 2
Note G2 grade tumor, no protein detected (Aulmann et al., 2003).
Cytogenetics 14 bp insertion at AA D91, see figure 2.
  
  
Entity Invasive ductal breast carcinoma, grade 3
Note G3 grade tumor (Aulmann et al., 2003).
Cytogenetics LOH and Q72H, figure 2.
  
  
Entity Breast cancer
Note Zinc finger mutation (Filippova et al., 2002).
Cytogenetics LOH and K343E, figure 2.
  
  
Entity Prostate cancer
Note Zinc finger mutation (Filippova et al., 2002).
Cytogenetics LOH and H344E, figure 2.
  
  
Entity Wilms tumor
Note Zinc finger mutation (Filippova et al., 2002).
Cytogenetics LOH and R339W or R448Q, figure 2.
  
  
Entity Acute myeloid leukemia (AML)
Note (Dolnik et al., 2012).
Cytogenetics indels.
  

Bibliography

CTCF gene mutations in invasive ductal breast cancer.
Aulmann S, Blaker H, Penzel R, Rieker RJ, Otto HF, Sinn HP.
Breast Cancer Res Treat. 2003 Aug;80(3):347-52.
PMID 14503807
 
Negative transcriptional regulation mediated by thyroid hormone response element 144 requires binding of the multivalent factor CTCF to a novel target DNA sequence.
Awad TA, Bigler J, Ulmer JE, Hu YJ, Moore JM, Lutz M, Neiman PE, Collins SJ, Renkawitz R, Lobanenkov VV, Filippova GN.
J Biol Chem. 1999 Sep 17;274(38):27092-8.
PMID 10480923
 
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.
Bao L, Zhou M, Cui Y.
Nucleic Acids Res. 2008 Jan;36(Database issue):D83-7. Epub 2007 Nov 2.
PMID 17981843
 
High-resolution profiling of histone methylations in the human genome.
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K.
Cell. 2007 May 18;129(4):823-37.
PMID 17512414
 
The protein CTCF is required for the enhancer blocking activity of vertebrate insulators.
Bell AC, West AG, Felsenfeld G.
Cell. 1999 Aug 6;98(3):387-96.
PMID 10458613
 
CTCF regulates asynchronous replication of the imprinted H19/Igf2 domain.
Bergstrom R, Whitehead J, Kurukuti S, Ohlsson R.
Cell Cycle. 2007 Feb 15;6(4):450-4. Epub 2007 Feb 12.
PMID 17329968
 
The molecular function and clinical phenotype of partial deletions of the IGF2/H19 imprinting control region depends on the spatial arrangement of the remaining CTCF-binding sites.
Beygo J, Citro V, Sparago A, De Crescenzo A, Cerrato F, Heitmann M, Rademacher K, Guala A, Enklaar T, Anichini C, Cirillo Silengo M, Graf N, Prawitt D, Cubellis MV, Horsthemke B, Buiting K, Riccio A.
Hum Mol Genet. 2013 Feb 1;22(3):544-57. doi: 10.1093/hmg/dds465. Epub 2012 Oct 30.
PMID 23118352
 
Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.
Botta M, Haider S, Leung IX, Lio P, Mozziconacci J.
Mol Syst Biol. 2010 Nov 2;6:426. doi: 10.1038/msb.2010.79.
PMID 21045820
 
CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin.
Burke LJ, Zhang R, Bartkuhn M, Tiwari VK, Tavoosidana G, Kurukuti S, Weth C, Leers J, Galjart N, Ohlsson R, Renkawitz R.
EMBO J. 2005 Sep 21;24(18):3291-300. Epub 2005 Aug 18.
PMID 16107875
 
Epigenetic inactivation of BRCA1 is associated with aberrant expression of CTCF and DNA methyltransferase (DNMT3B) in some sporadic breast tumours.
Butcher DT, Rodenhiser DI.
Eur J Cancer. 2007 Jan;43(1):210-9. Epub 2006 Oct 27.
PMID 17071074
 
CTCF, a candidate trans-acting factor for X-inactivation choice.
Chao W, Huynh KD, Spencer RJ, Davidow LS, Lee JT.
Science. 2002 Jan 11;295(5553):345-7. Epub 2001 Dec 6.
PMID 11743158
 
The role of CTCF in regulating V(D)J recombination.
Chaumeil J, Skok JA.
Curr Opin Immunol. 2012 Apr;24(2):153-9. doi: 10.1016/j.coi.2012.01.003. Epub 2012 Mar 15. (REVIEW)
PMID 22424610
 
Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome.
Chen H, Tian Y, Shu W, Bo X, Wang S.
PLoS One. 2012;7(7):e41374. doi: 10.1371/journal.pone.0041374. Epub 2012 Jul 19.
PMID 22829947
 
CDC25B mediates rapamycin-induced oncogenic responses in cancer cells.
Chen RQ, Yang QK, Lu BW, Yi W, Cantin G, Chen YL, Fearns C, Yates JR 3rd, Lee JD.
Cancer Res. 2009 Mar 15;69(6):2663-8. Epub 2009 Mar 10.
PMID 19276368
 
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, Loh YH, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung WK, Clarke ND, Wei CL, Ng HH.
Cell. 2008 Jun 13;133(6):1106-17.
PMID 18555785
 
CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide.
Chernukhin I, Shamsuddin S, Kang SY, Bergstrom R, Kwon YW, Yu W, Whitehead J, Mukhopadhyay R, Docquier F, Farrar D, Morrison I, Vigneron M, Wu SY, Chiang CM, Loukinov D, Lobanenkov V, Ohlsson R, Klenova E.
Mol Cell Biol. 2007 Mar;27(5):1631-48. Epub 2007 Jan 8.
PMID 17210645
 
Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF.
Cho DH, Thienes CP, Mahoney SE, Analau E, Filippova GN, Tapscott SJ.
Mol Cell. 2005 Nov 11;20(3):483-9.
PMID 16285929
 
Lysine acetylation targets protein complexes and co-regulates major cellular functions.
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
Science. 2009 Aug 14;325(5942):834-40. Epub 2009 Jul 16.
PMID 19608861
 
Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.
Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K.
Genome Res. 2009 Jan;19(1):24-32. Epub 2008 Dec 3.
PMID 19056695
 
Loss of imprinting of insulin-like growth factor-II in Wilms' tumor commonly involves altered methylation but not mutations of CTCF or its binding site.
Cui H, Niemitz EL, Ravenel JD, Onyango P, Brandenburg SA, Lobanenkov VV, Feinberg AP.
Cancer Res. 2001 Jul 1;61(13):4947-50.
PMID 11431321
 
Frequent aberrant methylation of the imprinted IGF2/H19 locus and LINE1 hypomethylation in ovarian carcinoma.
Dammann RH, Kirsch S, Schagdarsurengin U, Dansranjavin T, Gradhand E, Schmitt WD, Hauptmann S.
Int J Oncol. 2010 Jan;36(1):171-9.
PMID 19956846
 
Gain of DNA methylation is enhanced in the absence of CTCF at the human retinoblastoma gene promoter.
Davalos-Salas M, Furlan-Magaril M, Gonzalez-Buendia E, Valdes-Quezada C, Ayala-Ortega E, Recillas-Targa F.
BMC Cancer. 2011 Jun 10;11:232. doi: 10.1186/1471-2407-11-232.
PMID 21663659
 
H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: a pilot case-control analysis.
De Castro Valente Esteves LI, De Karla Cervigne N, Do Carmo Javaroni A, Magrin J, Kowalski LP, Rainho CA, Rogatto SR.
Int J Mol Med. 2006 Feb;17(2):397-404.
PMID 16391843
 
Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF.
De La Rosa-Velazquez IA, Rincon-Arano H, Benitez-Bribiesca L, Recillas-Targa F.
Cancer Res. 2007 Mar 15;67(6):2577-85
PMID 17363576
 
The human enhancer blocker CTC-binding factor interacts with the transcription factor Kaiso.
Defossez PA, Kelly KF, Filion GJ, Perez-Torrado R, Magdinier F, Menoni H, Nordgaard CL, Daniel JM, Gilson E.
J Biol Chem. 2005 Dec 30;280(52):43017-23. Epub 2005 Oct 17.
PMID 16230345
 
Differential expression and phosphorylation of CTCF, a c-myc transcriptional regulator, during differentiation of human myeloid cells.
Delgado MD, Chernukhin IV, Bigas A, Klenova EM, Leon J.
FEBS Lett. 1999 Feb 5;444(1):5-10.
PMID 10037138
 
CTCF promotes muscle differentiation by modulating the activity of myogenic regulatory factors.
Delgado-Olguin P, Brand-Arzamendi K, Scott IC, Jungblut B, Stainier DY, Bruneau BG, Recillas-Targa F.
J Biol Chem. 2011 Apr 8;286(14):12483-94. doi: 10.1074/jbc.M110.164574. Epub 2011 Feb 2.
PMID 21288905
 
A role for CTCF and cohesin in subtelomere chromatin organization, TERRA transcription, and telomere end protection.
Deng Z, Wang Z, Stong N, Plasschaert R, Moczan A, Chen HS, Hu S, Wikramasinghe P, Davuluri RV, Bartolomei MS, Riethman H, Lieberman PM.
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PMID 23010778
 
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
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Nature. 2012 Apr 11;485(7398):376-80. doi: 10.1038/nature11082.
PMID 22495300
 
Decreased poly(ADP-ribosyl)ation of CTCF, a transcription factor, is associated with breast cancer phenotype and cell proliferation.
Docquier F, Kita GX, Farrar D, Jat P, O'Hare M, Chernukhin I, Gretton S, Mandal A, Alldridge L, Klenova E.
Clin Cancer Res. 2009 Sep 15;15(18):5762-71. Epub 2009 Sep 8.
PMID 19737964
 
Commonly altered genomic regions in acute myeloid leukemia are enriched for somatic mutations involved in chromatin remodeling and splicing.
Dolnik A, Engelmann JC, Scharfenberger-Schmeer M, Mauch J, Kelkenberg-Schade S, Haldemann B, Fries T, Kronke J, Kuhn MW, Paschka P, Kayser S, Wolf S, Gaidzik VI, Schlenk RF, Rucker FG, Dohner H, Lottaz C, Dohner K, Bullinger L.
Blood. 2012 Nov 1;120(18):e83-92. doi: 10.1182/blood-2011-12-401471. Epub 2012 Sep 13.
PMID 22976956
 
Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch.
Donohoe ME, Zhang LF, Xu N, Shi Y, Lee JT.
Mol Cell. 2007 Jan 12;25(1):43-56.
PMID 17218270
 
The insulator binding protein CTCF associates with the nuclear matrix.
Dunn KL, Zhao H, Davie JR.
Exp Cell Res. 2003 Aug 1;288(1):218-23.
PMID 12878173
 
Regulation of the transcription factor, CTCF, by phosphorylation with protein kinase CK2.
El-Kady A, Klenova E.
FEBS Lett. 2005 Feb 28;579(6):1424-34.
PMID 15733852
 
DNA methylation in the CTCF-binding site I and the expression pattern of the H19 gene: does positive expression predict poor prognosis in early stage head and neck carcinomas?
Esteves LI, Javaroni AC, Nishimoto IN, Magrin J, Squire JA, Kowalski LP, Rainho CA, Rogatto SR.
Mol Carcinog. 2005 Oct;44(2):102-10.
PMID 16015666
 
Mutational analysis of the poly(ADP-ribosyl)ation sites of the transcription factor CTCF provides an insight into the mechanism of its regulation by poly(ADP-ribosyl)ation.
Farrar D, Rai S, Chernukhin I, Jagodic M, Ito Y, Yammine S, Ohlsson R, Murrell A, Klenova E.
Mol Cell Biol. 2010 Mar;30(5):1199-216. Epub 2009 Dec 28.
PMID 20038529
 
Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting.
Fedoriw AM, Stein P, Svoboda P, Schultz RM, Bartolomei MS.
Science. 2004 Jan 9;303(5655):238-40.
PMID 14716017
 
Genetics and epigenetics of the multifunctional protein CTCF.
Filippova GN.
Curr Top Dev Biol. 2008;80:337-60. (REVIEW)
PMID 17950379
 
The tumor suppressor role of CTCF.
Fiorentino FP, Giordano A.
J Cell Physiol. 2012 Feb;227(2):479-92. doi: 10.1002/jcp.22780. (REVIEW)
PMID 21465478
 
Allele-specific binding of CTCF to the multipartite imprinting control region KvDMR1.
Fitzpatrick GV, Pugacheva EM, Shin JY, Abdullaev Z, Yang Y, Khatod K, Lobanenkov VV, Higgins MJ.
Mol Cell Biol. 2007 Apr;27(7):2636-47. Epub 2007 Jan 22.
PMID 17242189
 
Aging and cancer-related loss of insulin-like growth factor 2 imprinting in the mouse and human prostate.
Fu VX, Dobosy JR, Desotelle JA, Almassi N, Ewald JA, Srinivasan R, Berres M, Svaren J, Weindruch R, Jarrard DF.
Cancer Res. 2008a Aug 15;68(16):6797-802.
PMID 18701505
 
The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
Fu Y, Sinha M, Peterson CL, Weng Z.
PLoS Genet. 2008b Jul 25;4(7):e1000138.
PMID 18654629
 
Functional role of CCCTC binding factor in insulin-stimulated cell proliferation.
Gao J, Li T, Lu L.
Cell Prolif. 2007 Dec;40(6):795-808.
PMID 18021171
 
Targeted deletion of multiple CTCF-binding elements in the human C-MYC gene reveals a requirement for CTCF in C-MYC expression.
Gombert WM, Krumm A.
PLoS One. 2009 Jul 1;4(7):e6109.
PMID 19568426
 
Gene-specific repression of the p53 target gene PUMA via intragenic CTCF-Cohesin binding.
Gomes NP, Espinosa JM.
Genes Dev. 2010 May 15;24(10):1022-34.
PMID 20478995
 
Loss of imprinting of IGF2 and H19, loss of heterozygosity of IGF2R and CTCF, and Helicobacter pylori infection in laryngeal squamous cell carcinoma.
Grbesa I, Marinkovic M, Ivkic M, Kruslin B, Novak-Kujundzic R, Pegan B, Bogdanovic O, Bedekovic V, Gall-Troselj K.
J Mol Med. 2008 Sep;86(9):1057-66. Epub 2008 Jul 5.
PMID 18604514
 
Loss of expression of chromosome 16q genes DPEP1 and CTCF in lobular carcinoma in situ of the breast.
Green AR, Krivinskas S, Young P, Rakha EA, Paish EC, Powe DG, Ellis IO.
Breast Cancer Res Treat. 2009 Jan;113(1):59-66. Epub 2008 Jan 23.
PMID 18213475
 
ADP-ribose polymer depletion leads to nuclear Ctcf re-localization and chromatin rearrangement(1).
Guastafierro T, Catizone A, Calabrese R, Zampieri M, Martella O, Bacalini MG, Reale A, Di Girolamo M, Miccheli M, Farrar D, Klenova E, Ciccarone F, Caiafa P.
Biochem J. 2013 Feb 1;449(3):623-30. doi: 10.1042/BJ20121429.
PMID 23116180
 
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B.
Nature. 2008 Jun 12;453(7197):948-51. doi: 10.1038/nature06947. Epub 2008 May 7.
PMID 18463634
 
CTCF-binding elements mediate control of V(D)J recombination.
Guo C, Yoon HS, Franklin A, Jain S, Ebert A, Cheng HL, Hansen E, Despo O, Bossen C, Vettermann C, Bates JG, Richards N, Myers D, Patel H, Gallagher M, Schlissel MS, Murre C, Busslinger M, Giallourakis CC, Alt FW.
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DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas.
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CTCF regulates allelic expression of Igf2 by orchestrating a promoter-polycomb repressive complex 2 intrachromosomal loop.
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CTCF cis-regulates trinucleotide repeat instability in an epigenetic manner: a novel basis for mutational hot spot determination.
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Citation

This paper should be referenced as such :
Piette, J
CTCF (CCCTC-binding factor (zinc finger protein))
Atlas Genet Cytogenet Oncol Haematol. 2013;17(12):802-810.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CTCFID40187ch16q22.html
History of this paper:
Piette, J. CTCF (CCCTC-binding factor (zinc finger protein)). Atlas Genet Cytogenet Oncol Haematol. 2011;15(11):907-913.
http://documents.irevues.inist.fr/bitstream/handle/2042/46051/04-2011-CTCFID40187ch16q22.pdf


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  Myeloid proliferations in Down syndrome


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Breast: Ductal carcinoma


External links

Nomenclature
HGNC (Hugo)CTCF   13723
Cards
AtlasCTCFID40187ch16q22
Entrez_Gene (NCBI)CTCF  10664  CCCTC-binding factor
AliasesMRD21
GeneCards (Weizmann)CTCF
Ensembl hg19 (Hinxton)ENSG00000102974 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000102974 [Gene_View]  chr16:67562407-67639185 [Contig_View]  CTCF [Vega]
ICGC DataPortalENSG00000102974
TCGA cBioPortalCTCF
AceView (NCBI)CTCF
Genatlas (Paris)CTCF
WikiGenes10664
SOURCE (Princeton)CTCF
Genetics Home Reference (NIH)CTCF
Genomic and cartography
GoldenPath hg38 (UCSC)CTCF  -     chr16:67562407-67639185 +  16q22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CTCF  -     16q22.1   [Description]    (hg19-Feb_2009)
EnsemblCTCF - 16q22.1 [CytoView hg19]  CTCF - 16q22.1 [CytoView hg38]
Mapping of homologs : NCBICTCF [Mapview hg19]  CTCF [Mapview hg38]
OMIM604167   615502   
Gene and transcription
Genbank (Entrez)AA814313 AB209793 AI753629 AK093395 AK314804
RefSeq transcript (Entrez)NM_001191022 NM_006565
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CTCF
Cluster EST : UnigeneHs.368367 [ NCBI ]
CGAP (NCI)Hs.368367
Alternative Splicing GalleryENSG00000102974
Gene ExpressionCTCF [ NCBI-GEO ]   CTCF [ EBI - ARRAY_EXPRESS ]   CTCF [ SEEK ]   CTCF [ MEM ]
Gene Expression Viewer (FireBrowse)CTCF [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10664
GTEX Portal (Tissue expression)CTCF
Protein : pattern, domain, 3D structure
UniProt/SwissProtP49711   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP49711  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP49711
Splice isoforms : SwissVarP49711
PhosPhoSitePlusP49711
Domaine pattern : Prosite (Expaxy)ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)CTCF
DMDM Disease mutations10664
Blocks (Seattle)CTCF
PDB (SRS)1X6H    2CT1   
PDB (PDBSum)1X6H    2CT1   
PDB (IMB)1X6H    2CT1   
PDB (RSDB)1X6H    2CT1   
Structural Biology KnowledgeBase1X6H    2CT1   
SCOP (Structural Classification of Proteins)1X6H    2CT1   
CATH (Classification of proteins structures)1X6H    2CT1   
SuperfamilyP49711
Human Protein AtlasENSG00000102974
Peptide AtlasP49711
HPRD05005
IPIIPI00027988   IPI00902532   IPI00953090   IPI00556456   
Protein Interaction databases
DIP (DOE-UCLA)P49711
IntAct (EBI)P49711
FunCoupENSG00000102974
BioGRIDCTCF
STRING (EMBL)CTCF
ZODIACCTCF
Ontologies - Pathways
QuickGOP49711
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  chromosome, centromeric region  condensed chromosome  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  protein binding  nucleus  nucleoplasm  nucleolus  DNA methylation  regulation of gene expression by genetic imprinting  transcription from RNA polymerase II promoter  chromosome segregation  zinc ion binding  maintenance of DNA methylation  positive regulation of gene expression  covalent chromatin modification  nucleosome positioning  regulation of histone methylation  regulation of histone acetylation  regulation of gene expression, epigenetic  regulation of molecular function, epigenetic  chromatin insulator sequence binding  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  regulation of centromeric sister chromatid cohesion  protein localization to chromosome, centromeric region  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  chromosome, centromeric region  condensed chromosome  RNA polymerase II core promoter proximal region sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  protein binding  nucleus  nucleoplasm  nucleolus  DNA methylation  regulation of gene expression by genetic imprinting  transcription from RNA polymerase II promoter  chromosome segregation  zinc ion binding  maintenance of DNA methylation  positive regulation of gene expression  covalent chromatin modification  nucleosome positioning  regulation of histone methylation  regulation of histone acetylation  regulation of gene expression, epigenetic  regulation of molecular function, epigenetic  chromatin insulator sequence binding  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  regulation of centromeric sister chromatid cohesion  protein localization to chromosome, centromeric region  
Pathways : BIOCARTACTCF: First Multivalent Nuclear Factor [Genes]   
REACTOMEP49711 [protein]
REACTOME PathwaysR-HSA-5617472 [pathway]   
NDEx NetworkCTCF
Atlas of Cancer Signalling NetworkCTCF
Wikipedia pathwaysCTCF
Orthology - Evolution
OrthoDB10664
GeneTree (enSembl)ENSG00000102974
Phylogenetic Trees/Animal Genes : TreeFamCTCF
HOVERGENP49711
HOGENOMP49711
Homologs : HomoloGeneCTCF
Homology/Alignments : Family Browser (UCSC)CTCF
Gene fusions - Rearrangements
Fusion : MitelmanCTCF/CES2 [16q22.1/16q22.1]  
Fusion: TCGACTCF 16q22.1 CES2 16q22.1 SKCM
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCTCF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CTCF
dbVarCTCF
ClinVarCTCF
1000_GenomesCTCF 
Exome Variant ServerCTCF
ExAC (Exome Aggregation Consortium)CTCF (select the gene name)
Genetic variants : HAPMAP10664
Genomic Variants (DGV)CTCF [DGVbeta]
DECIPHERCTCF [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCTCF 
Mutations
ICGC Data PortalCTCF 
TCGA Data PortalCTCF 
Broad Tumor PortalCTCF
OASIS PortalCTCF [ Somatic mutations - Copy number]
Cancer Gene: CensusCTCF 
Somatic Mutations in Cancer : COSMICCTCF  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDCTCF
intOGen PortalCTCF
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch CTCF
DgiDB (Drug Gene Interaction Database)CTCF
DoCM (Curated mutations)CTCF (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CTCF (select a term)
intoGenCTCF
NCG5 (London)CTCF
Cancer3DCTCF(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604167    615502   
Orphanet22327   
MedgenCTCF
Genetic Testing Registry CTCF
NextProtP49711 [Medical]
TSGene10664
GENETestsCTCF
Target ValidationCTCF
Huge Navigator CTCF [HugePedia]
snp3D : Map Gene to Disease10664
BioCentury BCIQCTCF
ClinGenCTCF
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10664
Chemical/Pharm GKB GenePA26998
Clinical trialCTCF
Miscellaneous
canSAR (ICR)CTCF (select the gene name)
Other databaseCTCFBSDB 2.0: a database for CTCF-binding sites and genome organization (Ziebarth et al., 2013).
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=CTCF
Probes
Litterature
PubMed210 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCTCF
EVEXCTCF
GoPubMedCTCF
iHOPCTCF
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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