CCCTC-Binding Factor. Synonyms. Definition. Characteristics

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1 C CCCTC-Binding Factor Elena Klenova 1, Dmitri Loukinov 2 and Victor Lobanenkov 2 1 Department of Biological Sciences, University of Essex, Colchester, Essex, UK 2 Section of Molecular Pathology, Laboratory of Immunopathology, NIAID, National Institutes of Health, Bethesda, MD, USA Synonyms CTCF Definition CTCF (acronym for a CCCTC-binding factor ) is a highly conserved and ubiquitous protein with multiple functions, which include regulation of transcription, chromatin insulation, and genomic imprinting. Characteristics The CTCF protein was originally identified for its ability to bind to a promoter element of the chicken c-myc gene. The sequence recognized by CTCF contained the CCCTC repeats and therefore the protein was defined as CTCF (the CCCTC-binding factor). However, it was later discovered that other CTCF-target sequences (or CTSs) were remarkably dissimilar, and the term multivalent transcription factor was coined for CTCF. Another unusual feature of the CTSs is their length: the analysis of binding patterns of CTCF to multiple sites demonstrated that CTCF requires about bp-long sequence to form a complex with DNA. The ability of CTCF to bind such diverse targets has been attributed to its DNA-binding domain, which is composed of 11 zinc fingers (ZFs), 10 of them of the C 2 H 2 class and 1 ZF of C 2 HC class (Fig. 1a, b). According to this model, the combinatorial utilization of different ZFs results in binding to diverse DNA targets. In addition, CTCF-DNA complex formation can be regulated by DNA methylation, if symmetrically methylated CpG dinucleotides present on both DNA-strands within any given CTS coincide with the DNA bases required for the CTS recognition by a particular subset of CTCF fingers. Not all CTCF-target sequences contain CpG bp that can be modified by methylation, nevertheless the capability of CTCF to distinguish differentially methylated DNA targets is one of the major features of CTCF with a broad spectrum of functional implications. The CTSs have been identified in many genomic elements. It is estimated there may be well over 30,000 of CTSs in the human genome, with 14,000 localized in potential insulators. Many of these sites are methylation sensitive and map to promoter, intergenic and intragenic regions, # Springer-Verlag Berlin Heidelberg 2015 M. Schwab (ed.), Encyclopedia of Cancer, DOI / _902-2

2 2 CCCTC-Binding Factor and both exons and introns. Examples of CTCFtarget promoters include 5 0 -noncoding regions of the c-myc oncogene, chicken lysozyme, IRAK2, BRCA1, the amyloid precursor protein (APP), the exon regions of htert, and the intron regions of the serotonin transporter gene, SLC6A4. Other CTCF-driven regulatory elements include vertebrate enhancer-blocking elements (insulators), classic examples of which are chicken b-globin insulators that flank b-globin gene cluster. Such intergenic insulators seem to have a consensus binding motif for CTCF. CTCF sites are universally present in all mammalian differentially methylated domains/regions (DMD/DMR) or imprinting control regions (ICR), as exemplified by CTSs in ICRs of such imprinted gene clusters as IGF2/H19, Rasgfr, KvDMR, and other loci, deregulation of which through aberrant (biallelic) CTS-methylation or CTS-demethylation contributes to cancer. CTCF has now been cloned from various organisms which include insects, fish, amphibians, birds, rodents, and primates. The comparison between the proteins revealed a high degree of homology between the CTCF from different organisms, especially in the ZF DNA-binding domain. Thus, this domain is 100 % identical at the protein level among mouse, man, and chicken, whereas the full-length protein is 93 % identical in those three species; the Drosophila CTCF protein has a 46 % identity within the zincfinger regions and 27 % overall identity. Typically for a transcriptional factor, CTCF is localized to the nucleus. It is ubiquitously expressed in various tissues and cells in different organisms. Such conservation in the protein composition and also wide representation in cells/ tissues signifies the important and general cellular functions mediated by CTCF. The size of the CTCF protein varies depending on the organism. For example, the human CTCF protein is composed of 727 amino acids, chicken CTCF of 728, and Drosophila CTCF of 818 amino acids. The structure of the human CTCF is shown in Fig. 1 (panels a and b). The ZF DNA-binding domain is positioned in the center of CTCF and accounts for about one third of the protein s size. The N-terminal domain of human CTCF is composed of 268 amino acids and is rich in proline residues. The C-terminal domain is the smallest part of the molecule (150 amino acids) and is highly negatively charged. These CTCF domains play an important role in the modulation of CTCF functions in the regulation of transcription. In some cases, this regulation relies on posttranslational modifications. For example, the C-terminal domain contains the sites of phosphorylation by the protein kinase CK2 (former casein kinase II), whereas the N-terminal domain contains the sites for poly(adp-ribosyl)ation by the PARP-1 (poly(adp-ribose) polymerase-1). The sites for SUMOylation have been mapped to the N- and C-terminal domains of CTCF. The posttranslational modifications and interactions with protein partners have been demonstrated to modulate important functions of CTCF. For example, specific phosphorylation of CTCF by CK2 and SUMOylation affect the CTCF functions in transcriptional regulation. Poly(ADP-ribosyl)ation was found to be important for insulator function of CTCF, CTCFdependant nucleolar transcription, and barrier function. Posttranslational modifications of CTCF have also been implicated in human myeloid cell differentiation. Regulation of CTCF-dependent molecular processes also involves CTCF associations with other proteins. Thus, CTCF interactions with sin3 and YB-1 are shown to modulate CTCF function as a transcriptional repressor. Cooperation of CTCF with nucleophosmin, Kaiso, and helicase protein CHD8 has been linked to the control of insulator function of CTCF and epigenetic regulation. Cohesins and CTCF have been shown to co-localize genome wide; this association has been implicated in the insulator function of CTC- F. Interaction of CTCF with another transcription factor, YY-1, is required to control the X-chromosome inactivation, and cooperation of CTCF with RNA Polymerase II may be important for regulation of transcription. A testis-specific paralogue of CTCF has been reported. This protein was termed BORIS (the acronym for Brother of the Regulator of Imprinted Sites). BORIS possesses the 11 ZF

3 CCCTC-Binding Factor 3 CCCTC-Binding Factor, Fig. 1 (a) Schematic drawing of the CTCF protein. The three domains of CTCF are depicted as follows: N N-terminal domain (Patterned box), ZF ZF domain (box with half ovals designating 11 Zinc Fingers; the black half ovals refer to the C 2 H 2 class and the gray half oval refers to the C 2 HC class), C C-terminal domain (open box). The amino acid numbers for the start and the end of each domain are indicated above the diagram. (b) The cartoon illustration of the wild-type human CTCF protein represents the N-terminal and C-terminal domains of CTCF and the DNA-binding domain of CTCF composed of 10 ZF of C 2 H 2 class and 1 ZF of C 2 HC class. (c) The locations of the tumorspecific mutations in the CTCF protein are shown. The mutations CTCFHR, KE, and RW are located in ZF3, and the mutation CTCFRQ is located in ZF7. The position of the 14 bp insertion is indicated domain homologous to that of CTCF; the flanking N-and C-terminal domain, on the other hand, are dissimilar. These structural features indicate that BORIS could recognize the same

4 4 CCCTC-Binding Factor set of DNA targets as CTCF, while different flanking domains could be important for regulation of BORIS-specific functions. CTCF Functions A growing body of evidence suggests that CTCF is involved in the organization and regulation of a whole range of distinct genomic functions in three-dimensional nuclear space. They include gene activation, repression, and silencing; CTCF is also involved in the control of insulator function and imprinting. All vertebrate enhancerblocking elements tested so far contain CTCFbinding sites. The importance of the insulator function of CTCF was further demonstrated in the regulation of CTG/CAG repeats in the DM1 locus and in the X-chromosome inactivation. It is now generally accepted that the molecular basis for the insulator function of CTCF lies in the ability of CTCF to influence chromatin architecture by mediating long-range chromatin looping and modification of histones. Such alterations then settle the balance between active and repressive chromatin and influence gene expression. CTCF binding to many of its targets can be regulated by DNA methylation; the ability of CTCF to read such epigenetic marks contributes significantly to the versatility of CTCF functions. Several findings support the concept of CTCF being a tumor suppressor gene (TSG). Firstly, CTCF suppresses cell growth and proliferation, and, further, in some cell systems (for example, myeloid cells) induces cell differentiation. Secondly, the CTCF gene maps within the smallest region of overlap for loss of heterozygosity (LOH) that has been observed at chromosome 16q22.1 in breast, prostate, and Wilm s tumor (Fig. 1c). Finally, functionally significant, tumor-specific CTCF mutations in the ZF domain of CTCF were identified in various sporadic cancers including breast, prostate, and Wilm s tumor in the remaining allele (Fig. 1b). All four reported tumor-specific point mutations in the CTCF Zn finger domain result in a missense codon at a position predicted to be critical for ZF formation or DNA base recognition. Another reported tumor-specific mutation constituted of a 14 bp insertion in the N-terminal domain of CTCF (Fig. 1b). In familial non-brca1/ BRCA2 breast cancers, two sequence variants, G240A in the 5 0 untranslated region and C1455T (S388S) in exon 4, were also identified. The CTCF s function as a negative regulator of cell growth has been well documented on various cellular models. Thus, over-expression of CTCF leads to inhibition of cell growth and proliferation. Normal embryonic rat cells, made haploinsufficient for CTCF by the retroviral insertion into the intron upstream of the first coding exon, manifest all major features of cancerous transformation in vitro. The mechanism of this function of CTCF, at least in part, lies in the ability of CTCF to control genes responsible for regulation of cell growth and proliferation, negatively oncogenes and positively TSG. Examples of such CTCF-target genes include oncogenes MYC, PIM-1, PLK, E2F1, TERT, IGF2 and TSGs p19arf(p16/ink4a), BRCA1, p53, p21, and p27. Based on these findings, CTCF emerges as a key versatile element linking genetics, epigenetics, development, and disease. The ability of CTCF to interact with the repeated sequences and read epigenetic marks (DNA methylation) may provide a causal link not only to some forms of neoplasia but also to degenerative and neurological conditions. Epigenetic disturbances in these diseases are frequently associated with the instability of repeats, which is considered to be the hallmark of this pathology. Clinical Aspects A link between CTCF and the disease development has been generally recognized. Various genetic and epigenetic mechanisms that result in CTCF malfunction can lead to pathogenesis. The tumor-specific mutations in CTCF can dramatically change the normal biological functions of the wild-type CTCF protein. The sets of the genomic targets of the mutant CTCF variants may alter due to the loss of binding to the usual CTCF targets and/or binding of the mutants to the new targets, especially if the wild-type allele is lost. Each ZF mutation abrogates CTCF binding to a subset of target sites within the promoters and/or insulators of certain genes involved in

5 CCCTC-Binding Factor 5 regulating cell proliferation but do not alter binding to the regulatory sequences of other genes. These observations suggest that CTCF may represent a novel tumor suppressor gene that displays tumor-specific change of function rather than complete loss of function. The 14 bp insertion in the N-terminal domain, on the other hand, most likely leads to the loss of function of CTCF as it creates a premature stop codon, thus generating a truncated CTCF protein. The significance of the sequence variants in the familial breast cancers, however, is not yet clear. The genetic alterations in CTCF are rare events; therefore, considerable efforts are being currently made to identify epigenetic mechanisms responsible for inactivation of CTCF. The rationale behind these studies is that the binding of CTCF to its DNA targets is methylation sensitive, with the current view that the bound CTCF can protect the CpG islands of DNA against methylation. Indeed, it has been reported that derepression of the maternal IGF2 allele is linked to abnormal methylation of the CTCF target sites within the ICR H19 in a wide range of cancer types (breast, prostate, colorectal, Wilm s tumor). This has been explained by the inability of CTCF to bind to the methylated ICR H19 and therefore its failure to establish the chromatin insulator function on the maternal allele thus leading to activation of IGF2. There is a growing body of evidence to suggest that even mutations of a single CTCF site leads to dramatic biological consequences. For instance, mutations of the CTCF site in the Xist promoter that alter CTCF binding result in the skewed X-chromosome inactivation in affected families. Furthermore, deletions of CTCF sites in human ICR H19 lead to predisposition to Wilm s tumors in families with Beckwith-Wiedemann Syndrome (BWS). Finally, a mutation of the single CTCF site in the homologous ICR H19 predisposes the mice carrying such a mutation to colorectal cancer. Epigenetic inactivation of a number of cancer genes due to aberrant methylation of the CpG islands within their promoters has also been established. Interestingly, many of these genes are regulated by CTCF. As in the case with the ICR H19, CTCF may be necessary to protect the promoters of the TSGs from unwanted DNA methylation. According to another, yet to be proven, model, CTCF may demarcate the boundary between methylated and unmethylated genomic domains, as may be the case for the BRCA1 promoter. The utility of CTCF as a cancer biomarker is yet to be established, although there are indications that CTCF may be an interesting target for therapy in breast tumors where levels of CTCF were found elevated compared with breast cell lines with finite life span and normal breast tissues. Such upregulation of CTCF in breast cancer cells has been linked to resistance of these cells to apoptosis. The results of the experiments in breast cancer cell lines point to a possible link between CTCF expression and sensitivity to apoptosis; that is, higher levels of CTCF may be necessary to protect the more sensitive cancer cells from apoptotic stimuli. These findings may be relevant to the potential use of CTCF as a therapeutic target in breast cancers: reducing the levels of CTCF would then result in apoptotic cell death of cancer cells hopefully without affecting normal breast tissue; the effect of CTCF downregulation may be more dramatic in high grade breast tumors. On the other hand, elevated levels of CTCF in breast tumors may correlate with several clinical and/or pathological parameters, which make CTCF a potential prognostic marker. More research is needed to clarify the full potential of CTCF as a clinical target and a cancer biomarker. References Klenova EM, Morse HC, III HC, Ohlsson R et al (2002) The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer. Semin Cancer Biol 12:

6 6 CCCTC-Binding Factor Ohlsson R, Renkawitz R, Lobanenkov V (2001) CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet 17: Ohlsson R, Lobanenkov V, Klenova E (2010) Does CTCF mediate between nuclear organization and gene expression? Bioessays 32:37 50 Phillips JE, Corces VG (2009) CTCF: master weaver of the genome. Cell 137: Recillas-Targa F, De La Rosa-Velazquez IA, Soto-Reyes E et al (2006) Epigenetic boundaries of tumour suppressor gene promoters: the CTCF connection and its role in carcinogenesis. J Cell Mol Med 10:

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