Genomes and Genes
Gene Symbol: CTCF
Alias: CG8591, Dmel\CG8591, dCTCF, CTCF, CCCTC-binding factor, CG8591-PA, CTCF-PA
Species: fruit fly
- Bushey A, Ramos E, Corces V. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev. 2009;23:1338-50 pubmed publisher..Suppressor of Hair-wing [Su(Hw)] and Drosophila CTCF (dCTCF) insulators are found at distinct loci throughout the Drosophila melanogaster genome and function by recruiting an ..
- Negre N, Brown C, Shah P, Kheradpour P, Morrison C, Henikoff J, et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 2010;6:e1000814 pubmed publisher..We studied by ChIP-chip the genome-wide binding sites of 6 insulator-associated proteins-dCTCF, CP190, BEAF-32, Su(Hw), Mod(mdg4), and GAF-to obtain the first comprehensive map of insulator elements in ..
- Kyrchanova O, Ivlieva T, Toshchakov S, Parshikov A, Maksimenko O, Georgiev P. Selective interactions of boundaries with upstream region of Abd-B promoter in Drosophila bithorax complex and role of dCTCF in this process. Nucleic Acids Res. 2011;39:3042-52 pubmed publisher..The results show that all dCTCF-containing boundaries interact with each other...
- Moon H, Filippova G, Loukinov D, Pugacheva E, Chen Q, Smith S, et al. CTCF is conserved from Drosophila to humans and confers enhancer blocking of the Fab-8 insulator. EMBO Rep. 2005;6:165-70 pubmed..demonstrate that one of the insulators (Fab-8) in the Drosophila Abdominal-B locus mediates enhancer blocking by dCTCF. Therefore, the enhancer-blocking protein CTCF and, most probably, the mechanism of enhancer blocking mediated by ..
- Ong C, Van Bortle K, Ramos E, Corces V. Poly(ADP-ribosyl)ation regulates insulator function and intrachromosomal interactions in Drosophila. Cell. 2013;155:148-59 pubmed publisher..This modification is not essential for DNA occupancy of insulator DNA-binding proteins dCTCF and Su(Hw)...
- Lim S, Boyle P, Chinen M, Dale R, Lei E. Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res. 2013;41:2963-80 pubmed publisher..ChIP-seq in two different embryonic cell lines reveals extensive and specific overlap with the CP190, BEAF-32 and CTCF insulator proteins...
- Feller C, Prestel M, Hartmann H, Straub T, Söding J, Becker P. The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Res. 2012;40:1509-22 pubmed publisher..We conclude that the regulatory capacity of the NSL complex is highly context-dependent. Activation by the NSL complex requires a particular promoter architecture defined by combinations of chromatin regulators and core promoter motifs. ..
- Gerasimova T, Lei E, Bushey A, Corces V. Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila. Mol Cell. 2007;28:761-72 pubmedCTCF plays a central role in vertebrate insulators and forms part of the Fab-8 insulator in Drosophila. dCTCF is present at hundreds of sites in the Drosophila genome, where it is located at the boundaries between bands and interbands in ..
- Moshkovich N, Nisha P, Boyle P, Thompson B, Dale R, Lei E. RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev. 2011;25:1686-701 pubmed publisher..Intriguingly, AGO2 colocalizes extensively with CTCF/CP190 chromatin insulators but not with genomic regions corresponding to endogenous siRNA production...
- Schoborg T, Labrador M. The phylogenetic distribution of non-CTCF insulator proteins is limited to insects and reveals that BEAF-32 is Drosophila lineage specific. J Mol Evol. 2010;70:74-84 pubmed publisher..To date, six insulators and their associated proteins have been characterized, including Su(Hw), Zw5, CTCF, GAF, Mod(mdg4), and BEAF-32...
- Kyrchanova O, Toshchakov S, Podstreshnaya Y, Parshikov A, Georgiev P. Functional interaction between the Fab-7 and Fab-8 boundaries and the upstream promoter region in the Drosophila Abd-B gene. Mol Cell Biol. 2008;28:4188-95 pubmed publisher..Recently binding sites for the Drosophila homolog of the vertebrate insulator protein CTCF (dCTCF) were identified in the Fab-8 boundary and upstream of Abd-B promoter A, with no binding of CTCF to the Fab-7 ..
- Oliver D, Sheehan B, South H, Akbari O, Pai C. The chromosomal association/dissociation of the chromatin insulator protein Cp190 of Drosophila melanogaster is mediated by the BTB/POZ domain and two acidic regions. BMC Cell Biol. 2010;11:101 pubmed publisher..is essential to the function of at least three-types of chromatin insulator complexes organized by Su(Hw), CTCF and BEAF32...
- Mohan M, Bartkuhn M, Herold M, Philippen A, Heinl N, Bardenhagen I, et al. The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J. 2007;26:4203-14 pubmed..Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates...
- Ramos E, Torre E, Bushey A, Gurudatta B, Corces V. DNA topoisomerase II modulates insulator function in Drosophila. PLoS ONE. 2011;6:e16562 pubmed publisher..2 protein and its binding to polytene chromosomes are restored. Thus, Topo II is required to prevent Mod(mdg4)2.2 degradation and, consequently, to stabilize Su(Hw) insulator-mediated chromatin organization. ..
- Smith S, Wickramasinghe P, Olson A, Loukinov D, Lin L, Deng J, et al. Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev Biol. 2009;328:518-28 pubmed publisher..Based on this finding, we characterized the Fab-6 insulator element. In genome-wide analysis, we found that dCTCF-binding sites are often situated between closely positioned gene promoters, consistent with the role of CTCF as an ..
- Dai Q, Ren A, Westholm J, Duan H, Patel D, Lai E. Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Genes Dev. 2015;29:48-62 pubmed publisher..Altogether, our data define an array of common and distinct biochemical and functional properties of this new family of transcription factors. ..
- Sultana H, Verma S, Mishra R. A BEAF dependent chromatin domain boundary separates myoglianin and eyeless genes of Drosophila melanogaster. Nucleic Acids Res. 2011;39:3543-57 pubmed publisher..We also report that BEAF and GAF are the two major proteins responsible for the ME boundary function. Our studies demonstrate a rational approach to search for potential boundaries in genomic regions that are well annotated. ..
- Magbanua J, Runneburger E, Russell S, White R. A variably occupied CTCF binding site in the ultrabithorax gene in the Drosophila bithorax complex. Mol Cell Biol. 2015;35:318-30 pubmed publisherAlthough the majority of genomic binding sites for the insulator protein CCCTC-binding factor (CTCF) are constitutively occupied, a subset show variable occupancy...
- Rubin A, Green P. Expression-based segmentation of the Drosophila genome. BMC Genomics. 2013;14:812 pubmed publisher..Coexpression segments appear to reflect a level of regulatory organization related to, but below that of physical interaction domains, and depending in part on insulator binding. ..
- Maksimenko O, Kyrchanova O, Bonchuk A, Stakhov V, Parshikov A, Georgiev P. Highly conserved ENY2/Sus1 protein binds to Drosophila CTCF and is required for barrier activity. Epigenetics. 2014;9:1261-70 pubmed publisher..Drosophila insulator protein dCTCF marks active promoters and boundaries of many histone H3K27 trimethylation domains associated with repressed ..
- Vorobyeva N, Mazina M, Golovnin A, Kopytova D, Gurskiy D, Nabirochkina E, et al. Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome. Nucleic Acids Res. 2013;41:5717-30 pubmed publisher..Su(Hw) is the first example of such a protein. ..
- Chetverina D, Savitskaya E, Maksimenko O, Melnikova L, Zaytseva O, Parshikov A, et al. Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs. Nucleic Acids Res. 2008;36:929-37 pubmed
- MacDonald W, Menon D, Bartlett N, Sperry G, Rasheva V, MELLER V, et al. The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster. BMC Biol. 2010;8:105 pubmed publisherb>CTCF is a versatile zinc finger DNA-binding protein that functions as a highly conserved epigenetic transcriptional regulator...
- Philip P, Pettersson F, Stenberg P. Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster. BMC Genomics. 2012;13:97 pubmed publisher..High affinity sites seem to be responsible for initial recruitment of the complex to the X chromosome, but the targeting to and within individual genes is poorly understood...
- Bohla D, Herold M, Panzer I, Buxa M, Ali T, Demmers J, et al. A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS ONE. 2014;9:e107765 pubmed publisher..Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors...
- NÃ¡zer E, Lei E. Modulation of chromatin modifying complexes by noncoding RNAs in trans. Curr Opin Genet Dev. 2014;25:68-73 pubmed publisher..In this review, we discuss new insights into the mechanisms by which ncRNAs function in trans with respect to Polycomb Group, chromatin insulator, and dosage compensation complexes in mammals and/or Drosophila. ..
- Saberi S, FarrÃ© P, Cuvier O, Emberly E. Probing long-range interactions by extracting free energies from genome-wide chromosome conformation capture data. BMC Bioinformatics. 2015;16:171 pubmed publisher..PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin. ..
- Heger P, George R, Wiehe T. Successive gain of insulator proteins in arthropod evolution. Evolution. 2013;67:2945-56 pubmed publisher..While a single insulator protein, CTCF (CCCTC-binding factor), is known in vertebrates, Drosophila melanogaster utilizes six additional factors...
- Rohrbaugh M, Clore A, Davis J, Johnson S, Jones B, Jones K, et al. Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines. PLoS ONE. 2013;8:e53091 pubmed publisher..Information gained from the analysis of CG11138 Stwl, dNlp, and Df31 sets the stage for future studies of these proteins. ..
- Kalverda B, Fornerod M. Characterization of genome-nucleoporin interactions in Drosophila links chromatin insulators to the nuclear pore complex. Cell Cycle. 2010;9:4812-7 pubmed..This suggests that the NPC may have a function in the structural organization of the genome. ..
- Guerrero P, Maggert K. The CCCTC-binding factor (CTCF) of Drosophila contributes to the regulation of the ribosomal DNA and nucleolar stability. PLoS ONE. 2011;6:e16401 pubmed publisher..b>CTCF is a sequence-specific DNA binding protein which is thought to act as a transcriptional repressor, block enhancer-..
- Kyrchanova O, Zolotarev N, Mogila V, Maksimenko O, Schedl P, Georgiev P. Architectural protein Pita cooperates with dCTCF in organization of functional boundaries in Bithorax complex. Development. 2017;144:2663-2672 pubmed publisher..Mutation of the Mcp Pita site disrupts blocking activity and also eliminates dCTCF binding...
- Bonchuk A, Georgiev P, Maksimenko O. CTCF and Sgfl1 proteins form alternative complexes with ENY2 proteins. Dokl Biochem Biophys. 2016;468:180-2 pubmed publisher..Besides this, the interactions of ENY2 with DNA-binding insulator proteins Su(Hw) and dCTCF have been described as essential for the barrier activity of corresponding insulators [3, 4]...
- Van Bortle K, Peterson A, Takenaka N, O Connor M, Corces V. CTCF-dependent co-localization of canonical Smad signaling factors at architectural protein binding sites in D. melanogaster. Cell Cycle. 2015;14:2677-87 pubmed publisher..genome-wide in Kc cells and find that numerous sites for these factors overlap with the architectural protein CTCF. Depletion of CTCF by RNAi results in the disappearance of a subset of Smad sites, suggesting Smad proteins ..
- van Bemmel J, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven R, et al. The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS ONE. 2010;5:e15013 pubmed publisher..sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains...
- Demakov S, Vatolina T, Babenko V, Semeshin V, Belyaeva E, Zhimulev I. Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics. 2011;12:566 pubmed publisher..Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization. ..
- Bowman S, Deaton A, Domingues H, Wang P, Sadreyev R, Kingston R, et al. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. elife. 2014;3:e02833 pubmed publisher..The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains ..
- Franchini L, Ganko E, McDonald J. Retrotransposon-gene associations are widespread among D. melanogaster populations. Mol Biol Evol. 2004;21:1323-31 pubmed..Sequence analysis of an association allele present in all populations indicates that selection is a significant factor in the spread and/or maintenance of at least some of retroelement-gene associations in D. melanogaster. ..
- Navarro C, Lopez F, Cano C, Garcia Alcalde F, Blanco A. CisMiner: genome-wide in-silico cis-regulatory module prediction by fuzzy itemset mining. PLoS ONE. 2014;9:e108065 pubmed publisher..ugr.es/cisminer. CisMiner can be queried for the results presented in this work and can also perform a customized cis-regulatory module prediction on a query set of transcription factor binding sites provided by the user. ..
- Maksimenko O, Bartkuhn M, Stakhov V, Herold M, Zolotarev N, Jox T, et al. Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin. Genome Res. 2015;25:89-99 pubmed publisher..The Drosophila CP190 protein is a cofactor for the DNA-binding insulator proteins Su(Hw), CTCF, and BEAF-32...
- Padeken J, Mendiburo M, Chlamydas S, Schwarz H, Kremmer E, Heun P. The nucleoplasmin homolog NLP mediates centromere clustering and anchoring to the nucleolus. Mol Cell. 2013;50:236-49 pubmed publisher..flies, we identified a network of proteins, including the nucleoplasmin-like protein (NLP), the insulator protein CTCF, and the nucleolus protein Modulo, to be essential for the positioning of centromeres...
- FresÃ¡n U, Cuartero S, O Connor M, EspinÃ s M. The insulator protein CTCF regulates Drosophila steroidogenesis. Biol Open. 2015;4:852-7 pubmed publisherThe steroid hormone ecdysone is a central regulator of insect development. In this report we show that CTCF expression in the prothoracic gland is required for full transcriptional activation of the Halloween genes spookier, shadow and ..
- Naval SÃ¡nchez M, Potier D, Hulselmans G, Christiaens V, Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol. 2015;32:2441-55 pubmed publisher..In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence. ..
- Gurudatta B, Yang J, Van Bortle K, Donlin Asp P, Corces V. Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle. Cell Cycle. 2013;12:1605-15 pubmed publisher..Several DNA-binding insulator proteins have been described in Drosophila, including BEAF-32, dCTCF and Su(Hw)...
- Li G, Zhou L. Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PLoS ONE. 2013;8:e67156 pubmed publisher..However, boundary-associated insulator binding sites are distinctively flanked by nucleosome destabilizing sequences, which correlates with significantly decreased nucleosome density and increased binding of co-factors. ..
- Pascual García P, Debo B, Aleman J, Talamas J, Lan Y, Nguyen N, et al. Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts. Mol Cell. 2017;66:63-76.e6 pubmed publisher..Together, our data identify Nups as a class of architectural proteins for enhancers and supports a model in which animal genomes use the nuclear pore as an organizing scaffold for inducible poised genes. ..
- Bonchuk A, Maksimenko O, Kyrchanova O, Ivlieva T, Mogila V, Deshpande G, et al. Functional role of dimerization and CP190 interacting domains of CTCF protein in Drosophila melanogaster. BMC Biol. 2015;13:63 pubmed publisher..more about how insulators carry out their diverse functions, we have begun an analysis of the Drosophila CTCF (dCTCF). CTCF is one of the few insulator proteins known to be conserved from flies to man...
- Li L, Lyu X, Hou C, Takenaka N, Nguyen H, Ong C, et al. Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell. 2015;58:216-31 pubmed publisher..These results suggest that the TAD organization of metazoan genomes is plastic and can be reconfigured quickly. ..
- Pathak R, Srinivasan A, Mishra R. Genome-wide mapping of matrix attachment regions in Drosophila melanogaster. BMC Genomics. 2014;15:1022 pubmed publisher..We also identified sequence motifs and repeats that constitute MARs. Our data reveal the contact points of genome to the nuclear architecture and provide a link between nuclear functions and genomic packaging. ..
- Pascual García P, Jeong J, Capelson M. Nucleoporin Nup98 associates with Trx/MLL and NSL histone-modifying complexes and regulates Hox gene expression. Cell Rep. 2014;9:433-42 pubmed publisher..These findings introduce roles of Nup98 in epigenetic regulation that may underlie the basis of oncogenicity of Nup98 fusions in leukemia. ..
- Cuartero S, Fresán U, Reina O, Planet E, Espinàs M. Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function. EMBO J. 2014;33:637-47 pubmed publisher..In Drosophila different proteins, dCTCF, Su(Hw), and BEAF bind to specific subsets of insulators most of them having in common CP190...
- Ahanger S, Günther K, Weth O, Bartkuhn M, Bhonde R, Shouche Y, et al. Ectopically tethered CP190 induces large-scale chromatin decondensation. Sci Rep. 2014;4:3917 pubmed publisher..In contrast, dCTCF alone, is unable to cause such a decondensation, however, when CP190 is present, dCTCF recruits it to the lacO ..
- Korenjak M, Kwon E, Morris R, Anderssen E, Amzallag A, Ramaswamy S, et al. dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes. Nucleic Acids Res. 2014;42:8939-53 pubmed publisher..These findings suggest that dREAM functions in the organization of transcriptional domains. ..