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Volumn 17, Issue 1, 2016, Pages

CTCF-mediated chromatin loops enclose inducible gene regulatory domains

Author keywords

Chromatin looping; CTCF; Enhancers; Gene regulation; Inducible genes; Transcription factory

Indexed keywords

RNA POLYMERASE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR CTCF; CCCTC-BINDING FACTOR; CHROMATIN; REPRESSOR PROTEIN;

EID: 85007578386     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2516-6     Document Type: Article
Times cited : (47)

References (69)
  • 1
    • 0025675441 scopus 로고
    • A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene
    • Lobanenkov VV, Nicolas RH, Adler VV, Paterson H, Klenova EM, Polotskaja AV, Goodwin GH. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5'-flanking sequence of the chicken c-myc gene. Oncogene. 1990;5:1743-53.
    • (1990) Oncogene , vol.5 , pp. 1743-1753
    • Lobanenkov, V.V.1    Nicolas, R.H.2    Adler, V.V.3    Paterson, H.4    Klenova, E.M.5    Polotskaja, A.V.6    Goodwin, G.H.7
  • 2
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: master weaver of the genome
    • Phillips JE, Corces VG. CTCF: master weaver of the genome. Cell. 2009;137: 1194-211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 3
    • 0033529654 scopus 로고    scopus 로고
    • The protein CTCF is required for the enhancer blocking activity of vertebrate insulators
    • Bell AC, West AG, Felsenfeld G. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell. 1999;98:387-96.
    • (1999) Cell , vol.98 , pp. 387-396
    • Bell, A.C.1    West, A.G.2    Felsenfeld, G.3
  • 5
    • 84878188440 scopus 로고    scopus 로고
    • Chromatin insulators: linking genome organization to cellular function
    • Phillips-Cremins JE, Corces VG. Chromatin insulators: linking genome organization to cellular function. Mol Cell. 2013;50:461-74.
    • (2013) Mol Cell , vol.50 , pp. 461-474
    • Phillips-Cremins, J.E.1    Corces, V.G.2
  • 6
  • 7
    • 84856619909 scopus 로고    scopus 로고
    • CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement
    • Feeney AJ, Verma-Gaur J. CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement. Cell Res. 2012;22:280-2.
    • (2012) Cell Res , vol.22 , pp. 280-282
    • Feeney, A.J.1    Verma-Gaur, J.2
  • 8
    • 77956645612 scopus 로고    scopus 로고
    • CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus
    • Majumder P, Boss JM. CTCF controls expression and chromatin architecture of the human major histocompatibility complex class II locus. Mol Cell Biol. 2010;30:4211-23.
    • (2010) Mol Cell Biol , vol.30 , pp. 4211-4223
    • Majumder, P.1    Boss, J.M.2
  • 9
    • 35649000946 scopus 로고    scopus 로고
    • Evidence that homologous Xchromosome pairing requires transcription and Ctcf protein
    • Xu N, Donohoe ME, Silva SS, Lee JT. Evidence that homologous Xchromosome pairing requires transcription and Ctcf protein. Nat Genet. 2007;39:1390-6.
    • (2007) Nat Genet , vol.39 , pp. 1390-1396
    • Xu, N.1    Donohoe, M.E.2    Silva, S.S.3    Lee, J.T.4
  • 12
    • 0027362621 scopus 로고
    • CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms
    • Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 1993;13: 7612-24.
    • (1993) Mol Cell Biol , vol.13 , pp. 7612-7624
    • Klenova, E.M.1    Nicolas, R.H.2    Paterson, H.F.3    Carne, A.F.4    Heath, C.M.5    Goodwin, G.H.6    Neiman, P.E.7    Lobanenkov, V.V.8
  • 20
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84-98.
    • (2012) Cell , vol.148 , pp. 84-98
    • Li, G.1    Ruan, X.2    Auerbach, R.K.3    Sandhu, K.S.4    Zheng, M.5    Wang, P.6    Poh, H.M.7    Goh, Y.8    Lim, J.9    Zhang, J.10
  • 22
    • 84864008380 scopus 로고    scopus 로고
    • Dynamic reconfiguration of long human genes during one transcription cycle
    • Larkin JD, Cook PR, Papantonis A. Dynamic reconfiguration of long human genes during one transcription cycle. Mol Cell Biol. 2012;32:2738-47.
    • (2012) Mol Cell Biol , vol.32 , pp. 2738-2747
    • Larkin, J.D.1    Cook, P.R.2    Papantonis, A.3
  • 25
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 27
    • 84924533047 scopus 로고    scopus 로고
    • Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture
    • Vietri Rudan M, Barrington C, Henderson S, Ernst C, Odom DT, Tanay A, et al. Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture. Cell Rep. 2015;10:1297-309.
    • (2015) Cell Rep , vol.10 , pp. 1297-1309
    • Vietri Rudan, M.1    Barrington, C.2    Henderson, S.3    Ernst, C.4    Odom, D.T.5    Tanay, A.6
  • 28
    • 70450222694 scopus 로고    scopus 로고
    • A model for all genomes: the role of transcription factories
    • Cook PR. A model for all genomes: the role of transcription factories. J Mol Biol. 2010;395:1-10.
    • (2010) J Mol Biol , vol.395 , pp. 1-10
    • Cook, P.R.1
  • 29
    • 84873581550 scopus 로고    scopus 로고
    • H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
    • Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell. 2013;12:180-92.
    • (2013) Cell Stem Cell , vol.12 , pp. 180-192
    • Hu, G.1    Cui, K.2    Northrup, D.3    Liu, C.4    Wang, C.5    Tang, Q.6    Ge, K.7    Levens, D.8    Crane-Robinson, C.9    Zhao, K.10
  • 30
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: automating chromatin-state discovery and characterization
    • Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012;9:215-6.
    • (2012) Nat Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 32
    • 33845631171 scopus 로고    scopus 로고
    • 'Genome design' model and multicellular complexity: golden middle
    • Vinogradov AE. 'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res. 2006;34:5906-14.
    • (2006) Nucleic Acids Res , vol.34 , pp. 5906-5914
    • Vinogradov, A.E.1
  • 34
    • 84884416048 scopus 로고    scopus 로고
    • Human housekeeping genes, revisited
    • Eisenberg E, Levanon EY. Human housekeeping genes, revisited. Trends Genet. 2013;29:569-74.
    • (2013) Trends Genet , vol.29 , pp. 569-574
    • Eisenberg, E.1    Levanon, E.Y.2
  • 39
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-80.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 44
  • 46
    • 84939240549 scopus 로고    scopus 로고
    • A CTCF Code for 3D Genome Architecture
    • Nichols MH, Corces VG. A CTCF Code for 3D Genome Architecture. Cell. 2015;162:703-5.
    • (2015) Cell , vol.162 , pp. 703-705
    • Nichols, M.H.1    Corces, V.G.2
  • 48
    • 79952259195 scopus 로고    scopus 로고
    • Fixing the model for transcription: the DNA moves, not the polymerase
    • Papantonis A, Cook PR. Fixing the model for transcription: the DNA moves, not the polymerase. Transcription. 2011;2:41-4.
    • (2011) Transcription , vol.2 , pp. 41-44
    • Papantonis, A.1    Cook, P.R.2
  • 55
    • 84889005653 scopus 로고    scopus 로고
    • Transcription factories: genome organization and gene regulation
    • Papantonis A, Cook PR. Transcription factories: genome organization and gene regulation. Chem Rev. 2013;113:8683-705.
    • (2013) Chem Rev , vol.113 , pp. 8683-8705
    • Papantonis, A.1    Cook, P.R.2
  • 56
    • 84906877432 scopus 로고    scopus 로고
    • Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation
    • Battistelli C, Busanello A, Maione R. Functional interplay between MyoD and CTCF in regulating long-range chromatin interactions during differentiation. J Cell Sci. 2014;127:3757-67.
    • (2014) J Cell Sci , vol.127 , pp. 3757-3767
    • Battistelli, C.1    Busanello, A.2    Maione, R.3
  • 62
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-2.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 64
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: accounting for selection bias
    • Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11:R14.
    • (2010) Genome Biol , vol.11 , pp. R14
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 67
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: scanning for occurrences of a given motif
    • Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27:1017-8.
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 69
    • 85007514436 scopus 로고    scopus 로고
    • CTCF loop analysis and prediction scripts and datasets
    • Oti M. CTCF loop analysis and prediction scripts and datasets. Zenodo. 2015. doi:10.5281/zenodo.29423.
    • (2015) Zenodo
    • Oti, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.