메뉴 건너뛰기




Volumn 10, Issue 10, 2014, Pages

Erratum: Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling (PLoS Comput Biol (2014) 10:10 (e1003877) DOI: 10.1371/journal.pcbi.1003877);Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling

Author keywords

[No Author keywords available]

Indexed keywords

COMPACTION; GENE EXPRESSION REGULATION; TRANSCRIPTION;

EID: 84908352990     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/JOURNAL.PCBI.1004716     Document Type: Erratum
Times cited : (53)

References (56)
  • 2
    • 84876838711 scopus 로고    scopus 로고
    • The Hierarchy of the 3D Genome
    • Gibcus JH, Dekker J, (2013) The Hierarchy of the 3D Genome. Molecular Cell 49: 773–782 doi:10.1016/j.molcel.2013.02.011
    • (2013) Molecular Cell , vol.49 , pp. 773-782
    • Gibcus, J.H.1    Dekker, J.2
  • 3
    • 84884294269 scopus 로고    scopus 로고
    • The spatial organization of the human genome
    • Bickmore WA, (2013) The spatial organization of the human genome. Annual review of genomics and human genetics 14: 67–84 doi:10.1146/annurev-genom-091212-153515
    • (2013) Annual review of genomics and human genetics , vol.14 , pp. 67-84
    • Bickmore, W.A.1
  • 4
    • 0035316574 scopus 로고    scopus 로고
    • Chromosome territories, nuclear architecture and gene regulation in mammalian cells
    • Cremer T, Cremer C, (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature reviews Genetics 2: 292–301 doi:10.1038/35066075
    • (2001) Nature reviews Genetics , vol.2 , pp. 292-301
    • Cremer, T.1    Cremer, C.2
  • 6
    • 35548975211 scopus 로고    scopus 로고
    • Functional organisation of the genome during interphase
    • Pombo A, Branco MR, (2007) Functional organisation of the genome during interphase. Current opinion in genetics & development 17: 451–455 doi:10.1016/j.gde.2007.08.008
    • (2007) Current opinion in genetics & development , vol.17 , pp. 451-455
    • Pombo, A.1    Branco, M.R.2
  • 7
    • 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, et al. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485: 376–380 doi:10.1038/nature11082
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5
  • 8
    • 84856747483 scopus 로고    scopus 로고
    • Three-dimensional folding and functional organization principles of the Drosophila genome
    • Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, et al. (2012) Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148: 458–472 doi:10.1016/j.cell.2012.01.010
    • (2012) Cell , vol.148 , pp. 458-472
    • Sexton, T.1    Yaffe, E.2    Kenigsberg, E.3    Bantignies, F.4    Leblanc, B.5
  • 9
    • 84861100147 scopus 로고    scopus 로고
    • Spatial partitioning of the regulatory landscape of the X-inactivation centre
    • Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, et al. (2012) Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 485: 381–385 doi:10.1038/nature11049
    • (2012) Nature , vol.485 , pp. 381-385
    • Nora, E.P.1    Lajoie, B.R.2    Schulz, E.G.3    Giorgetti, L.4    Okamoto, I.5
  • 10
    • 84869003748 scopus 로고    scopus 로고
    • Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains
    • Hou C, Li L, Qin ZS, Corces VG, (2012) Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Molecular cell 48: 471–484 doi:10.1016/j.molcel.2012.08.031
    • (2012) Molecular cell , vol.48 , pp. 471-484
    • Hou, C.1    Li, L.2    Qin, Z.S.3    Corces, V.G.4
  • 11
    • 84878860751 scopus 로고    scopus 로고
    • Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
    • Phillips-Cremins JE, Sauria MEG, Sanyal A, Gerasimova TI, Lajoie BR, et al. (2013) Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment. Cell 153: 1281–1295 doi:10.1016/j.cell.2013.04.053
    • (2013) Cell , vol.153 , pp. 1281-1295
    • Phillips-Cremins, J.E.1    Sauria, M.E.G.2    Sanyal, A.3    Gerasimova, T.I.4    Lajoie, B.R.5
  • 12
    • 84868127488 scopus 로고    scopus 로고
    • 3D chromatin conformation correlates with replication timing and is conserved in resting cells
    • Moindrot B, Audit B, Klous P, Baker A, Thermes C, et al. (2012) 3D chromatin conformation correlates with replication timing and is conserved in resting cells. Nucleic Acids Research 40: 9470–9481 doi:10.1093/nar/gks736
    • (2012) Nucleic Acids Research , vol.40 , pp. 9470-9481
    • Moindrot, B.1    Audit, B.2    Klous, P.3    Baker, A.4    Thermes, C.5
  • 13
    • 77952994784 scopus 로고    scopus 로고
    • Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
    • Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, et al. (2010) Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome research 20: 761–770 doi:10.1101/gr.099655.109
    • (2010) Genome research , vol.20 , pp. 761-770
    • Ryba, T.1    Hiratani, I.2    Lu, J.3    Itoh, M.4    Kulik, M.5
  • 15
    • 84887402678 scopus 로고    scopus 로고
    • The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture
    • Pope BD, Gilbert DM, (2013) The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture. Journal of molecular biology 425: 4690–4695 doi:10.1016/j.jmb.2013.04.014
    • (2013) Journal of molecular biology , vol.425 , pp. 4690-4695
    • Pope, B.D.1    Gilbert, D.M.2
  • 17
    • 84885617426 scopus 로고    scopus 로고
    • Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
    • Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, et al. (2013) Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502: 59–64 doi:10.1038/nature12593
    • (2013) Nature , vol.502 , pp. 59-64
    • Nagano, T.1    Lubling, Y.2    Stevens, T.J.3    Schoenfelder, S.4    Yaffe, E.5
  • 18
    • 79952807125 scopus 로고    scopus 로고
    • Chromatin folding–from biology to polymer models and back
    • Tark-Dame M, Van Driel R, Heermann DW, (2011) Chromatin folding–from biology to polymer models and back. Journal of cell science 124: 839–845 doi:10.1242/jcs.077628
    • (2011) Journal of cell science , vol.124 , pp. 839-845
    • Tark-Dame, M.1    Van Driel, R.2    Heermann, D.W.3
  • 19
    • 84860381688 scopus 로고    scopus 로고
    • Higher-order chromatin structure: bridging physics and biology
    • Fudenberg G, Mirny LA, (2012) Higher-order chromatin structure: bridging physics and biology. Current opinion in genetics & development 22: 115–124 doi:10.1016/j.gde.2012.01.006
    • (2012) Current opinion in genetics & development , vol.22 , pp. 115-124
    • Fudenberg, G.1    Mirny, L.A.2
  • 20
  • 21
    • 84891109077 scopus 로고    scopus 로고
    • Computational models of large-scale genome architecture
    • Rosa A, Zimmer C, (2014) Computational models of large-scale genome architecture. International review of cell and molecular biology 307: 275–349 doi:10.1016/B978-0-12-800046-5.00009-6
    • (2014) International review of cell and molecular biology , vol.307 , pp. 275-349
    • Rosa, A.1    Zimmer, C.2
  • 22
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, NY) 326: 289–293 doi:10.1126/science.1181369
    • (2009) Science (New York, NY) , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    Van Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5
  • 24
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
    • Dekker J, Marti-Renom MA, Mirny LA, (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nature reviews Genetics 14: 390–403 doi:10.1038/nrg3454
    • (2013) Nature reviews Genetics , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 25
    • 77957867310 scopus 로고    scopus 로고
    • Diffusion-driven looping provides a consistent framework for chromatin organization
    • Bohn M, Heermann DW, (2010) Diffusion-driven looping provides a consistent framework for chromatin organization. PloS one 5: e12218 doi:10.1371/journal.pone.0012218
    • (2010) PloS one , vol.5 , pp. e12218
    • Bohn, M.1    Heermann, D.W.2
  • 26
    • 84870387601 scopus 로고    scopus 로고
    • A model for the 3D chromatin architecture of pro and eukaryotes
    • Heermann DW, Jerabek H, Liu L, Li Y, (2012) A model for the 3D chromatin architecture of pro and eukaryotes. Methods (San Diego, Calif) 58: 307–314 doi:10.1016/j.ymeth.2012.04.010
    • (2012) Methods (San Diego, Calif) , vol.58 , pp. 307-314
    • Heermann, D.W.1    Jerabek, H.2    Liu, L.3    Li, Y.4
  • 27
    • 79251574319 scopus 로고    scopus 로고
    • Repulsive forces between looping chromosomes induce entropy-driven segregation
    • Bohn M, Heermann DW, (2011) Repulsive forces between looping chromosomes induce entropy-driven segregation. PloS one 6: e14428 doi:10.1371/journal.pone.0014428
    • (2011) PloS one , vol.6 , pp. e14428
    • Bohn, M.1    Heermann, D.W.2
  • 28
    • 79957818768 scopus 로고    scopus 로고
    • Physical nuclear organization: loops and entropy
    • Heermann DW, (2011) Physical nuclear organization: loops and entropy. Current opinion in cell biology 23: 332–337 doi:10.1016/j.ceb.2011.03.010
    • (2011) Current opinion in cell biology , vol.23 , pp. 332-337
    • Heermann, D.W.1
  • 29
    • 84875207723 scopus 로고    scopus 로고
    • Chromatin movement in the maintenance of genome stability
    • Dion V, Gasser SM, (2013) Chromatin movement in the maintenance of genome stability. Cell 152: 1355–1364 doi:10.1016/j.cell.2013.02.010
    • (2013) Cell , vol.152 , pp. 1355-1364
    • Dion, V.1    Gasser, S.M.2
  • 30
    • 84861389548 scopus 로고    scopus 로고
    • Expression-dependent folding of interphase chromatin
    • Jerabek H, Heermann DW, (2012) Expression-dependent folding of interphase chromatin. PloS one 7: e37525 doi:10.1371/journal.pone.0037525
    • (2012) PloS one , vol.7 , pp. e37525
    • Jerabek, H.1    Heermann, D.W.2
  • 32
    • 84879208137 scopus 로고    scopus 로고
    • Cohesin at active genes: a unifying theme for cohesin and gene expression from model organisms to humans
    • Dorsett D, Merkenschlager M, (2013) Cohesin at active genes: a unifying theme for cohesin and gene expression from model organisms to humans. Current opinion in cell biology 25: 327–333 doi:10.1016/j.ceb.2013.02.003
    • (2013) Current opinion in cell biology , vol.25 , pp. 327-333
    • Dorsett, D.1    Merkenschlager, M.2
  • 33
    • 84875127327 scopus 로고    scopus 로고
    • CTCF and cohesin: linking gene regulatory elements with their targets
    • Merkenschlager M, Odom DT, (2013) CTCF and cohesin: linking gene regulatory elements with their targets. Cell 152: 1285–1297 doi:10.1016/j.cell.2013.02.029
    • (2013) Cell , vol.152 , pp. 1285-1297
    • Merkenschlager, M.1    Odom, D.T.2
  • 34
    • 39149121436 scopus 로고    scopus 로고
    • Cohesin mediates transcriptional insulation by CCCTC-binding factor
    • Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, et al. (2008) Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451: 796–801 doi:10.1038/nature06634
    • (2008) Nature , vol.451 , pp. 796-801
    • Wendt, K.S.1    Yoshida, K.2    Itoh, T.3    Bando, M.4    Koch, B.5
  • 35
    • 38849121606 scopus 로고    scopus 로고
    • Cohesins functionally associate with CTCF on mammalian chromosome arms
    • Parelho V, Hadjur S, Spivakov M, Leleu M, Sauer S, et al. (2008) Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132: 422–433 doi:10.1016/j.cell.2008.01.011
    • (2008) Cell , vol.132 , pp. 422-433
    • Parelho, V.1    Hadjur, S.2    Spivakov, M.3    Leleu, M.4    Sauer, S.5
  • 36
    • 84892934183 scopus 로고    scopus 로고
    • Cohesin and CTCF Differentially Affect Chromatin Architecture and Gene Expression in Human Cells
    • Zuin J, Dixon JR, Van der Reijden MIJA, Ye Z, Kolovos P, et al. (2014) Cohesin and CTCF Differentially Affect Chromatin Architecture and Gene Expression in Human Cells. PNAS 111: 996–1001.
    • (2014) PNAS , vol.111 , pp. 996-1001
    • Zuin, J.1    Dixon, J.R.2    Van Der Reijden, M.I.J.A.3    Ye, Z.4    Kolovos, P.5
  • 37
    • 84890566970 scopus 로고    scopus 로고
    • Cohesin-mediated interactions organize chromosomal domain architecture
    • Sofueva S, Yaffe E, Chan W-C, Georgopoulou D, Vietri Rudan M, et al. (2013) Cohesin-mediated interactions organize chromosomal domain architecture. The EMBO journal 32: 3119–3129 doi:10.1038/emboj.2013.237
    • (2013) The EMBO journal , vol.32 , pp. 3119-3129
    • Sofueva, S.1    Yaffe, E.2    Chan, W.-C.3    Georgopoulou, D.4    Vietri Rudan, M.5
  • 38
    • 84890504911 scopus 로고    scopus 로고
    • Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
    • Seitan VC, Faure AJ, Zhan Y, McCord RP, Lajoie BR, et al. (2013) Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome research 23: 2066–2077 doi:10.1101/gr.161620.113
    • (2013) Genome research , vol.23 , pp. 2066-2077
    • Seitan, V.C.1    Faure, A.J.2    Zhan, Y.3    McCord, R.P.4    Lajoie, B.R.5
  • 39
    • 73649145481 scopus 로고    scopus 로고
    • Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus
    • Nativio R, Wendt KS, Ito Y, Huddleston JE, Uribe-Lewis S, et al. (2009) Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus. PLoS genetics 5: e1000739 doi:10.1371/journal.pgen.1000739
    • (2009) PLoS genetics , vol.5 , pp. e1000739
    • Nativio, R.1    Wendt, K.S.2    Ito, Y.3    Huddleston, J.E.4    Uribe-Lewis, S.5
  • 41
    • 77951836691 scopus 로고    scopus 로고
    • A CTCF-independent role for cohesin in tissue-specific transcription
    • Schmidt D, Schwalie PC, Ross-Innes CS, Hurtado A, Brown GD, et al. (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome research 20: 578–588 doi:10.1101/gr.100479.109
    • (2010) Genome research , vol.20 , pp. 578-588
    • Schmidt, D.1    Schwalie, P.C.2    Ross-Innes, C.S.3    Hurtado, A.4    Brown, G.D.5
  • 42
    • 0035895502 scopus 로고    scopus 로고
    • The human transcriptome map: clustering of highly expressed genes in chromosomal domains
    • Caron H, Van Schaik B, Van der Mee M, Baas F, Riggins G, et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science (New York, NY) 291: 1289–1292 doi:10.1126/science.1056794
    • (2001) Science (New York, NY) , vol.291 , pp. 1289-1292
    • Caron, H.1    Van Schaik, B.2    Van Der Mee, M.3    Baas, F.4    Riggins, G.5
  • 43
    • 84866421324 scopus 로고    scopus 로고
    • Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse
    • Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, et al. (2012) Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Human molecular genetics doi:10.1093/hmg/dds232
    • (2012) Human molecular genetics
    • Pope, B.D.1    Chandra, T.2    Buckley, Q.3    Hoare, M.4    Ryba, T.5
  • 44
    • 34250172721 scopus 로고    scopus 로고
    • The three-dimensional structure of human interphase chromosomes is related to the transcriptome map
    • Goetze S, Mateos-Langerak J, Gierman HJ, De Leeuw W, Giromus O, et al. (2007) The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Molecular and cellular biology 27: 4475–4487 doi:10.1128/MCB.00208-07
    • (2007) Molecular and cellular biology , vol.27 , pp. 4475-4487
    • Goetze, S.1    Mateos-Langerak, J.2    Gierman, H.J.3    De Leeuw, W.4    Giromus, O.5
  • 45
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
    • Rhee HS, Pugh BF, (2011) Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell 147: 1408–1419 doi:10.1016/j.cell.2011.11.013
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 46
    • 39449123232 scopus 로고    scopus 로고
    • Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP
    • Takizawa T, Gudla PR, Guo L, Lockett S, Misteli T, (2008) Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP. Genes & development 22: 489–498 doi:10.1101/gad.1634608
    • (2008) Genes & development , vol.22 , pp. 489-498
    • Takizawa, T.1    Gudla, P.R.2    Guo, L.3    Lockett, S.4    Misteli, T.5
  • 48
    • 79959699992 scopus 로고    scopus 로고
    • CTCF-mediated functional chromatin interactome in pluripotent cells
    • Handoko L, Xu H, Li G, Ngan CY, Chew E, et al. (2011) CTCF-mediated functional chromatin interactome in pluripotent cells. Nature genetics 43: 630–638 doi:10.1038/ng.857
    • (2011) Nature genetics , vol.43 , pp. 630-638
    • Handoko, L.1    Xu, H.2    Li, G.3    Ngan, C.Y.4    Chew, E.5
  • 50
    • 84867498711 scopus 로고    scopus 로고
    • A fractal model for nuclear organization: current evidence and biological implications
    • Bancaud A, Lavelle C, Huet S, Ellenberg J, (2012) A fractal model for nuclear organization: current evidence and biological implications. Nucleic acids research 40: 8783–8792 doi:10.1093/nar/gks586
    • (2012) Nucleic acids research , vol.40 , pp. 8783-8792
    • Bancaud, A.1    Lavelle, C.2    Huet, S.3    Ellenberg, J.4
  • 51
    • 0029129565 scopus 로고
    • Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus
    • Yokota H, Van den Engh G, Hearst JE, Sachs RK, Trask BJ, (1995) Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus. The Journal of cell biology 130: 1239–1249.
    • (1995) The Journal of cell biology , vol.130 , pp. 1239-1249
    • Yokota, H.1    Van Den Engh, G.2    Hearst, J.E.3    Sachs, R.K.4    Trask, B.J.5
  • 53
    • 33645286183 scopus 로고    scopus 로고
    • Polymer chain models of DNA and chromatin
    • Langowski J, (2006) Polymer chain models of DNA and chromatin. The European physical journal E, Soft matter 19: 241–249 doi:10.1140/epje/i2005-10067-9
    • (2006) The European physical journal E, Soft matter , vol.19 , pp. 241-249
    • Langowski, J.1
  • 54
    • 0004147488 scopus 로고    scopus 로고
    • Monte Carlo Simulations in Statistical Physics
    • Heermann DW, Binder K (2010) Monte Carlo Simulations in Statistical Physics. fifth. Heidelberg: Springer. doi:10.1007/978-3-642-03163-2.
    • (2010)
    • Heermann, D.W.1    Binder, K.2
  • 55
    • 0024071054 scopus 로고
    • The Bond Fluctuation Method: A New Effective Algorithm for the Dynamics of Polymers in All Spatial Dimensions
    • Carmesin I, Kremer K, (1988) The Bond Fluctuation Method: A New Effective Algorithm for the Dynamics of Polymers in All Spatial Dimensions. Macromolecules 21: 2819–2823.
    • (1988) Macromolecules , vol.21 , pp. 2819-2823
    • Carmesin, I.1    Kremer, K.2
  • 56
    • 18644371834 scopus 로고
    • Interdiffusion and self-diffusion in polymer mixtures: A Monte Carlo study
    • Deutsch HP, Binder K, (1991) Interdiffusion and self-diffusion in polymer mixtures: A Monte Carlo study. J Chem Phys 94: 2294–2304.
    • (1991) J Chem Phys , vol.94 , pp. 2294-2304
    • Deutsch, H.P.1    Binder, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.