{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T02:09:05Z","timestamp":1772503745537,"version":"3.50.1"},"reference-count":56,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2014,10,9]],"date-time":"2014-10-09T00:00:00Z","timestamp":1412812800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003877","type":"journal-article","created":{"date-parts":[[2014,10,9]],"date-time":"2014-10-09T17:59:29Z","timestamp":1412877569000},"page":"e1003877","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":58,"title":["Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling"],"prefix":"10.1371","volume":"10","author":[{"given":"Mariliis","family":"Tark-Dame","sequence":"first","affiliation":[]},{"given":"Hansjoerg","family":"Jerabek","sequence":"additional","affiliation":[]},{"given":"Erik M. M.","family":"Manders","sequence":"additional","affiliation":[]},{"given":"Dieter W.","family":"Heermann","sequence":"additional","affiliation":[]},{"given":"Roel","family":"van Driel","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,10,9]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/nsmb.2474","article-title":"Functional implications of genome topology","volume":"20","author":"G Cavalli","year":"2013","journal-title":"Nature structural & molecular biology"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.molcel.2013.02.011","article-title":"The Hierarchy of the 3D Genome","volume":"49","author":"JH Gibcus","year":"2013","journal-title":"Molecular Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1146\/annurev-genom-091212-153515","article-title":"The spatial organization of the human genome","volume":"14","author":"WA Bickmore","year":"2013","journal-title":"Annual review of genomics and human genetics"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/35066075","article-title":"Chromosome territories, nuclear architecture and gene regulation in mammalian cells","volume":"2","author":"T Cremer","year":"2001","journal-title":"Nature reviews Genetics"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"a003889","DOI":"10.1101\/cshperspect.a003889","article-title":"Chromosome territories","volume":"2","author":"T Cremer","year":"2010","journal-title":"Cold Spring Harbor perspectives in biology"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1016\/j.gde.2007.08.008","article-title":"Functional organisation of the genome during interphase","volume":"17","author":"A Pombo","year":"2007","journal-title":"Current opinion in genetics & development"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1038\/nature11082","article-title":"Topological domains in mammalian genomes identified by analysis of chromatin interactions","volume":"485","author":"JR Dixon","year":"2012","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.cell.2012.01.010","article-title":"Three-dimensional folding and functional organization principles of the Drosophila genome","volume":"148","author":"T Sexton","year":"2012","journal-title":"Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the X-inactivation centre","volume":"485","author":"EP Nora","year":"2012","journal-title":"Nature"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1016\/j.molcel.2012.08.031","article-title":"Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains","volume":"48","author":"C Hou","year":"2012","journal-title":"Molecular cell"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.cell.2013.04.053","article-title":"Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment","volume":"153","author":"JE Phillips-Cremins","year":"2013","journal-title":"Cell"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"9470","DOI":"10.1093\/nar\/gks736","article-title":"3D chromatin conformation correlates with replication timing and is conserved in resting cells","volume":"40","author":"B Moindrot","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1101\/gr.099655.109","article-title":"Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types","volume":"20","author":"T Ryba","year":"2010","journal-title":"Genome research"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1007\/s10577-009-9100-8","article-title":"Domain-wide regulation of DNA replication timing during mammalian development","volume":"18","author":"BD Pope","year":"2010","journal-title":"Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"4690","DOI":"10.1016\/j.jmb.2013.04.014","article-title":"The replication domain model: regulating replicon firing in the context of large-scale chromosome architecture","volume":"425","author":"BD Pope","year":"2013","journal-title":"Journal of molecular biology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1073\/pnas.0809501106","article-title":"Spatially confined folding of chromatin in the interphase nucleus","volume":"106","author":"J Mateos-Langerak","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nature12593","article-title":"Single-cell Hi-C reveals cell-to-cell variability in chromosome structure","volume":"502","author":"T Nagano","year":"2013","journal-title":"Nature"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1242\/jcs.077628","article-title":"Chromatin folding\u2013from biology to polymer models and back","volume":"124","author":"M Tark-Dame","year":"2011","journal-title":"Journal of cell science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.gde.2012.01.006","article-title":"Higher-order chromatin structure: bridging physics and biology","volume":"22","author":"G Fudenberg","year":"2012","journal-title":"Current opinion in genetics & development"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/B978-0-12-800046-5.00013-8","article-title":"Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture","volume":"307","author":"S Huet","year":"2014","journal-title":"International review of cell and molecular biology"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/B978-0-12-800046-5.00009-6","article-title":"Computational models of large-scale genome architecture","volume":"307","author":"A Rosa","year":"2014","journal-title":"International review of cell and molecular biology"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range interactions reveals folding principles of the human genome","volume":"326","author":"E Lieberman-Aiden","year":"2009","journal-title":"Science (New York, NY)"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s10577-010-9177-0","article-title":"The fractal globule as a model of chromatin architecture in the cell","volume":"19","author":"LA Mirny","year":"2011","journal-title":"Chromosome research: an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/nrg3454","article-title":"Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data","volume":"14","author":"J Dekker","year":"2013","journal-title":"Nature reviews Genetics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"e12218","DOI":"10.1371\/journal.pone.0012218","article-title":"Diffusion-driven looping provides a consistent framework for chromatin organization","volume":"5","author":"M Bohn","year":"2010","journal-title":"PloS one"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1016\/j.ymeth.2012.04.010","article-title":"A model for the 3D chromatin architecture of pro and eukaryotes","volume":"58","author":"DW Heermann","year":"2012","journal-title":"Methods (San Diego, Calif)"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e14428","DOI":"10.1371\/journal.pone.0014428","article-title":"Repulsive forces between looping chromosomes induce entropy-driven segregation","volume":"6","author":"M Bohn","year":"2011","journal-title":"PloS one"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.ceb.2011.03.010","article-title":"Physical nuclear organization: loops and entropy","volume":"23","author":"DW Heermann","year":"2011","journal-title":"Current opinion in cell biology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1016\/j.cell.2013.02.010","article-title":"Chromatin movement in the maintenance of genome stability","volume":"152","author":"V Dion","year":"2013","journal-title":"Cell"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e37525","DOI":"10.1371\/journal.pone.0037525","article-title":"Expression-dependent folding of interphase chromatin","volume":"7","author":"H Jerabek","year":"2012","journal-title":"PloS one"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"20120369","DOI":"10.1098\/rstb.2012.0369","article-title":"CTCF: the protein, the binding partners, the binding sites and their chromatin loops","volume":"368","author":"SJB Holwerda","year":"2013","journal-title":"Philosophical transactions of the Royal Society of London Series B, Biological sciences"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.ceb.2013.02.003","article-title":"Cohesin at active genes: a unifying theme for cohesin and gene expression from model organisms to humans","volume":"25","author":"D Dorsett","year":"2013","journal-title":"Current opinion in cell biology"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1016\/j.cell.2013.02.029","article-title":"CTCF and cohesin: linking gene regulatory elements with their targets","volume":"152","author":"M Merkenschlager","year":"2013","journal-title":"Cell"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/nature06634","article-title":"Cohesin mediates transcriptional insulation by CCCTC-binding factor","volume":"451","author":"KS Wendt","year":"2008","journal-title":"Nature"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/j.cell.2008.01.011","article-title":"Cohesins functionally associate with CTCF on mammalian chromosome arms","volume":"132","author":"V Parelho","year":"2008","journal-title":"Cell"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1073\/pnas.1317788111","article-title":"Cohesin and CTCF Differentially Affect Chromatin Architecture and Gene Expression in Human Cells","volume":"111","author":"J Zuin","year":"2014","journal-title":"PNAS"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"3119","DOI":"10.1038\/emboj.2013.237","article-title":"Cohesin-mediated interactions organize chromosomal domain architecture","volume":"32","author":"S Sofueva","year":"2013","journal-title":"The EMBO journal"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1101\/gr.161620.113","article-title":"Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments","volume":"23","author":"VC Seitan","year":"2013","journal-title":"Genome research"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e1000739","DOI":"10.1371\/journal.pgen.1000739","article-title":"Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus","volume":"5","author":"R Nativio","year":"2009","journal-title":"PLoS genetics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3651","DOI":"10.1073\/pnas.0912087107","article-title":"Cell type specificity of chromatin organization mediated by CTCF and cohesin","volume":"107","author":"C Hou","year":"2010","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1101\/gr.100479.109","article-title":"A CTCF-independent role for cohesin in tissue-specific transcription","volume":"20","author":"D Schmidt","year":"2010","journal-title":"Genome research"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1126\/science.1056794","article-title":"The human transcriptome map: clustering of highly expressed genes in chromosomal domains","volume":"291","author":"H Caron","year":"2001","journal-title":"Science (New York, NY)"},{"key":"ref43","article-title":"Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse","author":"BD Pope","year":"2012","journal-title":"Human molecular genetics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"4475","DOI":"10.1128\/MCB.00208-07","article-title":"The three-dimensional structure of human interphase chromosomes is related to the transcriptome map","volume":"27","author":"S Goetze","year":"2007","journal-title":"Molecular and cellular biology"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1016\/j.cell.2011.11.013","article-title":"Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution","volume":"147","author":"HS Rhee","year":"2011","journal-title":"Cell"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1101\/gad.1634608","article-title":"Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP","volume":"22","author":"T Takizawa","year":"2008","journal-title":"Genes & development"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"a000588","DOI":"10.1101\/cshperspect.a000588","article-title":"Gene positioning","volume":"2","author":"C Ferrai","year":"2010","journal-title":"Cold Spring Harbor perspectives in biology"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/ng.857","article-title":"CTCF-mediated functional chromatin interactome in pluripotent cells","volume":"43","author":"L Handoko","year":"2011","journal-title":"Nature genetics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"16173","DOI":"10.1073\/pnas.1204799109","article-title":"Complexity of chromatin folding is captured by the strings and binders switch model","volume":"109","author":"M Barbieri","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"8783","DOI":"10.1093\/nar\/gks586","article-title":"A fractal model for nuclear organization: current evidence and biological implications","volume":"40","author":"A Bancaud","year":"2012","journal-title":"Nucleic acids research"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1083\/jcb.130.6.1239","article-title":"Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0\/G1 interphase nucleus","volume":"130","author":"H Yokota","year":"1995","journal-title":"The Journal of cell biology"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1126\/science.1236083","article-title":"Organization of the mitotic chromosome","volume":"342","author":"N Naumova","year":"2013","journal-title":"Science (New York, NY)"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1140\/epje\/i2005-10067-9","article-title":"Polymer chain models of DNA and chromatin","volume":"19","author":"J Langowski","year":"2006","journal-title":"The European physical journal E, Soft matter"},{"key":"ref54","doi-asserted-by":"crossref","unstructured":"Heermann DW, Binder K (2010) Monte Carlo Simulations in Statistical Physics. fifth. Heidelberg: Springer. doi:10.1007\/978-3-642-03163-2.","DOI":"10.1007\/978-3-642-03163-2"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2819","DOI":"10.1021\/ma00187a030","article-title":"The Bond Fluctuation Method: A New Effective Algorithm for the Dynamics of Polymers in All Spatial Dimensions","volume":"21","author":"I Carmesin","year":"1988","journal-title":"Macromolecules"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"2294","DOI":"10.1063\/1.459901","article-title":"Interdiffusion and self-diffusion in polymer mixtures: A Monte Carlo study","volume":"94","author":"HP Deutsch","year":"1991","journal-title":"J Chem Phys"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1004716","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2016,1,15]],"date-time":"2016-01-15T00:00:00Z","timestamp":1452816000000}}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003877","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T03:33:23Z","timestamp":1588995203000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003877"}},"subtitle":[],"editor":[{"given":"Marc A.","family":"Marti-Renom","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,10,9]]},"references-count":56,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2014,10,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003877","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1004716","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,9]]}}}