Show simple item record

dc.contributor.authorQi, Yifeng
dc.contributor.authorZhang, Bin
dc.date.accessioned2020-05-22T13:49:31Z
dc.date.available2020-05-22T13:49:31Z
dc.date.issued2019-06
dc.identifier.issn1553-7358
dc.identifier.issn1553-734X
dc.identifier.urihttps://hdl.handle.net/1721.1/125406
dc.description.abstractWe introduce a computational model to simulate chromatin structure and dynamics. Starting from one-dimensional genomics and epigenomics data that are available for hundreds of cell types, this model enables de novo prediction of chromatin structures at five-kilo-base resolution. Simulated chromatin structures recapitulate known features of genome organization, including the formation of chromatin loops, topologically associating domains (TADs) and compartments, and are in quantitative agreement with chromosome conformation capture experiments and super-resolution microscopy measurements. Detailed characterization of the predicted structural ensemble reveals the dynamical flexibility of chromatin loops and the presence of cross-talk among neighboring TADs. Analysis of the model’s energy function uncovers distinct mechanisms for chromatin folding at various length scales and suggests a need to go beyond simple A/B compartment types to predict specific contacts between regulatory elements using polymer simulations.en_US
dc.description.sponsorshipNational Science Foundation (U.S.) (Grant MCB-1715859)en_US
dc.language.isoen
dc.publisherPublic Library of Science (PLoS)en_US
dc.relation.isversionof10.1371/journal.pcbi.1007024en_US
dc.rightsCreative Commons Attribution 4.0 International licenseen_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.sourcePLoSen_US
dc.titlePredicting three-dimensional genome organization with chromatin statesen_US
dc.typeArticleen_US
dc.identifier.citationQi, Yifeng and Bin Zhang. “Predicting three-dimensional genome organization with chromatin states.” PLOS computational biology 15 (2019): e1007024 © 2019 The Author(s)en_US
dc.contributor.departmentMassachusetts Institute of Technology. Department of Chemistryen_US
dc.relation.journalPLOS computational biologyen_US
dc.eprint.versionFinal published versionen_US
dc.type.urihttp://purl.org/eprint/type/JournalArticleen_US
eprint.statushttp://purl.org/eprint/status/PeerRevieweden_US
dc.date.updated2020-01-14T14:12:14Z
dspace.date.submission2020-01-14T14:12:16Z
mit.journal.volume15en_US
mit.journal.issue6en_US


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record