Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming

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• dc.contributor.author Krijger, Peter Hugo Lodewijkca
• dc.contributor.author Di Stefano, Bruno, 1984-ca
• dc.contributor.author de Wit, Elzoca
• dc.contributor.author Limone, Francescoca
• dc.contributor.author van Oevelen, Chrisca
• dc.contributor.author de Laat, Wouterca
• dc.contributor.author Graf, T. (Thomas)ca
• dc.date.accessioned 2016-06-01T13:33:53Z
• dc.date.available 2016-06-01T13:33:53Z
• dc.date.issued 2016
• dc.description.abstract Forced expression of reprogramming factors can convert somatic cells into induced pluripotent stem cells (iPSCs). Here we studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale topologically associated domain (TAD) repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic-cell-specific genome structures while establishing an embryonic stem-cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable recognition of their cell of origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin-dependent gene expression patterns.ca
• dc.description.sponsorship This work was supported by an NWO/CW TOP grant (714.012.002), an NWO VICI grant 724.012.003, a NanoNextNL grant, and a European Research Council Starting Grant (209700, ‘‘4C’’) to W.d.L.; a Ministerio de Educacion y Ciencia, SAF.2012-37167, Fundació La Marató TV3 120410, AGAUR SGR 1136, and European Research Council Synergy Grant (‘‘4D-Genome) to T.G.; and an ERC Stg (637587, ‘‘HAP-PHEN’’) to E.d.W
• dc.format.mimetype application/pdfca
• dc.identifier.citation Krijger PH, Di Stefano B, de Wit E, Limone F, van Oevelen C, de Laat W et al. Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming. Cell Stem Cell. 2016; 18(5): 597-610. DOI 10.1016/j.stem.2016.01.007ca
• dc.identifier.doi http://dx.doi.org/10.1016/j.stem.2016.01.007
• dc.identifier.issn 1934-5909
• dc.identifier.uri http://hdl.handle.net/10230/26793
• dc.language.iso engca
• dc.publisher Elsevierca
• dc.relation.ispartof Cell Stem Cell. 2016; 18(5): 597-610
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SAF2012-37167
• dc.rights This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/ca
• dc.subject.other Cèl·lules somàtiquesca
• dc.title Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogrammingca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca