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

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 doma...

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Detalles Bibliográficos
Autores: Krijger, Peter Hugo Lodewijk, Di Stefano, Bruno, 1984-, de Wit, Elzo, Limone, Francesco, van Oevelen, Chris, de Laat, Wouter, Graf, T. (Thomas)
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2016
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/26793
Acceso en línea:http://hdl.handle.net/10230/26793
http://dx.doi.org/10.1016/j.stem.2016.01.007
Access Level:acceso abierto
Palabra clave:Cèl·lules somàtiques
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spelling Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogrammingKrijger, Peter Hugo LodewijkDi Stefano, Bruno, 1984-de Wit, ElzoLimone, Francescovan Oevelen, Chrisde Laat, WouterGraf, T. (Thomas)Cèl·lules somàtiquesForced 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.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.WElsevier201620162016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/26793http://dx.doi.org/10.1016/j.stem.2016.01.007reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésCell Stem Cell. 2016; 18(5): 597-610info:eu-repo/grantAgreement/ES/3PN/SAF2012-37167This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/267932026-05-29T05:05:01Z
dc.title.none.fl_str_mv Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
title Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
spellingShingle Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
Krijger, Peter Hugo Lodewijk
Cèl·lules somàtiques
title_short Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
title_full Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
title_fullStr Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
title_full_unstemmed Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
title_sort Cell-of-origin-specific 3D genome structure acquired during somatic cell reprogramming
dc.creator.none.fl_str_mv Krijger, Peter Hugo Lodewijk
Di Stefano, Bruno, 1984-
de Wit, Elzo
Limone, Francesco
van Oevelen, Chris
de Laat, Wouter
Graf, T. (Thomas)
author Krijger, Peter Hugo Lodewijk
author_facet Krijger, Peter Hugo Lodewijk
Di Stefano, Bruno, 1984-
de Wit, Elzo
Limone, Francesco
van Oevelen, Chris
de Laat, Wouter
Graf, T. (Thomas)
author_role author
author2 Di Stefano, Bruno, 1984-
de Wit, Elzo
Limone, Francesco
van Oevelen, Chris
de Laat, Wouter
Graf, T. (Thomas)
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv Cèl·lules somàtiques
topic Cèl·lules somàtiques
description 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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016
2016
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/26793
http://dx.doi.org/10.1016/j.stem.2016.01.007
url http://hdl.handle.net/10230/26793
http://dx.doi.org/10.1016/j.stem.2016.01.007
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Cell Stem Cell. 2016; 18(5): 597-610
info:eu-repo/grantAgreement/ES/3PN/SAF2012-37167
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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