Promoter-like epigenetic signatures in exons displaying cell type-specific splicing

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• dc.contributor.author Curado, Joaoca
• dc.contributor.author Iannone, Camilla, 1984-ca
• dc.contributor.author Tilgner, Hagen, 1980-ca
• dc.contributor.author Valcárcel, J. (Juan)ca
• dc.contributor.author Guigó Serra, Rodericca
• dc.date.accessioned 2015-11-20T10:03:58Z
• dc.date.available 2015-11-20T10:03:58Z
• dc.date.issued 2015ca
• dc.description Un erratum d'aquest article s'ha publicat a Erratum to: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing-Genome biology, 2016, 17(1), 52. DOI: 10.1186/s13059-016-0890-7 i també està disponible a http://hdl.handle.net/10230/26093
• dc.description.abstract Background. Pre-mRNA splicing occurs mainly co-transcriptionally, and both nucleosome density and histone modifications have been proposed to play a role in splice site recognition and regulation. However, the extent and mechanisms behind this interplay remain poorly understood./nResults. We use transcriptomic and epigenomic data generated by the ENCODE project to investigate the association between chromatin structure and alternative splicing. We find a strong and significant positive association between H3K9ac, H3K27ac, H3K4me3, epigenetic marks characteristic of active promoters, and exon inclusion in a small but well-defined class of exons, representing approximately 4 % of all regulated exons. These exons are systematically maintained at comparatively low levels of inclusion across cell types, but their inclusion is significantly enhanced in particular cell types when in physical proximity to active promoters./nConclusion. Histone modifications and other chromatin features that activate transcription can be co-opted to participate in the regulation of the splicing of exons that are in physical proximity to promoter regions.
• dc.description.sponsorship We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’, SEV-2012-0208. JC was supported by a SFRH/BD/33535/2008 from the Portuguese Foundation to Science and Technology. CI was supported by a La Caixa predoctoral fellowship. Work in JV’s lab was supported by Fundación Botín, by Banco de Santander through its Santander Universities Global Division and by Consolider RNAREG, MINECO, and AGAUR. We thank Anshul Kundaje, Ben Brown, Michael Snyder, Thomas Gingeras, and Alberto Kornblihtt for useful discussions and access to data, and Romina Garrido for administrative assistance.
• dc.format.mimetype application/pdfca
• dc.identifier.citation Curado J, Iannone C, Tilgner H, Valcárcel J, Guigó R. Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biology. 2015;16:236. DOI: 10.1186/s13059-015-0797-8ca
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0797-8
• dc.identifier.issn 1465-6906ca
• dc.identifier.uri http://hdl.handle.net/10230/25168
• dc.language.iso engca
• dc.publisher BioMed Centralca
• dc.relation.ispartof Genome Biology. 2015;16:236
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
• dc.relation.uri http://hdl.handle.net/10230/26093
• dc.rights © 2015 Curado et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Chromatin
• dc.subject.keyword Splicing
• dc.subject.keyword Histone
• dc.subject.keyword Modifications
• dc.subject.keyword Promoters
• dc.subject.keyword Proximity
• dc.subject.keyword Transcription
• dc.subject.keyword Epigenetic
• dc.subject.keyword RNA
• dc.subject.keyword ENCODE
• dc.subject.other Cromatina
• dc.subject.other Histones
• dc.subject.other Epigènesi
• dc.title Promoter-like epigenetic signatures in exons displaying cell type-specific splicingca
• dc.type info:eu-repo/semantics/articleca
• dc.type.version info:eu-repo/semantics/publishedVersionca