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

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dc.contributor.author Curado, Joao
dc.contributor.author Iannone, Camilla, 1984-
dc.contributor.author Tilgner, Hagen, 1980-
dc.contributor.author Valcárcel, J. (Juan)
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2015-11-20T10:03:58Z
dc.date.available 2015-11-20T10:03:58Z
dc.date.issued 2015
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.
dc.identifier.issn 1465-6906
dc.identifier.uri http://hdl.handle.net/10230/25168
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/pdf
dc.language.iso eng
dc.publisher BioMed Central
dc.relation http://hdl.handle.net/10230/26093
dc.relation.ispartof Genome Biology. 2015;16:236
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.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Cromatina
dc.subject.other Histones
dc.subject.other Epigènesi
dc.title Promoter-like epigenetic signatures in exons displaying cell type-specific splicing
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/s13059-015-0797-8
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.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/SEV2012-0208
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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