IRFinder: assessing the impact of intron retention on mammalian gene expression
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- dc.contributor.author Middleton, Robertca
- dc.contributor.author Gao, Dadica
- dc.contributor.author Thomas, Aubinca
- dc.contributor.author Singh, Babita, 1986-ca
- dc.contributor.author Au, Amyca
- dc.contributor.author Wong, Justin J.-L.ca
- dc.contributor.author Bomane, Alexandraca
- dc.contributor.author Cosson, Bertrandca
- dc.contributor.author Eyras Jiménez, Eduardoca
- dc.contributor.author Rasko, John E.J.ca
- dc.contributor.author Ritchie, Williamca
- dc.date.accessioned 2017-05-23T08:06:03Z
- dc.date.available 2017-05-23T08:06:03Z
- dc.date.issued 2017
- dc.description.abstract Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
- dc.description.sponsorship This work was supported by the Agence Nationale de la Recherche (ANR 143683); the National Health and Medical Research Council (grant #1061906, #1080530, #1128175, #1126306). BS and EE were supported by grants BIO2014-52566-R from the MINECO (Spanish Government) and FEDER funds, by AGAUR (2014-SGR1121), and by the Sandra Ibarra Foundation for Cancer (FSI2013).
- dc.format.mimetype application/pdfca
- dc.identifier.citation Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ-L et al. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biology. 2017;18:51. DOI: 10.1186/s13059-017-1184-4
- dc.identifier.doi http://dx.doi.org/10.1186/s13059-017-1184-4
- dc.identifier.issn 1474-760X
- dc.identifier.uri http://hdl.handle.net/10230/32143
- dc.language.iso eng
- dc.publisher BioMed Centralca
- dc.relation.ispartof Genome Biology. 2017;18:51
- dc.rights © The Author(s). 2017. 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.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword mRNA splicing
- dc.subject.keyword Intron retention
- dc.subject.keyword Gene regulation
- dc.title IRFinder: assessing the impact of intron retention on mammalian gene expressionca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion