IRFinder: assessing the impact of intron retention on mammalian gene expression

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dc.contributor.author	Middleton, Robert
dc.contributor.author	Gao, Dadi
dc.contributor.author	Thomas, Aubin
dc.contributor.author	Singh, Babita, 1986-
dc.contributor.author	Au, Amy
dc.contributor.author	Wong, Justin J.-L.
dc.contributor.author	Bomane, Alexandra
dc.contributor.author	Cosson, Bertrand
dc.contributor.author	Eyras Jiménez, Eduardo
dc.contributor.author	Rasko, John E.J.
dc.contributor.author	Ritchie, William
dc.date	2017
dc.identifier.citation	Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJ-L, Bomane A, Cosson B, Eyras Jiménez E, Rasko JEJ, Ritchie W. 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.citation	1474-760X
dc.identifier.citation	http://dx.doi.org/10.1186/s13059-017-1184-4
dc.identifier.uri	http://hdl.handle.net/10230/32143
dc.format	application/pdf
dc.language.iso	eng
dc.publisher	BioMed Central
dc.relation	Genome Biology. 2017; 18:51
dc.rights	info:eu-repo/semantics/openAccess
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	http://creativecommons.org/licenses/by/4.0/
dc.subject	mRNA splicing
dc.subject	Intron retention
dc.subject	Gene regulation
dc.title	IRFinder: assessing the impact of intron retention on mammalian gene expression
dc.type	info:eu-repo/semantics/article
dc.type	info:eu-repo/semantics/publishedVersion
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.abstract	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).

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