title: IRFinder: assessing the impact of intron retention on mammalian gene expression.
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.
authors.affiliation: Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.
authors.forename: Robert
authors.initials: R
authors.lastname: Middleton
authors.affiliation: Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.|Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.|Boston & Harvard Medical School, Boston, MA, USA.|Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.
authors.forename: Dadi
authors.initials: D
authors.lastname: Gao
authors.affiliation: CNRS, UPR 1142, Montpellier, 34094, France.
authors.forename: Aubin
authors.initials: A
authors.lastname: Thomas
authors.affiliation: Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.
authors.forename: Babita
authors.initials: B
authors.lastname: Singh
authors.affiliation: Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.|Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.
authors.forename: Amy
authors.initials: A
authors.lastname: Au
authors.affiliation: Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.|Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.|Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.
authors.forename: Justin J-L
authors.initials: JJ
authors.lastname: Wong
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Bomane
authors.affiliation: Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Cosson
authors.affiliation: Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.|Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, E08010, Barcelona, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
authors.affiliation: Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.|Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.|Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia.
authors.forename: John E J
authors.initials: JE
authors.lastname: Rasko
authors.affiliation: Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. william.ritchie@igh.cnrs.fr.|CNRS, UPR 1142, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.|CNRS, UMR 5203, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.
authors.forename: William
authors.identifier: 0000-0001-8162-1439
authors.initials: W
authors.lastname: Ritchie
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001665:Binding Sites; D002453:Cell Cycle / Q000235:genetics; D002454:Cell Differentiation / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D005091:Exons; D005786:Gene Expression Regulation; D006801:Humans; D007438:Introns; D059372:Nucleotide Motifs; D012326:RNA Splicing; D016601:RNA-Binding Proteins / Q000378:metabolism; D012984:Software
chemical_list: D016601:RNA-Binding Proteins
keywords: Gene regulation; Intron retention; mRNA splicing