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Genome Biol. 2017 Mar 15;18(1):51. doi: 10.1186/s13059-017-1184-4.

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

Middleton R1, Gao D1,2,3,4, Thomas A5, Singh B6, Au A4,7, Wong JJ4,7,8, Bomane A9, Cosson B9, Eyras E6,10, Rasko JE4,7,11, Ritchie W12,13,14.

Author information

1
Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.
2
Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.
3
Boston & Harvard Medical School, Boston, MA, USA.
4
Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.
5
CNRS, UPR 1142, Montpellier, 34094, France.
6
Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.
7
Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.
8
Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia.
9
Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France.
10
Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, E08010, Barcelona, Spain.
11
Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia.
12
Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. william.ritchie@igh.cnrs.fr.
13
CNRS, UPR 1142, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.
14
CNRS, UMR 5203, Montpellier, 34094, France. william.ritchie@igh.cnrs.fr.

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.

KEYWORDS:

Gene regulation; Intron retention; mRNA splicing

PMID:
28298237
PMCID:
PMC5353968
DOI:
10.1186/s13059-017-1184-4
[Indexed for MEDLINE]
Free PMC Article

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