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

R Middleton (1) , D Gao (2, 3, 1) , A Thomas (4) , B Singh (5) , A Au (1) , Justin J.-L. Wong (1) , A Bomane (6) , B Cosson (6) , E Eyras (5, 7) , John E. J. Rasko , William Ritchie (4, 8, 1)

1 Centenary Institute [Sidney]
2 Massachusetts General Hospital [Boston]
3 UMASS - University of Massachusetts Medical School [Worcester]
4 IGH - Institut de génétique humaine
5 UPF - Universitat Pompeu Fabra [Barcelona]
6 EDC - Centre épigénétique et destin cellulaire
7 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
8 IGF - Institut de Génomique Fonctionnelle

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 intronretaining transcripts that escape nonsense-mediated decay are not actively translated.

Mots clés: mRNA splicing; Intron retention; Gene regulation

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]; Bio-Informatique, Biologie Systémique [q-bio.QM]

R Middleton, D Gao, A Thomas, B Singh, A Au, et al.. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biology, 2017, 18 (1), pp.51. ⟨10.1186/s13059-017-1184-4⟩. ⟨hal-01497240⟩