Journal Article

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

Middleton, Robert, Cosson, Bertrand, Wong, Justin J-L, Gao, Dadi, Au, Amy, Singh, Babita, Bomane, Alexandra, Ritchie, William, Thomas, Aubin, Eyras, Eduardo, Rasko, John E. J.

2017

Overview

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.

• Publisher: BioMed Central,Springer Nature B.V
• Subject: Algorithms / Alternative Splicing / Animal Genetics and Genomics / Animals / Archives & records / Binding Sites / Biochemistry, Molecular Biology / Bioinformatics / Biomedical and Life Sciences / Cell cycle / Cell Cycle - genetics / cell differentiation / Cell Differentiation - genetics / Computational Biology - methods / Data processing / Evolutionary Biology / Exons / Experiments / Gene expression / Gene Expression Regulation / Gene regulation / Genomes / Genomics / Human Genetics / Humans / Intron retention / Introns / Life Sciences / mammals / messenger RNA / Microbial Genetics and Genomics / mRNA splicing / Nucleotide Motifs / Plant Genetics and Genomics / Proteins / Quantitative Methods / Retention / RNA Splicing / RNA-binding protein / RNA-binding proteins / RNA-Binding Proteins - metabolism / Software / tissues / transcription (genetics)