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

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

doi:10.1186/s13059-017-1184-4

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

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

161 Citations (Scopus)

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.

Original language	English
Article number	51
Journal	Genome Biology
Volume	18
Issue number	1
DOIs	https://doi.org/10.1186/s13059-017-1184-4
Publication status	Published - 15 Mar 2017
Externally published	Yes

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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.",

keywords = "Gene regulation, Intron retention, MRNA splicing",

author = "Robert Middleton and Dadi Gao and Aubin Thomas and Babita Singh and Amy Au and Wong, {Justin J.L.} and Alexandra Bomane and Bertrand Cosson and Eduardo Eyras and Rasko, {John E.J.} and William Ritchie",

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month = mar,

day = "15",

doi = "10.1186/s13059-017-1184-4",

language = "English",

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TY - JOUR

T1 - IRFinder

T2 - Assessing the impact of intron retention on mammalian gene expression

AU - Middleton, Robert

AU - Gao, Dadi

AU - Thomas, Aubin

AU - Singh, Babita

AU - Au, Amy

AU - Wong, Justin J.L.

AU - Bomane, Alexandra

AU - Cosson, Bertrand

AU - Eyras, Eduardo

AU - Rasko, John E.J.

AU - Ritchie, William

PY - 2017/3/15

Y1 - 2017/3/15

N2 - 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.

AB - 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.

KW - Gene regulation

KW - Intron retention

KW - MRNA splicing

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U2 - 10.1186/s13059-017-1184-4

DO - 10.1186/s13059-017-1184-4

M3 - Article

SN - 1474-7596

VL - 18

JO - Genome Biology

JF - Genome Biology

IS - 1

M1 - 51

ER -

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

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