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Open Access Research

The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA

Vicky Cho15, Yan Mei1, Arleen Sanny3, Stephanie Chan1, Anselm Enders4, Edward M Bertram5, Andy Tan123, Christopher C Goodnow15* and T Daniel Andrews15*

Author Affiliations

1 Immunogenomics Laboratory, John Curtin School of Medical Research, Australian National University, GPO Box 334, Canberra City ACT 2601, Australia

2 Immunology Groups, Bioprocessing Technology Institute, 20 Biopolis Way, Centros, 138668 Singapore, Singapore

3 Microarray Groups, Bioprocessing Technology Institute, 20 Biopolis Way, Centros, 138668 Singapore, Singapore

4 Ramaciotti Immunisation Genomics Laboratory, John Curtin School of Medical Research, Australian National University, GPO Box 334, Canberra City ACT 2601, Australia

5 Australian Phenomics Facility, Hugh Ennor Building, Australian National University, Garran Road, ACT 0200 Canberra, Australia

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Genome Biology 2014, 15:R26  doi:10.1186/gb-2014-15-1-r26

Published: 29 January 2014

Abstract

Background

Retention of a subset of introns in spliced polyadenylated mRNA is emerging as a frequent, unexplained finding from RNA deep sequencing in mammalian cells.

Results

Here we analyze intron retention in T lymphocytes by deep sequencing polyadenylated RNA. We show a developmentally regulated RNA-binding protein, hnRNPLL, induces retention of specific introns by sequencing RNA from T cells with an inactivating Hnrpll mutation and from B lymphocytes that physiologically downregulate Hnrpll during their differentiation. In Ptprc mRNA encoding the tyrosine phosphatase CD45, hnRNPLL induces selective retention of introns flanking exons 4 to 6; these correspond to the cassette exons containing hnRNPLL binding sites that are skipped in cells with normal, but not mutant or low, hnRNPLL. We identify similar patterns of hnRNPLL-induced differential intron retention flanking alternative exons in 14 other genes, representing novel elements of the hnRNPLL-induced splicing program in T cells. Retroviral expression of a normally spliced cDNA for one of these targets, Senp2, partially corrects the survival defect of Hnrpll-mutant T cells. We find that integrating a number of computational methods to detect genes with differentially retained introns provides a strategy to enrich for alternatively spliced exons in mammalian RNA-seq data, when complemented by RNA-seq analysis of purified cells with experimentally perturbed RNA-binding proteins.

Conclusions

Our findings demonstrate that intron retention in mRNA is induced by specific RNA-binding proteins and suggest a biological significance for this process in marking exons that are poised for alternative splicing.