Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.

TitleIntegrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Publication TypeJournal Article
Year of Publication2012
AuthorsHuelga SC, Vu AQ, Arnold JD, Liang TY, Liu PP, Yan BY, Donohue J P, Shiue L, Hoon S, Brenner S, Ares M, Yeo GW
JournalCell Rep
Volume1
Issue2
Pagination167-178
Date Published2012 Feb 23
ISSN2211-1247
Abstract

Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and auto-regulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells.

DOI10.1016/j.celrep.2012.02.001
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/22574288?dopt=Abstract
PMCPMC3345519
Alternate JournalCell Rep
PubMed ID22574288