Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

Brooks, Angela N.; Duff, Michael O.; May, Gemma; Yang, Li; Bolisetty, Mohan; Landolin, Jane; Wan, Ken; Sandler, Jeremy; Booth, Benjamin W.; Celniker, Susan E.; Graveley, Brenton R.; Brenner, Steven E.

doi:10.1101/gr.192518.115

Title: Regulation of alternative splicing in Drosophila by 56 RNA binding proteins

Journal Article · Thu Aug 20 00:00:00 EDT 2015 · Genome Research

DOI:https://doi.org/10.1101/gr.192518.115· OSTI ID:1257380

Brooks, Angela N. ^[1]; Duff, Michael O. ^[2]; May, Gemma ^[2]; Yang, Li ^[2]; Bolisetty, Mohan ^[2]; Landolin, Jane ^[3]; Wan, Ken ^[3]; Sandler, Jeremy ^[3]; Booth, Benjamin W. ^[3]; Celniker, Susan E. ^[3]; Graveley, Brenton R. ^[2]; Brenner, Steven E. ^[4]

Univ. of California, Berkeley, CA (United States). Dept. of Molecular and Cell Biology; Broad Inst. Cambridge, MA (United States); Dana-Farber Cancer Inst., Boston, MA (United States). Dept. of Medical Oncology
Univ. of Connecticut Health Center, Farmington, CT (United States). Dept. of Genetics and Genome Sciences and Inst. for Systems Genomics
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Dept. of Genome Dynamics
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology

Alternative splicing is regulated by RNA binding proteins (RBPs) that recognize pre-mRNA sequence elements and activate or repress adjacent exons. Here, we used RNA interference and RNA-seq to identify splicing events regulated by 56 Drosophila proteins, some previously unknown to regulate splicing. Nearly all proteins affected alternative first exons, suggesting that RBPs play important roles in first exon choice. Half of the splicing events were regulated by multiple proteins, demonstrating extensive combinatorial regulation. We observed that SR and hnRNP proteins tend to act coordinately with each other, not antagonistically. We also identified a cross-regulatory network where splicing regulators affected the splicing of pre-mRNAs encoding other splicing regulators. This large-scale study substantially enhances our understanding of recent models of splicing regulation and provides a resource of thousands of exons that are regulated by 56 diverse RBPs.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); Damon Runyon Cancer Research Foundation, New York City, NY (United States)

Grant/Contract Number:: AC02-05CH11231; DRG-2138-12; U01 HG004271

OSTI ID:: 1257380

Alternate ID(s):: OSTI ID: 1474888

Journal Information:: Genome Research, Vol. 25, Issue 11; ISSN 1088-9051

Publisher:: Cold Spring Harbor Laboratory PressCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 57 works

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