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RNA Biol. 2016;13(4):400-11. doi: 10.1080/15476286.2015.1138030. Epub 2016 Jan 13.

High-throughput analyses of hnRNP H1 dissects its multi-functional aspect.

Author information

1
a Molecular and Computational Biology , Department of Biological Sciences, University of Southern California , CA , USA.
2
b Department of Cellular and Structural Biology , University of Texas Health Science Center at San Antonio , TX , USA.
3
c Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio , TX , USA.
4
d Center for Genomics and Systems Biology , Department of Biology, New York University , NY , USA.

Abstract

hnRNPs are polyvalent RNA binding proteins that have been implicated in a range of regulatory roles including splicing, mRNA decay, translation, and miRNA metabolism. A variety of genome wide studies have taken advantage of methods like CLIP and RIP to identify the targets and binding sites of RNA binding proteins. However, due to the complex nature of RNA-binding proteins, these studies are incomplete without assays that characterize the impact of RBP binding on mRNA target expression. Here we used a suite of high-throughput approaches (RIP-Seq, iCLIP, RNA-Seq and shotgun proteomics) to provide a comprehensive view of hnRNP H1s ensemble of targets and its role in splicing, mRNA decay, and translation. The combination of RIP-Seq and iCLIP allowed us to identify a set of 1,086 high confidence target transcripts. Binding site motif analysis of these targets suggests the TGGG tetramer as a prevalent component of hnRNP H1 binding motif, with particular enrichment around intronic hnRNP H1 sites. Our analysis of the target transcripts and binding sites indicates that hnRNP H1s involvement in splicing is 2-fold: it directly affects a substantial number of splicing events, but also regulates the expression of major components of the splicing machinery and other RBPs with known roles in splicing regulation. The identified mRNA targets displayed function enrichment in MAPK signaling and ubiquitin mediated proteolysis, which might be main routes by which hnRNP H1 promotes tumorigenesis.

KEYWORDS:

Integrated analysis; Proteomics; RIP-seq; RNA-binding proteins; RNA-seq; hnRNP H1; iCLIP

PMID:
26760575
PMCID:
PMC4841607
DOI:
10.1080/15476286.2015.1138030
[Indexed for MEDLINE]
Free PMC Article

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