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High-throughput analyses of hnRNP H1 dissects its multi-functional aspect
Philip J Uren1, Emad Bahrami-Samani1, Patricia Rosa de Araujo2,3
1a Molecular and Computational Biology , Department of Biological Sciences, University of Southern California , CA , USA.
RNA Biology
|January 14, 2016
Summary
Heterogeneous nuclear ribonucleoproteins (hnRNPs) regulate gene expression. This study comprehensively maps hnRNP H1 targets, revealing its dual role in splicing and potential links to cancer via MAPK signaling and proteolysis.
Area of Science:
- Molecular Biology
- Gene Regulation
- Cancer Biology
Background:
- Heterogeneous nuclear ribonucleoproteins (hnRNPs) are crucial RNA-binding proteins involved in diverse cellular processes like splicing, mRNA decay, and translation.
- Genome-wide studies using CLIP and RIP identify RNA-binding protein targets, but often lack functional context regarding mRNA expression impact.
Purpose of the Study:
- To comprehensively profile hnRNP H1 targets and elucidate its roles in splicing, mRNA decay, and translation.
- To integrate multiple high-throughput methods for a complete understanding of hnRNP H1's regulatory network.
Main Methods:
- Utilized a suite of high-throughput techniques including RIP-Seq, individual-nucleotide resolution crosslinking immunoprecipitation sequencing (iCLIP), RNA-Sequencing (RNA-Seq), and shotgun proteomics.
- Combined RIP-Seq and iCLIP to identify high-confidence hnRNP H1 target transcripts.
- Performed binding site motif analysis and functional enrichment analysis on identified targets.
Main Results:
- Identified 1,086 high-confidence hnRNP H1 target transcripts.
- Discovered a prevalent TGGG tetramer motif in hnRNP H1 binding sites, particularly near intronic sites.
- hnRNP H1 directly influences numerous splicing events and regulates key splicing machinery components and other RNA-binding proteins (RBPs).
Conclusions:
- hnRNP H1 plays a significant role in splicing regulation through direct target modulation and control of splicing factors.
- Enriched functions of hnRNP H1 targets in MAPK signaling and ubiquitin-mediated proteolysis suggest potential roles in tumorigenesis.
- This study provides a comprehensive view of hnRNP H1's regulatory landscape and its implications in cancer biology.
