Yeo Lab @ UCSD, IGM, SCRM, A*STAR


Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins

SUPPLEMENTARY ONLINE WEB TOOL

Stephanie C. Huelga1,2, Anthony Q. Vu1,2, Justin D. Arnold1,2, Tiffany Y. Liang1,2, Patrick P. Liu1,2, Bernice Y. Yan1,2, John Paul Donohue3, Lily Shiue3, Shawn Hoon4, Sydney Brenner4, Manuel Ares, Jr.3, Gene W. Yeo1,2,4

1Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, 92093, USA
2Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, California, 92093, USA
3RNA Center, Department of Molecular, Cell and Developmental Biology, Sinsheimer Labs, University of California, Santa Cruz, California, 95064, USA
4Molecular Engineering Lab, Agency for Science Technology and Research, Singapore


Enter Gene Name (ex: hnrnpu)

Enter Sequence Within Gene (Optional)


				
			

DESCRIPTION

A tool to visualize hnRNP dependent splicing events and hnRNP binding sites within genes as determined by custom splicing-sensitive microarrays (Affymetrix) and CLIP-seq.

Summary

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 autoregulation 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.

Highlights

  • Thousands of binding sites and splicing events identified for major hnRNP proteins
  • HnRNP proteins act cooperatively, regulating cassette exons in similar directions
  • HnRNP proteins cross and auto-regulate
  • HnRNP proteins regulate other RNA binding proteins and cancer related genes
  • Data Downloads

    Raw sequencing data is available under GEO accession number GSE34996.
    HnRNP CLIP-derived clusters can be downloaded in .BED (hg18) format here: CDCs.
    A table of all scored hnRNP splicing changes is available here: Events
    A table of all PWMs from Figure 3A is available here: PWMs

    Please cite Huelga et. al. Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins, Cell Reports, 2012 when using materials from this website for publications and talks.


    FUNDING

    This work was supported by grants from US National Institutes of Health (HG004659 and GM084317) and the Stem Cell Program at the University of California, San Diego. S.C.H. is funded by a National Science Foundation Graduate Research Fellowship. G.W.Y is an Alfred P. Sloan research fellow.


    For questions about and requests for datasets, please contact Gene Yeo or Stephanie Huelga.
    Developed by Patrick Liu. Please email for questions or comments. Last updated July 17, 2014.