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| Status |
Public on Feb 20, 2012 |
| Title |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| 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 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.
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| Overall design |
In triplicate, polyA-selected RNA was extracted from control, hnRNP A1, hnRNP A2/B1, hnRNP H1, hnRNP F, hnRNP M, and hnRNP U siRNA treated human 293T cells, and hybridized to custom splice-junction arrays
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| Contributor(s) |
Huelga SC, Yeo GW |
| Citation(s) |
22574288 |
| Submission date |
Jan 10, 2012 |
| Last update date |
Jun 21, 2012 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
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| Organization name |
UCSD
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| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platforms (1) |
| GPL15106 |
[hjay] Affymetrix GeneChip Human HJAY Array |
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| Samples (21)
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| This SubSeries is part of SuperSeries: |
| GSE34996 |
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins |
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| Relations |
| BioProject |
PRJNA156299 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34992_RAW.tar |
655.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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