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| Status |
Public on Feb 16, 2012 |
| Title |
Nuclear Matrix Factor hnRNP U/SAF-A Exerts a Global Control of Alternative Splicing by Regulating U2 snRNP Maturation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The nuclear matrix associated hnRNP U/SAF-A protein has been implicated in diverse pathways from transcriptional regulation to telomere length control to X inactivation, but the precise mechanism underlying each of these processes has remained elusive. Here, we report hnRNP U as a regulator of SMN2 splicing from a custom RNAi screen. Genome-wide analysis by CLIP-seq reveals that hnRNP U binds virtually to all classes of regulatory non-coding RNAs, including all snRNAs required for splicing of both major and minor classes of introns, leading to the discovery that hnRNP U regulates U2 snRNP maturation and Cajal body morphology in the nucleus. Global analysis of hnRNP U-dependent splicing by RNA-seq coupled with bioinformatic analysis of associated splicing signals suggests a general rule for splice site selection through modulating the core splicing machinery. These findings exemplify hnRNP U/SAF-A as a potent regulator of nuclear ribonucleoprotein particles in diverse gene expression pathways.
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| Overall design |
Examination of hnRNP U regulated splicing in Hela cells with CLIP-seq (two biological replicates) and paired-end RNA-seq (control and hnRNP U knockdown)
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| Contributor(s) |
Xiao R, Tang P, Yang B, Huang J, Zhou Y, Shao C, Li H, Sun H, Zhang Y, Fu X |
| Citation(s) |
22325991 |
| |
| Submission date |
Dec 16, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiang-Dong Fu |
| Organization name |
UC San Diego
|
| Department |
CMM
|
| Lab |
George Palade Laboratories
|
| Street address |
9500 Gilman Drive, Room 231
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0651 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (4)
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| Relations |
| SRA |
SRP009861 |
| BioProject |
PRJNA151321 |
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