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Series GSE34491 Query DataSets for GSE34491
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
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.
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)
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
Platforms (2)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (4)
GSM850170 Hela_hnRNPU_CLIP_rep1
GSM850171 Hela_hnRNPU_CLIP_rep2
GSM850172 Hela_hnRNPU_RNAseq_control
SRA SRP009861
BioProject PRJNA151321

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Supplementary file Size Download File type/resource
GSE34491_RAW.tar 1.4 Gb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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