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Series GSE24179 Query DataSets for GSE24179
Status Public on Sep 29, 2010
Title Transcriptome changes in splicing inhibited cells
Organism Homo sapiens
Experiment type Expression profiling by genome tiling array
Summary In eukaryotes, U1 small nuclear ribonucleoprotein (snRNP) forms spliceosomes in equal stoichiometry with U2, U4, U5 and U6 snRNPs; however, its abundance in human far exceeds that of the other snRNPs. Here we used antisense morpholino oligonucleotide to U1 snRNA to achieve functional U1 snRNP knockdown in HeLa cells, and identified accumulated unspliced pre-mRNAs by genomic tiling microarrays. In addition to inhibiting splicing, U1 snRNP knockdown caused premature cleavage and polyadenylation in numerous pre-mRNAs at cryptic polyadenylation signals, frequently in introns near (<5 kilobases) the start of the transcript. This did not occur when splicing was inhibited with U2 snRNA antisense morpholino oligonucleotide or the U2-snRNP-inactivating drug spliceostatin A unless U1 antisense morpholino oligonucleotide was also included. We further show that U1 snRNA–pre-mRNA base pairing was required to suppress premature cleavage and polyadenylation from nearby cryptic polyadenylation signals located in introns. These findings reveal a critical splicing-independent function for U1 snRNP in protecting the transcriptome, which we propose explains its overabundance.
 
Overall design Treated HeLa cells with antisense oligos for U1 snRNP or U2 snRNP or control oligo, or methanol or spliceosotain A for 8 hours followed by analysis of total RNA on human tiling 2.0R E array. Three biological replicates were used for each treatment.
 
Contributor(s) Kaida D, Dreyfuss G
Citation(s) 20881964
Submission date Sep 16, 2010
Last update date Mar 22, 2012
Contact name Daisuke Kaida
E-mail(s) kaida@med.u-toyama.ac.jp
Organization name University of Toyama
Department Frontier Research Core for Life Sciences
Street address 2630 Sugitani
City Toyama
State/province Toyama
ZIP/Postal code 930-0194
Country Japan
 
Platforms (1)
GPL4914 [Hs35b_P05R] Affymetrix Human Tiling 2.0R Set, Array 5
Samples (3)
GSM594831 U1 vs control
GSM594832 U2 vs control
GSM594833 spliceostatin A vs methanol
Relations
BioProject PRJNA130103

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24179_RAW.tar 582.0 Mb (http)(custom) TAR (of BAR, CEL)
Processed data provided as supplementary file

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