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GEO help: Mouse over screen elements for information. |
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Status |
Public on Sep 29, 2010 |
Title |
Transcriptome changes in splicing inhibited cells |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by genome tiling array
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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.
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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.
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Contributor(s) |
Kaida D, Dreyfuss G |
Citation(s) |
20881964 |
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Submission date |
Sep 16, 2010 |
Last update date |
Mar 22, 2012 |
Contact name |
Daisuke Kaida |
E-mail(s) |
kaida@med.u-toyama.ac.jp
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Organization name |
University of Toyama
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Department |
Frontier Research Core for Life Sciences
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Street address |
2630 Sugitani
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City |
Toyama |
State/province |
Toyama |
ZIP/Postal code |
930-0194 |
Country |
Japan |
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Platforms (1) |
GPL4914 |
[Hs35b_P05R] Affymetrix Human Tiling 2.0R Set, Array 5 |
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Samples (3) |
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Relations |
BioProject |
PRJNA130103 |
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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