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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 28, 2008 |
| Title |
Small RNA profile in fully grown mammalian oocytes |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
We aim to comprehensively characterize the small RNA population in oocytes
Pseudogenes populate the mammalian genome as remnants of artifactual incorporation of coding mRNAs into transposon pathways 1. Here, we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. In these cases, endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from protein coding genes to antisense transcripts from homologous pseudogenes. In at least one case, an inverted repeat pseudogene gives rise to abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting in concert with piwi-interacting RNAs (piRNAs). Loss of Dicer increases expression of endo-siRNA targets, demonstrating the regulatory activity of these small RNAs. Our findings provide a function for pseudogenes in regulating gene expression via the RNAi pathway and may, in part, explain the evolutionary pressure to conserve Argonaute-mediated catalysis in mammals.
Keywords: small RNAs profile
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| Overall design |
Total RNA was isolated and size-fractionated by PAGE either into 19-24nt and 24-30nt, or 19-30nt. These were independently processed and sequenced on Illumina 1G platform.
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| Contributor(s) |
Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachindanandam R, Schultz RM, Hannon GJ |
| Citation(s) |
18404147 |
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| Submission date |
Feb 01, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
ravi Sachidanandam |
| E-mail(s) |
sachidan@cshl.edu
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| Phone |
516 367 8864
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| Fax |
516 367 8389
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| URL |
http://katahdin.cshl.org:9331
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| Organization name |
Cold Spring Harbor Laboratory
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| Department |
N/A
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| Lab |
sachidanandam
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| Street address |
1 bungtown road
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| City |
Cold spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platforms (1) |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (3) |
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| Relations |
| SRA |
SRP000733 |
| BioProject |
PRJNA105627 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10364_RAW.tar |
109.0 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data included within Sample table |
| Raw data are available in SRA |
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