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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 25, 2010 |
| Title |
Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Messenger RNAs are regulated by a variety of degradation mechanisms in mammalian cells. In the canonical animal microRNA pathway, microRNAs in complex with Argonaute proteins bind to many mRNA targets with imperfect complementarity, leading to degradation of the mRNA through the regular decay machinery. The ancestral “slicer” endonuclease activity of Argonaute2 itself, which requires more extensive complementarity with the target RNA, is not used in this pathway, and has only been observed in two microRNA-guided cases. Nevertheless, the cleavage capacity of mammalian Ago2 is conserved and essential for viability. Here, we assess the endonucleolytic function of Ago2 and other nucleases by identifying cleavage products retaining 5`-phosphate groups in mouse ES cells on a transcriptome-wide scale. We detect a significant signature of Ago2-dependent cleavage events and validate several targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in this mode of mRNA regulation. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events, including one in the Dgcr8 mRNA, that functionally regulate mRNA levels in mES cells. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals.
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| Overall design |
Global 5`-phosphate-dependent RACE in WT, Ago2-KO and Drosha-excised mouse ES cells and human 293S cells
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| Contributor(s) |
Karginov FV, Hannon GJ |
| Citation(s) |
20620951 |
| Submission date |
May 24, 2010 |
| Last update date |
Mar 04, 2023 |
| Contact name |
Fedor Karginov |
| E-mail(s) |
karginov@ucr.edu
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| Organization name |
UC Riverside
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| Department |
MCSB
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| Street address |
900 University Ave
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| City |
Riverside |
| State/province |
California |
| ZIP/Postal code |
92521 |
| Country |
USA |
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| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (27)
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| Relations |
| SRA |
SRP002543 |
| BioProject |
PRJNA127179 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data not applicable for this record |
| Raw data are available in SRA |
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