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| Status |
Public on Apr 05, 2012 |
| Title |
Effects of ADARs on small RNA processing pathways in C. elegans |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Adenosine deaminases that act on RNA (ADARs) are RNA editing enzymes that convert adenosine to inosine in double-stranded RNA (dsRNA). To evaluate effects of ADARs on small RNAs that derive from dsRNA precursors, we performed deep-sequencing, comparing small RNAs from wildtype and ADAR mutant C. elegans. While editing in small RNAs was rare, at least 40% of microRNAs had altered levels in at least one ADAR mutant strain, and miRNAs with significantly altered levels had mRNA targets with correspondingly affected levels. About 40% of siRNAs derived from endogenous genes (endo-siRNAs) also had altered levels in at least one mutant strain, including 63% of Dicer-dependent endo-siRNAs. The 26G class of endo-siRNAs was significantly affected by ADARs, and many altered 26G loci had intronic reads, and histone modifications associated with transcriptional silencing. Our data indicate ADARs, through both direct and indirect mechanisms, are important for maintaining wildtype levels of many small RNAs in C. elegans.
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| |
|
| Overall design |
Deep sequencing of small RNAs in wild-type (N2), adr-1 null, adr-2 null and adr-1;adr-2 null mixed stage C. elegans
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| |
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| Contributor(s) |
Warf MB, Johnson WE, Bass BL |
| Citation(s) |
22673872 |
| |
| Submission date |
Apr 27, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Bryan Warf |
| E-mail(s) |
warf@biochem.utah.edu
|
| Phone |
801-585-3110
|
| Organization name |
University of Utah
|
| Department |
Biochemistry
|
| Lab |
Brenda Bass
|
| Street address |
15 N Medical Dr East, room 4800
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9269 |
Illumina Genome Analyzer II (Caenorhabditis elegans) |
|
| Samples (5)
|
|
| Relations |
| SRA |
SRP006489 |
| BioProject |
PRJNA140639 |
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