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| Status |
Public on Oct 31, 2009 |
| Title |
Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway |
| Organism |
Drosophila melanogaster |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
Other
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| Summary |
In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character—as is found in small interfering RNAs (siRNAs)—directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired central region and requires both Dcr-2 and R2D2. Those miRNA and miRNA* sequences bound to Ago2, like siRNAs diced in vivo from long double-stranded RNA, typically begin with cytidine, whereas Ago1-bound miRNA and miRNA* disproportionately begin with uridine. Consequently, some pre-miRNA generate two or more isoforms from the same side of the stem that differentially partition between Ago1 and Ago2. Our findings provide the first genome-wide test for the idea that Drosophila small RNAs are sorted between Ago1 and Ago2 according to their duplex structure and the identity of their first nucleotide.
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| Overall design |
Sequencing of small RNAs (either total small RNAs or Ago1-associated small RNAs) in wild-type, dcr-2 and r2d2 mutant flies. Small RNA sequencing, Small RNAs (18-29 nt long), Size selection (18 to 30 nt).
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| Contributor(s) |
Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD |
| Citation(s) |
19917635, 20558712 |
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| Submission date |
Oct 29, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia Xu |
| E-mail(s) |
Jia.Xu@umassmed.edu
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| Organization name |
UMASSMED
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| Department |
Program in Bioinformatics and Integrative Biology
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| Lab |
Weng
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| Street address |
55 Lake Avenue North
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| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
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| Platforms (1) |
| GPL9058 |
Illumina Genome Analyzer (Drosophila melanogaster) |
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| Samples (11)
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| GSM466487 |
Total small RNAs from Oregon R |
| GSM466488 |
2´-O-methylated small RNAs from Oregon R |
| GSM466489 |
Ago1-associated small RNAs from Oregon R |
| GSM466490 |
Total small RNAs from dcr-2 heterozygous flies |
| GSM466491 |
2´-O-methylated small RNAs from dcr-2 heterozygous flies |
| GSM466492 |
Total small RNAs from dcr-2 homozygous flies |
| GSM466493 |
2´-O-methylated small RNAs from dcr-2 homozygous flies |
| GSM466494 |
Total small RNAs from r2d2 heterozygous flies |
| GSM466495 |
2´-O-methylated small RNAs from r2d2 heterozygous flies |
| GSM466496 |
Total small RNAs from r2d2 homozygous flies |
| GSM466497 |
2´-O-methylated small RNAs from r2d2 homozygous flies |
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| Relations |
| SRA |
SRP001536 |
| BioProject |
PRJNA121221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE18806_RAW.tar |
125.3 Mb |
(http)(custom) |
TAR (of TAR, TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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