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Series GSE18806 Query DataSets for GSE18806
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
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.
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).
Contributor(s) Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD
Citation(s) 19917635, 20558712
Submission date Oct 29, 2009
Last update date May 15, 2019
Contact name Jia Xu
Organization name UMASSMED
Department Program in Bioinformatics and Integrative Biology
Lab Weng
Street address 55 Lake Avenue North
City Worcester
State/province MA
ZIP/Postal code 01655
Country USA
Platforms (1)
GPL9058 Illumina Genome Analyzer (Drosophila melanogaster)
Samples (11)
GSM466487 Total small RNAs from Oregon R
GSM466488 2´-O-methylated small RNAs from Oregon R
GSM466489 Ago1-associated small RNAs from Oregon R
SRA SRP001536
BioProject PRJNA121221

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GSE18806_RAW.tar 125.3 Mb (http)(custom) TAR (of TAR, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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