Unknown

Dataset Information

34

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway


ABSTRACT: 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).

REANALYSED by: GSE117217

INSTRUMENT(S): Illumina Genome Analyzer (Drosophila melanogaster)

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Jia Xu  

PROVIDER: GSE18806 | GEO | 2009-10-31

SECONDARY ACCESSION(S): PRJNA121221

REPOSITORIES: GEO

Similar Datasets

2009-10-31 | E-GEOD-18806 | ArrayExpress
2011-02-10 | GSE26230 | GEO
2011-02-10 | E-GEOD-26230 | ArrayExpress
2012-03-16 | E-GEOD-36449 | ArrayExpress
2018-06-22 | GSE104015 | GEO
2014-01-01 | E-GEOD-52961 | ArrayExpress
| GSE52961 | GEO
2018-09-10 | PXD010197 | Pride
2009-07-31 | GSE17171 | GEO
2010-08-03 | GSE12462 | GEO