Transcriptomics

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Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform


ABSTRACT: Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are ~22-23-nt, ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of ~24-28-nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These ~21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a co-factor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1/Loqs-PB complexes and Dcr-2/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively. Small RNA profiling by high throughput sequencing Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE into 19-24nt. These were independently processed and sequenced using the Illumina GAII platform. In total, six libraries were analyzed.

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: James A Wohlschlegel   Ravi Sachindanandam  Norbert Perrimon  Benjamin Czech  Julius Brennecke  Rui Zhou  Gregory J Hannon 

PROVIDER: E-GEOD-17171 | ArrayExpress | 2009-07-30

SECONDARY ACCESSION(S): SRP001305GSE17171PRJNA119663

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform.

Zhou Rui R   Czech Benjamin B   Brennecke Julius J   Sachidanandam Ravi R   Wohlschlegel James A JA   Perrimon Norbert N   Hannon Gregory J GJ  

RNA (New York, N.Y.) 20090727 10


Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are approximately 22-23 nucleotides (nt), ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of approximately 24-28 nt associate with Piwi-family p  ...[more]

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