Drosophila retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations

Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon (retroTn) mobility in Drosophila somatic cells. EsiRNAs are primarily generated from transposon and inverted repeat (hairpin) loci in Drosophila culture cells. After discovering a nucleus specific physical interaction between the essential esiRNA cleavage enzyme Dcr2 and Symplekin, a component of the core cleavage complex (CCC) required for 3’ end processing of mRNAs, we investigated cellular localization of esiRNA biogenesis and overlap between these pathways. We found that knockdown of CCC components perturbs esiRNA levels and that retroTn precursor transcripts are highly enriched in the nucleus while hairpin RNAs are predominantly cytoplasmic. Additionally, retroTn and hairpin-derived esiRNAs have distinct physical characteristics. Combined, these observations support a novel mechanism in which differences in localization of esiRNA precursors impacts esiRNA biogenesis; hairpin-derived esiRNAs are generated in the cytoplasm independent of Dcr2-Symplekin interactions, while retroTns are processed in the nucleus. This submission includes 18 raw data files. Two samples (Blank control, Symplekin and CPSF73 RNAi-depleted) are represented by three technical triplicate raw data files. RNA-seq and small RNA-seq data are provided for each sample.