An endogenous small interfering RNA pathway in Drosophila

Abstract

In this work, Czech et al. identify a new class of small RNAs in Drosophila: endogenous short interfering RNAs (endo-siRNAs). These RNAs are present in both somatic and gonadal cells. Their processing is different than that of miRNAs or piRNAs; it requires Dcr2 and, unusually, Loqs, the Dcr1 partner, rather than R2D2, the usual partner of Dcr2. The processed endo-siRNAs are the first small RNAs found to associate preferentially with the Argonaute protein AGO2, and this complex targets genes that encode proteins as well as mobile elements. This paper identifies a class of small RNAs in fly: endogenous siRNAs (endo-siRNAs). These RNAs are present in both somatic and gonadal cells, and their processing is different than that of miRNAs or piRNAs. Drosophila endogenous small RNAs are categorized according to their mechanisms of biogenesis and the Argonaute protein to which they bind. MicroRNAs are a class of ubiquitously expressed RNAs of ∼22 nucleotides in length, which arise from structured precursors through the action of Drosha–Pasha and Dicer-1–Loquacious complexes1,2,3,4,5,6,7. These join Argonaute-1 to regulate gene expression8,9. A second endogenous small RNA class, the Piwi-interacting RNAs, bind Piwi proteins and suppress transposons10,11. Piwi-interacting RNAs are restricted to the gonad, and at least a subset of these arises by Piwi-catalysed cleavage of single-stranded RNAs12,13. Here we show that Drosophila generates a third small RNA class, endogenous small interfering RNAs, in both gonadal and somatic tissues. Production of these RNAs requires Dicer-2, but a subset depends preferentially on Loquacious1,4,5 rather than the canonical Dicer-2 partner, R2D2 (ref. 14). Endogenous small interfering RNAs arise both from convergent transcription units and from structured genomic loci in a tissue-specific fashion. They predominantly join Argonaute-2 and have the capacity, as a class, to target both protein-coding genes and mobile elements. These observations expand the repertoire of small RNAs in Drosophila, adding a class that blurs distinctions based on known biogenesis mechanisms and functional roles.