The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

Abstract

Short interfering RNAs (siRNAs) target cleavage of mRNAs with complementary sequences. In this work, Okamura et al. show that the Drosophila genome encodes endogenous siRNAs. Derived from long RNA hairpin genes, these siRNAs downregulate protein expression. Their processing pathway from the hairpin into the mature 21-nucleodite long siRNA involves factors of two pathways thought to be distinct. This paper shows that the Drosophila genome encodes endogenous siRNAs. Derived from long hairpin RNA genes, these siRNAs downregulate protein expression. Their processing pathway from the hairpin into the mature ∼21-nucleotide siRNA involves factors of two pathways thought to be distinct. In contrast to microRNAs and Piwi-associated RNAs, short interfering RNAs (siRNAs) are seemingly dispensable for host-directed gene regulation in Drosophila. This notion is based on the fact that mutants lacking the core siRNA-generating enzyme Dicer-2 or the predominant siRNA effector Argonaute 2 are viable, fertile and of relatively normal morphology1,2. Moreover, endogenous Drosophila siRNAs have not yet been identified. Here we report that siRNAs derived from long hairpin RNA genes (hpRNAs) programme Slicer complexes that can repress endogenous target transcripts. The Drosophila hpRNA pathway is a hybrid mechanism that combines canonical RNA interference factors (Dicer-2, Hen1 (known as CG12367) and Argonaute 2) with a canonical microRNA factor (Loquacious) to generate ∼21-nucleotide siRNAs. These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila.