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An endogenous small interfering RNA pathway in Drosophila


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.

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Figure 1: AGO2 binds endogenous small RNAs.
Figure 2: A subset of endo-siRNAs originates from transposons.
Figure 3: Two types of genic endo-siRNA loci in Drosophila.
Figure 4: Genetic requirements for siRNA biogenesis.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

Small RNA sequences were deposited in the Gene Expression Omnibus ( under accession number GSE11086.


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We thank R. Carthew, H. Siomi, P. Zamore and D. Smith for reagents. We are grateful to M. Rooks, E. Hodges and D. McCombie for help with deep sequencing. B.C. was supported by the German Academic Exchange Service. C.D.M. is a Beckman fellow of the Watson School of Biological Sciences and is supported by an NSF Graduate Research Fellowship. R.Z. is a Special Fellow of the Leukemia and Lymphoma Society. M.D. is an Engelhorn fellow of the Watson School of Biological Sciences. J.B. is supported by the Ernst Schering foundation. A.S. is supported by an HFSP fellowship. This work was supported in part from grants from the NIH to G.J.H. and N.P. and a gift from K. W. Davis (G.J.H.).

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Correspondence to Gregory J. Hannon or Julius Brennecke.

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The file contains Supplementary Methods, Supplementary Tables S1-S2, Supplementary Figures S1-S13 and additional references. (PDF 1479 kb)

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Czech, B., Malone, C., Zhou, R. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–802 (2008).

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