RNA silencing is a conserved mechanism in which small RNAs trigger various forms of sequence-specific gene silencing by guiding Argonaute complexes to target RNAs by means of base pairing1,2. RNA silencing is thought to have evolved as a form of nucleic-acid-based immunity to inactivate viruses and transposable elements. Although the activity of transposable elements in animals has been thought largely to be restricted to the germ line, recent studies have shown that they may also actively transpose in somatic cells, creating somatic mosaicism in animals3. In the Drosophila germ line, Piwi-interacting RNAs arise from repetitive intergenic elements including retrotransposons by a Dicer-independent pathway and function through the Piwi subfamily of Argonautes to ensure silencing of retrotransposons4,5,6,7,8,9. Here we show that, in cultured Drosophila S2 cells, Argonaute 2 (AGO2), an AGO subfamily member of Argonautes, associates with endogenous small RNAs of 20–22 nucleotides in length, which we have collectively named endogenous short interfering RNAs (esiRNAs). esiRNAs can be divided into two groups: one that mainly corresponds to a subset of retrotransposons, and the other that arises from stem–loop structures. esiRNAs are produced in a Dicer-2-dependent manner from distinctive genomic loci, are modified at their 3′ ends and can direct AGO2 to cleave target RNAs. Mutations in Dicer-2 caused an increase in retrotransposon transcripts. Together, our findings indicate that different types of small RNAs and Argonautes are used to repress retrotransposons in germline and somatic cells in Drosophila.
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We are grateful to T. Suzuki and members of the Siomi laboratory for discussion and comments on this manuscript. We thank K. Yamada and E. Hattori for expert assistance in AGO2-associated small RNA mapping and annotation, N. Iwanami and T. Hirose for help in qRT–PCR, and M. Itakura for continuous support and encouragement. This work was supported by MEXT grants to M.C.S. and H.S., a MEXT (Ministry of Education, Culture, Sports, Science and Technology, Japan) 21st COE (Centers of Excellence) postdoctoral fellowship to K.S. and T.S., and NEDO (New Energy and Industrial Technology Development Organization) grants to M.C.S., T.K. and K.A. M.C.S. is supported by CREST from JST. H.S. is a member of the Genome Network Project (MEXT).
Author Contributions Y.K., K.S., T.N.O. and M.C.S. performed AGO2 immunoprecipitations, northern blotting, RNAi, the in vitro cleavage assay, β-elimination and qRT–PCR, and prepared the AGO2-associated small RNA library. T.S. characterized and purified the AGO2 antibody. The bioinformatics analyses of AGO2-associated small RNAs were designed and carried out by T.K., K.S., Y.O. and K.A. M.C.S., K.S., Y.K. and H.S. designed the experiments, discussed the interpretation of the results and co-wrote the manuscript.
The file contains Supplementary Figures 1-9 with Legends, Supplementary Tables 1-3 and additional references.