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Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo

Abstract

Piwi-associated RNAs (piRNAs), a specific class of 24- to 30-nucleotide-long RNAs produced by the Piwi-type of Argonaute proteins, have a specific germline function in repressing transposable elements. This repression is thought to involve heterochromatin formation and transcriptional and post-transcriptional silencing1,2,3,4,5,6. The piRNA pathway has other essential functions in germline stem cell maintenance7 and in maintaining germline DNA integrity8,9,10. Here we uncover an unexpected function of the piRNA pathway in the decay of maternal messenger RNAs and in translational repression in the early embryo. A subset of maternal mRNAs is degraded in the embryo at the maternal-to-zygotic transition. In Drosophila, maternal mRNA degradation depends on the RNA-binding protein Smaug and the deadenylase CCR411,12,13, as well as the zygotic expression of a microRNA cluster14. Using mRNA encoding the embryonic posterior morphogen Nanos (Nos) as a paradigm to study maternal mRNA decay, we found that CCR4-mediated deadenylation of nos depends on components of the piRNA pathway including piRNAs complementary to a specific region in the nos 3′ untranslated region. Reduced deadenylation when piRNA-induced regulation is impaired correlates with nos mRNA stabilization and translational derepression in the embryo, resulting in head development defects. Aubergine, one of the Argonaute proteins in the piRNA pathway, is present in a complex with Smaug, CCR4, nos mRNA and piRNAs that target the nos 3′ untranslated region, in the bulk of the embryo. We propose that piRNAs and their associated proteins act together with Smaug to recruit the CCR4 deadenylation complex to specific mRNAs, thus promoting their decay. Because the piRNAs involved in this regulation are produced from transposable elements, this identifies a direct developmental function for transposable elements in the regulation of gene expression.

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Figure 1: The piRNA pathway is required for nos mRNA deadenylation and decay as well as translational repression in the bulk cytoplasm of the embryo.
Figure 2: Aub is present in the bulk of the embryo and the piRNA pathway is required for CCR4 and Smg cytoplasmic distributions.
Figure 3: Aub, Ago3, Smg, CCR4 and nos mRNA are present in a common complex in the bulk of the embryo.
Figure 4: piRNAs target a specific region in nos 3′ UTR that is required for nos mRNA deadenylation.

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Acknowledgements

We are grateful to A. Nakamura, M. Siomi, H. Siomi, C. Smibert, H. Lin, P. Macdonald, T. Schüpbach, W. Theurkauf, R. Wharton and P. Zamore, for their gifts of antibodies or Drosophila stocks. We thank M. Benkirane for the gift of 2′-O-methyl anti-miR129. This work was supported by the Centre National de la Recherche Scientifique UPR1142, the Agence Nationale de la Recherche (ANR Blanche ANR-06-BLAN-0343), the Fondation pour la Recherche Médicale (FRM, Equipe FRM 2007) and the Association pour la Recherche sur le Cancer (ARC Libre 2009) to M.S. and by the National Institutes of Health (NIH R01-GM083300) to E.C.L. C.R., A.C.M. and B.F. held salaries from ANR Blanche.

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C.R. and C.P. designed and performed the experiments, analysed the data and contributed equally to the study. A.-C.M. contributed to the generation of DNA constructs, B.F. contributed to poly(A) test assays in Fig. 1. A.B., N.R. and E.C.L. performed the bioinformatic analyses. A.P. performed northern blots. M.S. designed the study, analysed data and wrote the paper. All authors discussed the results and commented on the manuscript.

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Correspondence to Martine Simonelig.

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Rouget, C., Papin, C., Boureux, A. et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467, 1128–1132 (2010). https://doi.org/10.1038/nature09465

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