Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

The Piwi-interacting RNA (piRNA) pathway plays an essential role in the repression of transposons in the germline. Other functions of piRNAs such as post-transcriptional regulation of mRNAs are now emerging. Here, we perform iCLIP with the PIWI protein Aubergine (Aub) and identify hundreds of maternal mRNAs interacting with Aub in the early Drosophila embryo. Gene expression profiling reveals that a proportion of these mRNAs undergo Aub-dependent destabilization during the maternal-to-zygotic transition. Strikingly, Aub-dependent unstable mRNAs encode germ cell determinants. iCLIP with an Aub mutant that is unable to bind piRNAs confirms piRNA-dependent binding of Aub to mRNAs. Base pairing between piRNAs and mRNAs can induce mRNA cleavage and decay that are essential for embryonic development. These results suggest general regulation of maternal mRNAs by Aub and piRNAs, which plays a key developmental role in the embryo through decay and localization of mRNAs encoding germ cell determinants. [Display omitted] •Aub binds to maternal mRNAs in early Drosophila embryos•Interaction between Aub and maternal mRNAs depends on piRNAs•aub mutants are defective in mRNA decay during the MZT•Aub-dependent unstable mRNAs encode germ cell determinants Using iCLIP, Barckmann et al. identify several hundred maternal mRNAs that interact with Aub in early embryos. A number of these mRNAs undergo Aub-dependent destabilization in the soma during the maternal-to-zygotic transition and encode germ cell determinants.