Journal Article

Genetic and mechanistic diversity of piRNA 3′-end formation

Schnabl, Jakob, Handler, Dominik, Ameres, Stefan L., Mohn, Fabio, Brennecke, Julius, Hayashi, Rippei

2016

Overview

Drosophila have two pathways for PIWI-interacting RNA (piRNA) 3′-end formation—depending on which pathway is used, piRNA biogenesis is directed towards either cytoplasmic or nuclear PIWI protein effectors, which balances post-transcriptional versus transcriptional transposon silencing. Twin track of piRNA 3′-end formation Unlike microRNAs and short interfering RNAs, PIWI-interacting RNAs (piRNAs) are not generated by Dicer cleavage. The process leading to the 5′ ends of piRNAs is known, but mediating the formation of the 3′-ends has been difficult. Julius Brennecke and colleagues now show that there are two pathways in Drosophila capable of 3′-end formation. Depending on which pathway is used, the piRNA product is directed to either a cytoplasmic or a nuclear PIWI protein effector, which determines whether the piRNA functions in post-transcriptional or transcriptional events. Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing 1 . Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI-interacting RNAs (piRNAs)—the 22–30-nt-long guides for PIWI-clade Ago proteins that silence transposons in animal gonads—are generated independently of Dicer from single-stranded precursors 2 , 3 . piRNA 5′ ends are defined either by Zucchini, the Drosophila homologue of mitoPLD—a mitochondria-anchored endonuclease 4 , 5 , or by piRNA-guided target cleavage 6 , 7 . Formation of piRNA 3′ ends is poorly understood. Here we report that two genetically and mechanistically distinct pathways generate piRNA 3′ ends in Drosophila . The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub) or Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3′ ends 8 , 9 , Aub/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3′-to-5′ exoribonuclease Nibbler ( Drosophila homologue of Mut-7) 10 , 11 , 12 , 13 . The relative activity of these two pathways dictates the extent to which piRNAs are directed to cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Notably, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway in which piRNA 5′ and 3′ ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data reveal a coherent model for piRNA biogenesis, and should aid the mechanistic dissection of the processes that govern piRNA 3′-end formation.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/208/505 / 631/337/505 / Animals / Argonaute Proteins - metabolism / Biosynthesis / Cytoplasm - metabolism / Drosophila melanogaster - enzymology / Drosophila melanogaster - genetics / Drosophila melanogaster - metabolism / Drosophila Proteins - deficiency / Drosophila Proteins - metabolism / Endoribonucleases - deficiency / Endoribonucleases - metabolism / Exoribonucleases - deficiency / Exoribonucleases - metabolism / Female / Gene expression / Genes / Genetic aspects / Gonads / Humanities and Social Sciences / letter / Mitochondria / multidisciplinary / Nuclear Proteins - metabolism / Ovaries / Peptide Initiation Factors - metabolism / Proteins / Ribonucleic acid / RNA / RNA Processing, Post-Transcriptional / RNA sequencing / RNA, Guide, CRISPR-Cas Systems / RNA, Small Interfering - biosynthesis / RNA, Small Interfering - chemistry / RNA, Small Interfering - genetics / RNA, Small Interfering - metabolism / Science / Transcription, Genetic