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Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

Science  03 Aug 2012:
Vol. 337, Issue 6094, pp. 574-578
DOI: 10.1126/science.1220952

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Secondary Endogenous Small and Interfering

In many eukaryotes, Piwi proteins bind small noncoding Piwi-interacting RNAs (piRNAs) that function to silence transposons in the germ line and protect the germ line from transposable element–driven recombination and mutation. Bagijn et al. (p. 574, published online 14 June; see the Perspective by Xiol and Pillai) show that in the nematode, Caenorhabditis elegans, a messenger RNA (mRNA) that contains a piRNA target sequence gives rise to a second, downstream class of small RNAs known as secondary endogenous small interfering RNAs, or endo siRNAs. These endo siRNAs map to the vicinity of the piRNA complementary sequence in the mRNA target and depend on both Piwi and on factors involved in the related RNA interference pathway for their genesis, but not on the Piwi slicer activity. Mapping the endo siRNAs reveals that piRNAs can target imperfectly matched targets and that piRNAs target a subset of both transposons and endogenous genes for silencing.

Abstract

Piwi-interacting RNAs (piRNAs) are small RNAs required to maintain germline integrity and fertility, but their mechanism of action is poorly understood. Here we demonstrate that Caenorhabditis elegans piRNAs silence transcripts in trans through imperfectly complementary sites. Target silencing is independent of Piwi endonuclease activity or “slicing.” Instead, piRNAs initiate a localized secondary endogenous small interfering RNA (endo-siRNA) response. Endogenous protein-coding gene and transposon transcripts exhibit Piwi-dependent endo-siRNAs at sites complementary to piRNAs and are derepressed in Piwi mutants. Genomic loci of piRNA biogenesis are depleted of protein-coding genes and tend to overlap the start and end of transposons in sense and antisense, respectively. Our data suggest that nematode piRNA clusters are evolving to generate piRNAs against active mobile elements. Thus, piRNAs provide heritable, sequence-specific triggers for RNA interference in C. elegans.

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