Abstract
Piwi-interacting RNAs (piRNA) are small regulatory RNAs with essential roles in maintaining genome integrity in animals and protists. Most Caenorhabditis elegans piRNAs are transcribed from two genomic clusters that likely contain thousands of individual transcription units; however, their biogenesis is not understood. Here we identify and characterize prde-1 (piRNA silencing-defective) as the first essential C. elegans piRNA biogenesis gene. Analysis of prde-1 provides the first direct evidence that piRNA precursors are 28- to 29-nucleotide (nt) RNAs initiating 2 nt upstream of mature piRNAs. PRDE-1 is a nuclear germline-expressed protein that localizes to chromosome IV. PRDE-1 is required specifically for the production of piRNA precursors from genomic loci containing an 8-nt upstream motif, the Ruby motif. The expression of a second class of motif-independent piRNAs is unaffected in prde-1 mutants. We exploited this finding to determine the targets of the motif-independent class of piRNAs. Together, our data provide new insights into both the biogenesis and function of piRNAs in gene regulation.
Highlights
Piwi-interacting RNAs have an evolutionarily conserved role in maintaining the genetic and epigenetic integrity of the germline in many organisms (Malone and Hannon 2009). piRNAs in ciliates are involved in genome editing (Chalker and Yao 2011), and in planaria, piRNAs are involved in regeneration and neoblast function (Reddien et al 2005; Palakodeti et al 2008)
We developed an in vivo assay for piRNA function in the germline of C. elegans using a ‘‘piRNA sensor’’ transgene expressing a histone-GFP fusion protein in the germline that is responsive to the endogenous piRNA 21UR-1
We identified a first gene, prde-1, that is essential for the production of piRNA precursors upstream of PRG-1 in C. elegans
Summary
Piwi-interacting RNAs (piRNAs) have an evolutionarily conserved role in maintaining the genetic and epigenetic integrity of the germline in many organisms (Malone and Hannon 2009). piRNAs in ciliates are involved in genome editing (Chalker and Yao 2011), and in planaria, piRNAs are involved in regeneration and neoblast function (Reddien et al 2005; Palakodeti et al 2008). Despite these similarities to piRNAs in other organisms, C. elegans piRNAs differ in both their mechanism of action and their production: C. elegans piRNAs silence transposons and protein-coding genes in a manner that is independent of Piwi endonuclease activity or ‘‘slicing.’’ Instead, C. elegans piRNAs silence transcripts in trans and often through imperfectly complementary sites by initiating a localized secondary endogenous siRNA (endosiRNA) response (Bagijn et al 2012; Lee et al 2012). The significance of the ability of piRNAs to target genes in such a manner remains poorly understood, as do the rules that determine which genes become targets of the piRNA pathway and which remain independent
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
