Poly(UG)-tailed RNAs are potent mediators of gene silencing in C. elegans

Abstract

Transposons are mobile genetic elements found in the genomes of nearly all organisms. Active transposons threaten genome integrity, and organisms have developed systems to inhibit transposon mobility. RNA interference (RNAi) is a biological process by which double stranded RNAs (dsRNAs) trigger the production of small interfering RNAs (siRNAs) which then promote post-transcriptional silencing of mRNAs. In Caenorhabditis elegans (C. elegans), several factors required for RNAi also contribute to transposon silencing, implicating RNAi as a mechanism for transposon silencing. One of these factors is RDE-3 (or MUT-2), a predicted ribonucleotidyltransferase. When tethered to RNAs in heterologous expression systems, RDE-3 adds long, non-templated, and alternating uridine (U) and guanosine (G) ribonucleotide repeats (pUG tails) to the 3′ termini of RNAs. Our lab has shown that in its natural context in C. elegans, RDE-3 adds pUG tails to targets of RNAi, as well as to transposon RNAs, generating pUG RNAs. My work characterizes pUG RNAs as a novel agent of gene silencing. 3’ pUG tails consisting of perfectly alternating U and G nucleotide repeats confer silencing activity to otherwise inert RNA fragments. pUG tails promote gene silencing by recruiting RNA-dependent RNA polymerases (RdRPs), which then use the preceding RNA fragments as templates to synthesize siRNAs. Cycles of pUG RNA-templated siRNA synthesis and siRNA-directed pUG RNA biogenesis underlie the dsRNA-triggered multigenerational silencing of germline genes observed in C. elegans. Thus, we propose pUG tails as a novel protein-recruiting RNA modification and pUG RNAs as an essential component of the siRNA-mediated gene silencing pathway that contribute to maintaining genome integrity in C. elegans.