A small RNA mechanism distinct from the RNAi and microRNA pathways silences selfish genetic elements in Drosophila.. Drosophila melanogaster

In flies, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Here, we show that while small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise mainly from the antisense strand. rasiRNA production appear not to require Dicer-1, which makes microRNAs, or Dicer-2, which makes siRNAs, and rasiRNAs lack the 2´,3´ hydroxy termini characteristic of animal siRNA and miRNA. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. Thus, rasiRNAs define a third RNA silencing pathway distinct from both the miRNA and RNAi pathways. Keywords: gene silencing; post-transcriptional gene regulation; short RNAs; RNAi; rasiRNAs; rasiRNA; microRNAs; microRNA; siRNAs; siRNA Overall design: Short RNAs homologous to several selfish genetic elements (including Su(Ste) and roo), as well as a transgenic inverse-repeat made of white exon 3, were detected using custom-made tiling microarrays. These arrays also detect microRNAs. We used them to quantify rasiRNAs and siRNAs in various genetic backgrounds. Su(Ste) rasiRNAs were quantified in crystal mutants vs. wt (two arrays, with color-reversal; wt samples for both arrays were prepared independently, as well as cry samples); in armitage mutants vs. wt (two arrays, with color-reversal; the same