Divergent regulatory impacts of endogenous siRNAs on host mRNAs in testis of closely related species

Summary Invertebrates use RNAi to fight viruses that replicate via dsRNA intermediates, which serve as precursors for producing anti-viral siRNAs. In addition, siRNAs are produced from a broad range of endogenous dsRNAs in Drosophila melanogaster . However, beyond the impacts of siRNAs derived from a handful of hairpin RNAs, the regulatory potential of most endo-siRNAs has been unknown. Here, we report that RNAi is far more potent in the close sister species Drosophila simulans . Consequently, endo-siRNAs repress less than a dozen transcripts in D. melanogaster , but hundreds of mRNAs in D. simulans testis. These regulatory interactions occur in cis (between pairs of bidirectionally transcribed loci), as well as in trans (between genomically unlinked siRNA-target pairs). We establish the molecular determinants of productive gene repression by siRNAs in vivo , including cleavage in trans via > 16-nt contiguous complementarity. Our data indicate that D. simulans spermatogenesis requires repression of numerous host mRNAs by endo-siRNAs. More generally, we reveal unexpectedly fast-evolving and broad regulatory impacts of endogenous RNAi in the male germline.