Interplay between small RNA pathways shapes chromatin landscapes in C. elegans

The nematode C. elegans contains numerous endogenous small RNAs produced by RNA-dependent RNA polymerase complexes. The DRH-3 helicase, a component of RdRP, is required for production of both 9silencing9 siRNAs bound by Worm-specific Argonautes (WAGO) and 9activating9 siRNAs bound by CSR-1. Here we show that in the drh-3(ne4253) mutant deficient in the RdRP-produced secondary endo-siRNAs there is an ectopic accumulation of H3K27me2 at highly expressed genes. Moreover, we observe ectopic H3K9me3 at the enhancer elements in both drh-3(ne4253) and csr-1(tm892) mutant backgrounds. Notably, our previous work described a global increase in antisense transcription upon csr-1 and drh-3 loss-of function, and now we also report an increase in enhancer RNA levels in these mutants. We propose that, in the absence of secondary siRNAs, elevated antisense transcription promotes nuclear dsRNA formation, which, in turn, can be cleaved by Dicer into primary siRNAs that guide deposition of silent chromatin marks. A change in the siRNA landscape in RdRP and drh-3(ne4253) mutants and accumulation of dsRNA in the nuclei of drh-3(ne4253) worms supports this model.