Abstract
The nematode C. elegans contains numerous classes of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase complexes (RdRP). Both “silencing” siRNAs bound by Worm-specific Argonautes (WAGO) and “activating” siRNAs bound by CSR-1 require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the histone mark H3K27me3 ectopically accumulates at highly expressed genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants. Correlating with these chromatin changes in the mutants, there is a global increase in antisense transcription and a specific increase in enhancer RNA levels. Finally, we detect siRNA landscape changes in RdRP and drh-3(ne4253) mutants and accumulation of dsRNA in the nuclei of drh-3(ne4253) worms. Our study suggests 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.