Abstract
In germ cells, small RNAs function as a defense system to silence invading RNAs like viruses and transposons to protect genome integrity. The ability of small RNAs to robustly silence diverse RNA sequences prompts the question of how endogenous mRNAs avoid this silencing. In C. elegans, small RNAs bound by the Argonaute CSR-1 protect endogenous mRNAs from silencing, while also fine-tuning a subset of these mRNAs. Here, we identify RNA Helicase A (RHA-1) as a key regulator of CSR-1 small RNA biogenesis and function in mRNA fine-tuning. RHA-1 localizes to germ granules dependent on EGO-1, which synthesizes CSR-1 small RNAs. We find RHA-1 promotes small RNA production from the 5' regions of mRNAs and small RNA sorting to CSR-1. Loss of RHA-1 leads to elevated CSR-1 target mRNA levels and compromised fertility. Our study highlights the importance of small RNA regulation, mediated by RHA-1, to protect endogenous gene expression programs and germ cell function.