Germ granule compartments coordinate specialized small RNA production

Germ granules are biomolecular condensates present in most animal germ cells. One function of germ granules is to help maintain germ cell totipotency by organizing mRNA regulatory machinery, including small RNA-based gene regulatory pathways. The C. elegans germ granule is compartmentalized into multiple subcompartments whose biological functions are largely unknown. Here, we identify a new subcompartment of the C. elegans germ granule, which we term the E compartment. The E compartment is nonrandomly positioned within the germ granule. We identified five proteins that localize to the E compartment, including the RNA-dependent RNA polymerase (RdRP) EGO-1, the Dicer-related helicase DRH-3, the Tudor domain-containing protein EKL-1, and two intrinsically disordered proteins, EGC-1 and ELLI-1. Localization of EGO-1 to the E granule enables synthesis of a specialized class of 22G RNAs, which derive exclusively from 5 ’ regions of a subset of germline-expressed mRNAs. Defects in E compartment assembly elicit disordered production of endogenous siRNAs, which disturbs fertility and the RNAi response. Our results define a new subcompartment of the C. elegans germ granule and suggest that one function of germ granule compartmentalization is to facilitate the localized production of specialized classes of small regulatory RNAs.