Germ Granules Promote Self Versus Non-Self RNA Recognition to Protect Fertility

Germ cells are uniquely capable of giving rise to an entirely new organism. This totipotency relies on their ability to assemble germ granules, RNA and protein condensates enriched with conserved RNA regulators. Among the conserved factors, small RNAs and their processing machinery play critical roles in germ cell identity, genome integrity, and gamete differentiation. To carry out these roles, several types of small RNAs function in RNA regulation to silence the expression of "non-self" genetic elements, like transposons, and regulate the timing and spatial expression of endogenous "self" mRNAs. How small RNAs distinguish "self" from "non-self" mRNAs during germ cell development remains poorly understood. While many steps of small RNA processing are spatially organized within germ granules, it is unclear how critical this organization is for the regulation and function of small RNA processes. In this dissertation, I investigate the regulation of small RNA pathways within germ cells and how environmental changes challenge these processes. First, I identify RNA helicase RHA-1/DHX9 as a key factor that promotes specialized small RNA biogenesis and sorting. This small RNA sorting enables germ cells to distinguish "self" from "non-self" mRNAs. Next, I explore sex-dependent differences in the response to environmental double-stranded RNAs. I find small RNA pathway competition limits the RNA interference activity in male germ cells. Finally, I examine how environmental stress impacts germ granule organization. Following heat stress, I find germ granules partially disassemble but also promote stress granule and P-body assembly at the nuclear periphery. I show that like stress granules, germ granules ensure the recovery of germ cell viability after stress. Overall, these findings improve our understanding of how germ granules and small RNAs coordinate the regulation of diverse RNA sequences to protect germ cells from an array of environmental challenges for future generations.