Caenorhabditis elegans germ granules are present in distinct configurations and assemble in a hierarchical manner.

RNA silencing pathways are complex, highly conserved, and perform crucial regulatory roles. In Caenorhabditis elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments - P granules, Z granules, SIMR foci, and Mutator foci - multiple of which form via phase separation. Although the functions of individual germ granule proteins have been extensively studied, the relationships between germ granule compartments (collectively, 'nuage') are less understood.

germ granules are present in distinct configurations that differentially associate with RNAi-targeted RNAs.

RNA silencing pathways are complex, highly conserved, and perform widespread, critical regulatory roles. In germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments-P granules, Z granules, SIMR foci, and foci-multiple of which form via phase separation and exhibit liquid-like properties. The functions of individual proteins within germ granules are well-studied, but the spatial organization, physical interaction, and coordination of biomolecule exchange between compartments within germ granule "nuage" is less understood.

Epitope tag-specific differences in the detection of COSA-1 marked crossover sites in spermatocytes.

Nascent crossover sites in meiocytes can be cytologically detected using epitope-tagged versions of the pro-crossover protein COSA-1. In spermatocytes, differences exist between cytologically-detected and genetically-detected double crossover rates. Here, we examine nascent crossovers using both GFP- and OLLAS-tagged COSA-1.

SIMR foci are found in the progenitor germ cells of embryos.

RNA interference is a widely conserved mechanism of gene regulation and silencing across eukaryotes. In , RNA silencing is coordinated through perinuclear nuage containing at least four granules: P granules, Z granules, foci, and SIMR foci. Embryonic localization of these granules is known for all except SIMR foci.

Foci Are Regulated by Developmental Stage, RNA, and the Germline Cell Cycle in .

RNA interference is a crucial gene regulatory mechanism in Phase-separated perinuclear germline compartments called foci are a key element of RNAi, ensuring robust gene silencing and transgenerational epigenetic inheritance. Despite their importance, foci regulation is not well understood, and observations of foci have been largely limited to adult hermaphrodite germlines. Here we reveal that punctate foci arise in the progenitor germ cells of early embryos and persist throughout all larval stages.

A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in .

piRNAs play a critical role in the regulation of transposons and other germline genes. In , regulation of piRNA target genes is mediated by the complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the complex are unknown.

Visualization and Quantification of Transposon Activity in RNAi Pathway Mutants.

RNA silencing pathways play critical roles in maintaining quiescence of transposons in germ cells to promote genome integrity. However the precise mechanism by which different types of transposons are recognized by these pathways is not fully understood. Furthermore, the location in the germline where this transposition occurs after disruption of transposon silencing was previously unknown.

Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci.

In C. elegans, efficient RNA silencing requires small RNA amplification mediated by RNA-dependent RNA polymerases (RdRPs). RRF-1, an RdRP, and other Mutator complex proteins localize to Mutator foci, which are perinuclear germline foci that associate with nuclear pores and P granules to facilitate small RNA amplification.