Transgenerational Epigenetic Inheritance Factors Localize to Spatiallyand Temporally Ordered Liquid Droplet Assemblages

Abstract

Epigenetic information can be inherited for multiple generations (termed transgenerational epigenetic inheritance or TEI) 1,2. Non-coding RNAs have emerged as important mediators of TEI, although the mechanism(s) by which non-coding RNAs mediate TEI remains poorly understood. dsRNA-mediated gene silencing (RNAi) in C. elegans is a robust example of RNA-directed TEI3-5. To further our understanding of RNA-directed TEI, we conducted a genetic screen in C. elegans to identify genes required for RNAi inheritance. Our screen identified the conserved RNA helicase/Zn finger protein ZNFX-1 and the Argonaute protein WAGO-4. We find that WAGO-4 and ZNFX-1 act cooperatively in inheriting generations to maintain small interfering (si)RNA expression over generational time. ZNFX-1/ WAGO-4 localize to a liquid droplet organelle termed the P granule in early germline blastomeres. Later in development, ZNFX-1/WAGO-4 appear to separate from P granules to form independent foci that are adjacent to, yet remain distinct, from P granules. ZNFX-1/WAGO-4 labeled foci exhibit properties reminiscent of liquid droplets and we name these foci Z granules. In the adult germline, Z granules assemble into ordered tri-droplet assemblages with P granules and another germline droplet-like foci termed the Mutator foci. This work identifies a conserved RNA-binding protein that drives RNA-directed TEI in C. elegans, defines a new germline foci that we term the Z granule, demonstrates that liquid droplet formation is under developmental control, and shows that liquid droplets can assemble into spatially ordered multi-droplet structures. We speculate that temporal and spatial ordering of liquid droplets helps cells organize and coordinate the complex RNA processing pathways underlying gene regulatory systems, such as RNA-directed TEI.