ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals

Abstract

Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In the germline, epigenetic factors are enriched in liquid-like perinuclear condensates called nuage. Here, we identify the deeply conserved helicase-domain protein, ZNFX-1, as an epigenetic regulator and component of nuage that interacts with Argonaute systems to balance epigenetic inheritance. Our findings suggest that ZNFX-1 promotes the 3' recruitment of machinery that propagates the small RNA epigenetic signal and thus counteracts a tendency for Argonaute targeting to shift 5' along the mRNA. These functional insights support the idea that recently identified subdomains of nuage, including ZNFX-1 granules or "Z-granules," may define spatial and temporal zones of molecular activity during epigenetic regulation.

Germ Granules Functions are Memorized by Transgenerationally Inherited Small RNAs

“…Germ granules were hypothesized to balance the levels of different small RNA species 21,22 , and it is well established that different small RNA pathways compete over limited biogenesis factors 7,8,[42][43][44] . To understand how germ granules regulate small RNA levels, we sequenced small RNAs from dissected germlines of germ granule-defective pptr-1 mutants (the mutants that we found to always exhibit strong RNAi inheritance).…”

“…Many of the factors which participate in transgenerational small RNA inheritance reside in germline-specific ribonucleoprotein complexes termed germ granules [17][18][19][20][21][22][23] . P granules are RNA-rich, cytoplasmic, perinuclear liquid-like condensates 24 , which are maternally deposited to the oocyte 25,26 , and following fertilization are asymmetrically segregated to the P lineage designated to become the germline 27 .…”

“…P granules are required for maintaining the identify of germ cells throughout development, by preventing ectopic expression of somatic genes [28][29][30] . P granules are localized adjacent to nuclear pores, to survey the expression of mRNA molecules exiting the nucleus 22,31,32 . Various P granules-associated proteins were found to be required for RNAi or for RNAi inheritance, including the P granule core-forming proteins PGL-1 33,34 , MEG-3 and MEG-4 20 , and the VASA homolog GLH-1 35 .…”

“…The Z granules co-localize with P granules, but during the mitotic stage in the adult germline the two granules separate, while remaining adjacent to each other 20 . Z granules contain the WAGO-4 argonaute 20,21 , and the ZNFX-1 protein 20,22 , needed for balanced small RNA amplification 22 . Both proteins were shown to be required for RNAi inheritance [20][21][22] .…”

Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans

“…Hence, DEPS-1 serves as a common factor in multiple small RNA pathways. Previous work shows that the absence of piRNAs leads to secondary endo-siRNAs being mis-loaded to Argonaute proteins (Phillips et al, 2015) and that the zinc-finger protein ZNFX-1 associates with multiple Argonaute proteins (Ishidate et al, 2018). Thus, balanced inputs of small RNAs compete for the small RNA machineries to achieve balanced epigenetic signals.…”