Proteolytic processing of Argonautes in multiphase condensates promotes transgenerational epigenetic inheritance

Epigenetic information can be memorized in perinuclear condenates to transmit across generations to modulate gene expression in descenent. Here, we identify a conserved N terminal proteolytic mechanism in Caenorhabditis elegans that is essential for small RNA-mediated transgenerational epigenetic inheritance (TEI) and for maintaining germline immortality. Two conserved, perinuclear germ granule subcompartments-enriched N-terminal processing peptidases, APP-1 and DPF-3, act cooperatively to trim N-terminal intrinsically disordered regions of the Argonaute proteins WAGO-1, WAGO-3, and WAGO-4. This processing shields these Argonautes from proteasome-mediated protein degradation, prevents the loss of their associated small RNAs, and promotes their accumulation in germ granules subcompartments. In contrast, unprocessed WAGOs are recognized and destabilized by the conserved E3 ubiquitin ligases RNF-1 and UBR-7. We propose that this cooperative proteolytic mechanism adds another layer of sspatiotemporal regulation over small RNA-directed epigenetic inheritance and may represents a broadly conserved strategy for regulating protein homeostasis and gene expression programs.