Nuclear Argonaute HRDE-1 Sustains Chromatin-Independent Transcriptional Silencing and Epigenetic Inheritance

Epigenetic inheritance of transcriptional silencing is typically attributed to chromatin-based mechanisms in which Argonaute-small RNA complexes recruit histone-modifying enzymes. Here we show that, in Caenorhabditis elegans, the nuclear Argonaute HRDE-1 sustains germline repression independently of canonical heterochromatin marks. Inducible HRDE-1 depletion combined with germline nuclear sorting, CUT&Tag, and nascent transcription analysis revealed endogenous genes that become transcriptionally activated in the absence of HRDE-1 despite retention of H3K9me3 and H3K23me3. HRDE-1 further promotes polyUG-dependent amplification of antisense 22G-RNAs in perinuclear condensates, redefining nuclear Argonautes as active drivers of small RNA biogenesis rather than passive acceptors. Loss of HRDE-1 triggers the progressive erosion of 22G-RNAs and prevents the rapid re-establishment of silencing, underscoring the necessity of nuclear-cytoplasmic coupling for epigenetic memory. Our findings challenge the long-standing assumption that heterochromatin is required for transcriptional repression and redefine the mechanism by which nuclear Argonautes enforce epigenetic inheritance.