The Drosophila nuclear Piwi-piRNA pathway enforces transposon silencing through dual mechanisms: the newly identified cofactors TEsup-1 and TEsup-2 both promote heterochromatin-based transcriptional repression and recruit nuclear RNA exosome adaptor complexes via proline-recognition domains to enable co-transcriptional degradation of nascent transposon RNAs, thereby resolving the paradox of how Piwi achieves robust silencing while requiring ongoing target transcription for its recruitment.

Nuclear Argonaute proteins safeguard genome integrity by directing transcriptional silencing and heterochromatin formation at transposon loci. Yet it remains unclear how Argonautes enforce robust repression while relying on target transcription for their own recruitment. Here we show that transposon silencing by the Drosophila nuclear Piwi–piRNA pathway requires degradation of target RNA by the nuclear exosome. Using proximity proteomics at endogenous Piwi target sites, we identify two previously uncharacterized paralogs, TEsup-1 and TEsup-2, as essential cofactors for Piwi-mediated silencing. TEsup proteins act in part by engaging nuclear exosome adaptor complexes at piRNA-targeted transcripts through a domain that recognizes proline-rich peptides. Disruption of the Piwi–TEsup–exosome axis leads to accumulation and nuclear export of piRNA-targeted transposon RNAs. Notably, the P-element—which evades heterochromatin-based repression—is silenced primarily through this RNA-decay pathway. Thus, the nuclear piRNA pathway couples target recognition to RNA degradation, reconciling small RNA–guided heterochromatin formation with ongoing transcription at target loci.