A developmental switch in the piRNA pathway ensures stage-specific transposon silencing in Drosophila

These TEs are targeted by a piRNA program that relies on promoter-driven piRNA clusters independently of Moonshiner, Kipferl, and H3K27me3. In the second phase, triggered at the transition to endocycling nurse cells, the coordinated upregulation of Moon, Kipferl, Nxf3, and Bootlegger combined with increased H3K27me3 deposition reconfigures the piRNA pathway for enhanced piRNA production from heterochromatic dual-strand clusters, targeting the additional TE families activated in the polyploid nurse cell environment.

Stage-specific chromatin profiling reveals that Piwi-dependent H3K9me3 deposition at TE loci requires their transcriptional activation. Importantly, silencing established by the early piRNA program can be maintained independently of piRNA pathway activity in later development, consistent with an epigenetic lock mechanism. Our findings establish that the piRNA pathway is not merely maintained but actively remodeled across germline development to match changing TE silencing demands.