piRNA direct the chromatin reader to its genomic targets

Abstract

The chromatin reader Rhino (Rhi) is an HP1-paralog and master regulator of piRNA biogenesis in Drosophila that drives the transcription of piRNA precursors. While Rhi binds the heterochromatic mark H3K9me3, this interaction is insufficient to explain its specific occupancy, as Rhi is excluded from the majority of H3K9me3-enriched loci. Instead, we find that Rhi recruitment is orchestrated by several competing pathways, including the piRNA-guided protein Panoramix (Panx) and the DNA-binding protein Kipferl (Kipf). We demonstrate that Panx functions as a piRNA-guided modular scaffold that directs Rhi to its targets through a dual-mode mechanism: its N-terminus recruits the H3K9 methyltransferase machinery, while its C-terminus directly binds the Rhi chromodomain. While H3K9me3 deposition provides a necessary foundation, it acts in synergy with the direct Panx-Rhi physical bridge to drive robust Rhi occupancy. Furthermore, Rhi recruitment is amplified by the cytoplasmic inheritance of maternal piRNAs, forming a transgenerational feed-forward loop. Our results reveal that the piRNA pathway imparts sequence-specificity to the H3K9me3 code, utilizing a direct physical bridge to program the genomic distribution of the chromatin reader Rhi.