Binding of heterochromatin protein Rhino to a subset of piRNA clusters depends on a combination of two histone marks

Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements (TEs) and maintain genome integrity. In Drosophila melanogaster germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in TE fragments, via an elaborate machinery centered on the Heterochromatin Protein 1 homolog, Rhino. Although Rhino binds to peptides carrying tri-methylated H3K9 in vitro, it is not fully understood why in vivo only a fraction of H3K9me3-decorated heterochromatin is occupied by Rhino. Recent work revealed that Rhino is recruited to a subset of piRNA clusters by Kipferl. Here we identify a Kipferl-independent mode of Rhino recruitment that, in addition to the previously established role of H3K9me3, also depends on the histone H3 lysine 27 methyltransferase Enhancer of Zeste. At Kipferl-independent sites, we find that Rhino specifically binds to loci marked by both H3K9me3 and H3K27me3 via its chromodomain. Although the exact mechanism of how Rhino binding is influenced by dual histone modifications remains unclear from a structural and biochemical perspective, our work suggests that combinatorial modifications may regulate the specificity of chromatin-binding protein interactions. These findings provide an enhanced understanding of how Rhino targets piRNA source loci, highlighting the sophisticated epigenetic landscape governing TE silencing in Drosophila germ cells. The authors reveal that, in fruit fly ovaries, the protein Rhino is guided to specific regions of the genome by a combination of two histone modifications, enhancing understanding of how cells protect their DNA from harmful virus-like elements.