A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci

Abstract

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 and maintain genome integrity. In Drosophila germ cells, the majority of piRNA populations originate from dual-strand piRNA clusters, genomic regions highly enriched in transposon fragments, via an elaborate protein machinery centred on the heterochromatin protein 1 homolog, Rhino. Although Rhino binds to peptides carrying trimethylated H3K9 in vitro, it is not fully understood why in vivo only a fraction of H3K9me3-decorated heterochromatin is occupied by Rhino. Recent work uncovered that Rhino is recruited to a subset of piRNA clusters by the zinc finger protein Kipferl. Here we identify a Kipferl-independent mode of Rhino targeting that is dependent on the histone H3 lysine 27 methyltransferase Enhancer of Zeste and the presence of H3K9me3 and H3K27me3 marks. At Kipferl-independent sites, we find that Rhino, through its dimeric chromodomain, specifically binds to loci marked by both H3K9me3 and H3K27me3. These results expand our understanding of the characteristic binding profile of the heterochromatin protein Rhino. Our work reveals a role for dual histone modifications in defining the binding specificity of a chromatin protein.

Small‐RNA‐guided histone modifications and somatic genome elimination in ciliates

“…Enhancer-of-zeste proteins, which are the catalytic subnits of PRC2, have recently been implicated in the transcriptional control of TEs in these organisms (Hisanaga et al, 2023), supporting the idea that this may constitute the ancestral function of PRC2 (Déléris et al, 2021). Beyond participating in transcriptional repression of TEs directly, PRC2 was recently found to contribute to small-RNA biogenesis (Akkouche et al, 2024), suggesting that H3K27me3 can help control TEs at multiple levels.…”

“…Cao et al, 2002;Kuzmichev et al, 2002;Lachner et al, 2001). The presence of regions marked by both H3K9me3 and H3K27me3 in Paramecium raises the possibility that the same chromodomain-containing protein reads the two marks, as has been shown for Rhino in Drosophila (Akkouche et al, 2024). Despite the large number of chromodomain proteins encoded in the Paramecium genome, or perhaps because they are so numerous, none has so far been linked to Pgm complex recruitment to eliminated regions.…”

“…Meanwhile, in germline cells, H3K9me3 also accumulates at the clusters that serve as the source of piRNAs, leading to the binding of a dedicated reader of this histone mark called Rhino (Klattenhoff et al, 2009). At most sites, Rhino is recruited by the recently described Rhino-associated zinc finger protein, Kipferl (Baumgartner et al, 2022), while at the Kipferl-independent sites, it requires dual recognition of H3K27me3 and H3K9me3 for binding (Akkouche et al, 2024). Rhino acts together with its partners Deadlock and Cutoff to promote the synthesis of new piRNA precursors (Le Thomas et al, 2014;Mohn et al, 2014;Z.…”

The Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line

“…elegans . In Drosophila, piRNA precursors located in dual-strand clusters are dependent on co-occupancy of H3K27me3 and H3K9me3 at the promoter, which leads to the recruitment of the Rhino protein and subsequent transcription of the precursor RNA [ 32 – 36 ]. Thus, H3K27me3 and USTC in C .…”