Evolutionary adaptation of the chromodomain of the HP1-protein Rhino allows the integration of chromatin and DNA sequence signals

Abstract

ABSTRACTMembers of the diverse heterochromatin protein 1 (HP1) family of proteins play crucial roles in heterochromatin formation and maintenance. Despite the similar affinities of their chromodomains for di- and tri-methylated histone H3 lysine 9 (H3K9me2/3), different HP1 proteins exhibit distinct chromatin binding patterns, presumably due to their interactions with various specificity factors. Here, we elucidate the molecular basis of the protein-protein interaction between the HP1 protein Rhino, a critical factor of theDrosophilapiRNA pathway, and Kipferl, a DNA sequence-specific C2H2zinc finger protein and Rhino guidance factor. Through phylogenetic analyses, structure prediction, andin vivogenetics, we identify a single amino acid change within Rhino’s chromodomain, G31D, that does not affect H3K9me2/3 binding but abolishes the specific interaction between Rhino and Kipferl. Flies carrying therhinoG31Dmutation phenocopykipferlmutant flies, with Rhino redistributing from piRNA clusters to satellite repeats, causing pronounced changes in the ovarian piRNA profile ofrhinoG31Dflies. Thus, Rhino’s chromodomain serves as a dual-specificity module, facilitating interactions with both a histone mark and a DNA-binding protein.