Molecular Insights into Inhibition of the Methylated Histone-Plant Homeodomain Complexes by Calixarenes

Abstract Plant homeodomain (PHD) finger-containing proteins are implicated in fundamental biological processes including transcriptional activation and repression, DNA damage repair, cell differentiation and survival. The PHD finger functions as an epigenetic reader that binds to posttranslationally modified or unmodified histone H3 tails, recruiting catalytic writers and erasers and other components of the epigenetic machinery to chromatin. Despite the critical role of the histone-PHD interaction in normal and pathological processes, selective inhibitors of this association have not been well developed. Here, we demonstrate that macrocyclic calixarenes can disrupt binding of PHD fingers to methylated histone H3K4 tail in vitro and in vivo. The inhibitory activity relies on differences in binding affinities of the PHD fingers for H3K4me and the methylation state of the histone ligand, whereas the composition of the aromatic H3K4me-binding site of the PHD fingers appears to have no effect. Our approach provides a novel tool for studying biological roles of the methyllysine readers in epigenetic signaling.