Logics for Developing Regioselective Histone Acetylating Catalysts

The combination of post-translational modifications (PTMs) of histones, a major component of chromatin, defines “histone code” having distinct impact on chromatin structures and gene expression. Therefore, methods to introduce histone PTMs at desired positions are useful tools for investigating the functions of epigenetic marks, especially to understand consequences of specific modifications in histones. Chemical catalysts, such as lysine (Lys)-acetylating catalysts, have been emerged to regioselectively promote histone PTMs without relying on histone-modifying enzymes. However, it has been poorly under-stood what factors determine Lys-residue selectivity of the histone acetylating catalysts. Here we show that the intrinsic reac-tivity, distance from the catalytically active site, and conformational flexibility of Lys residues, are the critical factors for determining acetylation yield and regioselectivity. Combining molecular dynamics simulations of catalyst-nucleosome com-plexes and experimental optimization of the catalyst structure, we developed three catalysts that selectively acetylated K43, K108, and K120 of H2B, respectively. Biochemical analyses of the regioselectively acetylated nucleosomes revealed that each Lys acetylation showed distinct impacts on inter-nucleosomal interactions and the affinity to a nucleosome-binding molecule. Our data provide a guideline for developing regioselective histone acetylation catalysts and may further accelerate studies of epigenetics regulated by histone PTMs.