Chemical catalyst/protein hybrid as artificial histone-modifying enzyme for epigenome manipulation

Chemical biology approaches that can manipulate the epigenome hold promise to elucidate the role of epigenetics in gene regulation and may have utility in translational research. However, there are few methods to artificially introduce epigenetic modifications in living cells without reliance on endogenous enzymes. Here, we develop a chemical catalyst/protein hybrid promoting regioselective histone acylation, comprised of the cell-permeable lysine-acylating chemical catalyst TMP-BAHA and the nucleosome-binding fusion protein LANA-inserted eDHFR (LieD). Molecular modelling and molecular dynamics simulations with an atomistic model suggested that the catalyst-binding pocket of LieD was close to H2B lysine-120 (H2BK120). Consistent with this, TMP-BAHA bound to LieD and efficiently promoted H2BK120 acetylation in cells, which inhibited both H2BK120 ubiquitination and H3K79 dimethylation, active marks of gene transcription. Furthermore, the system incorporated other natural and unnatural acylations at target lysines, enabling study of endogenous histones. Our results suggest that a chemical catalyst/protein hybrid, such as the TMP-BAHA/LieD system, can function as an artificial histone-modifying enzyme and thus expands the toolbox of chemical biology for epigenome manipulation.