Nucleosome Turnover Establishes Histone Methylation Valence Status Genome-Wide

Despite extensive genome-wide, biochemical, and genetic characterizations, we do not fully understand how the epigenetic “landscape” is established in vivo or how chromatin modifiers interact to orchestrate unique biologic outcomes. Methylation of H3K79 is catalyzed by the DOT-complex, which despite being evolutionarily conserved and implicated in the development of Mixed Lineage Leukemia, remains poorly understood. Mono-, di-, and tri- H3K79 methylation marks are solely deposited by the DOT1L methyltransferase which is aberrantly retargeted in recurrent MLL-rearranged leukemia and critical for persistence of the disease. To define the minimal factors required to regulate histone methylation status, we inducibly tethered the OMLZ domain of the DOT-complex subunit AF10 to a synthetic DNA binding domain and used chemical-induced proximity (CIP) to selectively deposit H3K79me at endogenous, un-methylated genes in vivo. Through CIP, we characterize the kinetics of me1/me/me3 in real-time in diverse genomic contexts. We developed a Monte Carlo simulation coupling both the system of equations for processive methylation kinetics and nucleosome turnover and performed a meta-analysis on histone methylation to determine the contributions of histone turnover to methylation valency. We determine that nucleosome turnover is sufficient to establish varied methylation valency states and propose a conserved general principle for establishing the epigenetic landscape in both the presence and absence of active demethylation. Not only does our model support the genome-wide valency of H3K79 methylation, but when measurable parameters such as site-specific demethylation and rapid methylation are added, our model explains methylation states observed for other histone marks genome-wide, including both activating and repressive chromatin modifications in both diseased and conserved contexts. While the methylation dynamics we present are simple, histone methylation state appears to be characterized by processive-first order kinetics, governed by first-principles, and largely influenced by the rate of nucleosome turnover.