The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin

Oncogenic histone lysine-to-methionine mutations block the methylation of their corresponding lysine residues on wild-type histones. One attractive model is that these mutations sequester histone methyltransferases, but genome-wide studies show that mutant histones and histone methyltransferases often do not colocalize. Using chromatin immunoprecipitation sequencing (ChIP-seq), here, we show that, in fission yeast, even though H3K9M-containing nucleosomes are broadly distributed across the genome, the histone H3K9 methyltransferase Clr4 is mainly sequestered at pericentric repeats. This selective sequestration of Clr4 depends not only on H3K9M but also on H3K14 ubiquitylation (H3K14ub), a modification deposited by a Clr4-associated E3 ubiquitin ligase complex. In vitro, H3K14ub synergizes with H3K9M to interact with Clr4 and potentiates the inhibitory effects of H3K9M on Clr4 enzymatic activity. Moreover, binding kinetics show that H3K14ub overcomes the Clr4 aversion to H3K9M and reduces its dissociation. The selective sequestration model reconciles previous discrepancies and demonstrates the importance of protein-interaction kinetics in regulating biological processes. [Display omitted] •Clr4 is selectively sequestered by H3K9M at heterochromatin•H3K14ub synergizes with H3K9M to sequester Clr4 at heterochromatin in vivo•H3K14ub synergizes with H3K9M to promote interaction with Clr4 in vitro•H3K14ub changes the kinetics of the H3K9M-Clr4 interaction Shan et al. report that the selective sequestration of the H3K9 methyltransferase Clr4 by H3K9M at heterochromatin requires an additional histone modification, H3K14ub. In vitro characterization reveals that H3K14ub changes the kinetics of the Clr4-H3K9M interaction. This selective sequestration model reconciles previous discrepancies on the mechanism of histone lysine-to-methionine mutations.