Acquisition of drug resistance remains a chief impediment to successful
cancer therapy, and we previously described a transient drug-tolerant
cancer cell population (DTPs) whose survival is in part dependent on the activities of the
histone methyltransferases G9a/EHMT2 and EZH2, the latter being the catalytic component of the
polycomb repressive complex 2 (PRC2). Here, we apply multiple proteomic techniques to better understand the role of these
histone methyltransferases (HMTs) in the establishment of the DTP state.
Proteome-wide comparisons of
lysine methylation patterns reveal that DTPs display an increase in methylation on K116 of PRC member Jarid2, an event that helps stabilize and recruit PRC2 to
chromatin. We also find that EZH2, in addition to methylating
histone H3K27, also can methylate G9a at K185, and that methylated G9a better recruits repressive complexes to
chromatin. These complexes are similar to complexes recruited by
histone H3 methylated at K9. Finally, a detailed
histone post-translational modification (PTM) analysis shows that EZH2, either directly or through its ability to methylate G9a, alters H3K9 methylation in the context of H3
serine 10 phosphorylation, primarily in a
cancer cell subpopulation that serves as DTP precursors. We also show that combinations of
histone PTMs recruit a different set of complexes to
chromatin, shedding light on the temporal mechanisms that contribute to drug tolerance.