MYC interacts with the G9a histone methyltransferase to control transcriptional repression in cancer

MYC is a master regulator of transcriptional activation and repression that mediates diverse physiological and disease functions, including hematopoiesis, aging, and oncogenesis, yet its essential co-regulators remain unclear. We demonstrate that MYC interacts with and regulates the G9a H3K9 methyltransferase complex to control transcriptional repression in cancer. Inhibiting G9a hinders MYC binding, shifts repressive epigenetic locales to an active state, and de-represses gene expression to antagonize MYC-dependent cellular processes. MYC requires MYC Box II region for its interaction with G9a, providing a mechanism for this region essential for transcriptional repression. In treatment models of MYC-dependent basal breast cancer, genetically inhibiting G9a decreases tumour growth. Anti-proliferative sensitivity to G9a small molecule inhibitors correlates with sensitivity to MYC knockdown and associates with the basal subtype. Our findings illustrate an epigenetic model of MYC-mediated transcriptional repression in driving oncogenesis and establishes G9a as a therapeutic vulnerability in MYC-driven cancers. Genome-wide analysis comparing the effect of G9a knockdown (using two independent shRNAs) versus scramble control (shSCR) on MYC transcription factor binding in MCF10A breast epithelial cells transformed with ectopic PI3KH1047R and MYC (MCF10A.PM). ChIP-seq of three biological replicates immunoprecipitated with a MYC-specific antibody (N262) and respective DNA input for each shRNA condition was performed.