G9a-mediated methylation abrogates RUNX3 tumor suppressive activity to promote cancer cell survival under hypoxia [ChIP-seq]

Chronic hypoxia inhibits apoptosis to enhance survival of cancer cells. The mechanisms that prevent apoptosis under hypoxia are unclear. Here, we show that hypoxia induced G9a, a lysine methyltransferase, which methylates a tumor suppressor, Runt-related transcription factor 3 (RUNX3) at lysines 129 and 171. G9a-mediated methylation reduced transcriptional activity of RUNX3 by inhibiting interactions with its transcriptional cofactors, the core-binding factor-beta (CBF-beta) and p300, and also decreased the protein level of RUNX3 via Smurf1-mediated proteasomal degradation. Through ChIP-seq and gene expression profiling, G9a-mediated methylation inhibited expression of genes involved in apoptosis, thereby enhancing survival and proliferation of cancer cells both in vitro and vivo. Our results suggest G9a-dependent methylation of RUNX3 as a therapeutic target to control tumor growth. RUNX3 binding profiles of SNU484 cells at the following three conditions (2 replicates each) were examined by ChIP-sequencing: wild-type (WT), RUNX3 K129R mutant (K129R), and RUNX3 K171R mutant (K171R).