The catalytic efficiency of METTL16 affects cellular methyltransferase activities by governing the intracellular S-adenosylmethionine setpoint

S-adenosylmethionine (SAM) regulates multiple cell processes as the methyl donor for cellular methyltransferases. The N6-methyladenosine (m6A) methyltransferase METTL16 regulates the expression of the SAM synthetase MAT2A, but it has been unclear if this regulation supports SAM homeostasis in a physiologically relevant way. Here, we used a degron and complementation strategy in HCT116 cells to demonstrate that disruption of MAT2A regulation by METTL16 has consequences for a wide variety of SAM-dependent processes including histone methylation, translation, m6A and m6Am RNA methylation. We also identified several U6 snRNA psuedogenes, including those with non-canonical consensus motifs, that are methylated by METTL16. Complementation by a catalytically hyperactive METTL16 abrogates MAT2A regulation and decreases intracellular SAM concentrations. Moreover, these complemented cells are hypersensitive to treatment with a MAT2A inhibitor and to deletion of the MTAP gene, which is lost in nearly 15% of all cancers. These findings support the conclusion that the catalytic efficiency of METTL16 helps establish the SAM setpoint in cells and that this function could be exploited as a potential treatment for MTAP-deficient cancers. Overall design: 3 biological replicates of GLORI-Seq +/- 72 hr of auxin treatment in EV, K163A, and WT complemented METTL16-AID cells. Riboerased RNA.