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Gene methylation is an important mechanism regulating gene expression and genome stability. Our previous work showed that methylation of the nitrate reductase (NR) gene  NIA2  was dependent on chromomethylase 3 (CMT3). Here, we show that CMT3-mediated  NIA2  methylation is regulated by ammonium in  Arabidopsis thaliana . CHG sequences (where H can be A, T, or C) were methylated in  NIA2  but not in  NIA1 , and ammonium [(NH 4 ) 2 SO 4 ] treatment completely blocked CHG methylation in  NIA2 . By contrast, ammonium had no effect on  CMT3  methylation, indicating that ammonium negatively regulates CMT3-mediated  NIA2  methylation without affecting  CMT3  methylation. Ammonium upregulated  NIA2  mRNA expression, which was consistent with the repression of  NIA2  methylation by ammonium. Ammonium treatment also reduced the overall genome methylation level of wild-type  Arabidopsis . Moreover, CMT3 bound to specific promoter and intragenic regions of  NIA2 . These combined results indicate that ammonium inhibits CMT3-mediated methylation of  NIA2  and that of other target genes, and CMT3 selectively binds to target DNA sequences for methylation.

Ammonium Inhibits Chromomethylase 3-Mediated Methylation of the Arabidopsis Nitrate Reductase Gene NIA2