Quantitative profiling of mA at single base resolution across the life cycle of rice and Arabidopsis.

N-methyladenosine (mA) plays critical roles in regulating mRNA metabolism. However, comprehensive mA methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide mA maps at single-base resolution in different tissues of rice and Arabidopsis using mA-SAC-seq. Our analysis uncovers a total of 205,691 mA sites distributed across 22,574 genes in rice, and 188,282 mA sites across 19,984 genes in Arabidopsis. The evolutionarily conserved mA sites in rice and Arabidopsis ortholog gene pairs are involved in controlling tissue development, photosynthesis and stress response. We observe an overall mRNA stabilization effect by 3' UTR mA sites in certain plant tissues. Like in mammals, a positive correlation between the mA level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active mA deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA mA sites correlate with both translation promotion and translation suppression, depicting a more complicated regulatory picture. Our results therefore provide in-depth resources for relating single-base resolution mA sites with functions in plants and uncover a suppression-activation model controlling mA biogenesis across species.