Quantitative profiling of m⁶A at single base resolution across the life cycle of rice and Arabidopsis.

Abstract

N⁶-methyladenosine (m⁶A) plays critical roles in regulating mRNA metabolism. However, comprehensive m⁶A methylomes in different plant tissues with single-base precision have yet to be reported. Here, we present transcriptome-wide m⁶A maps at single-base resolution in different tissues of rice and Arabidopsis using m⁶A-SAC-seq. Our analysis uncovers a total of 205,691 m⁶A sites distributed across 22,574 genes in rice, and 188,282 m⁶A sites across 19,984 genes in Arabidopsis. The evolutionarily conserved m⁶A 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 m⁶A sites in certain plant tissues. Like in mammals, a positive correlation between the m⁶A level and the length of internal exons is also observed in plant mRNA, except for the last exon. Our data suggest an active m⁶A deposition process occurring near the stop codon in plant mRNA. In addition, the MTA-installed plant mRNA m⁶A 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 m⁶A sites with functions in plants and uncover a suppression-activation model controlling m⁶A biogenesis across species.