Natural Variation in RNA m(6)A Methylation and Its Relationship with Translational Status

N-6-methyladenosine (m(6)A) is the most abundant modification of eukaryotic mRNA. Although m(6)A has been demonstrated to affect almost all aspects of RNA metabolism, its global contribution to the post-transcriptional balancing of translational efficiency remains elusive in plants. In this study, we performed a parallel analysis of the transcriptome-wide mRNA m(6)A distribution and polysome profiling in two maize (Zea mays) inbred lines to assess the global correlation of m(6)A modification with translational status. m(6)A sites are widely distributed in thousands of protein-coding genes, confined to a consensus motif and primarily enriched in the 3' untranslated regions, and highly coordinated with alternative polyadenylation usage, suggesting a role of m(6)A modification in regulating alternative polyadenylation site choice. More importantly, we identified that the m(6)A modification shows multifaceted correlations with the translational status depending on its strength and genic location. Moreover, we observed a substantial intraspecies variation in m(6)A modification, and this natural variation was shown to be partly driven by gene-specific expression and alternative splicing. Together, these findings provide an invaluable resource for ascertaining transcripts that are subject to m(6)A modification in maize and pave the way to a better understanding of natural m(6)A variation in mediating gene expression regulation.