Shaping the landscape of N6-methyladenosine RNA methylation in Arabidopsis

As the most widespread internal modification on eukaryotic mRNAs, N6-methyladenosine (m6A) modification is deposited by evolutionarily conserved methyltransferases (writers). By far it remains elusive how individual m6A writers sculpt the overall landscape of m6A methylomes and the resulting biological impact in multicellular organisms. Here, we report a systematic survey of the quantitative m6A methylomes at single-nucleotide resolution and their correlated transcriptomes mediated by the individual components in the Arabidopsis m6A writer complex through nanopore direct RNA sequencing of the seedlings bearing respective impaired m6A writers grown under the same conditions. The m6A sites associated with the five Arabidopsis writers are located mostly within 3' UTR with peaks at around 100 bp downstream of stop codons. m6A predominantly promotes the usage of distal poly(A) sites, but has little effect on RNA splicing in Arabidopsis. Notably, impaired m6A writers result in hypomethylated and differentially expressed transcripts encoding most of the ribosomal proteins, indicating a strong correlation between m6A and protein translation. Besides the common effects on mRNA metabolism and biological functions uniquely exerted by different Arabidopsis m6A writers compared with their counterparts in human cell lines, our analyses also reveal functional specificity of individual Arabidopsis m6A writers in plant development and response to stresses. Our findings have uncovered the common and unique characteristics and impact of the methylomes and the correlated transcriptomes conferred by the five m6A writers in Arabidopsis, and gained unprecedented insights into the biological roles of various Arabidopsis m6A writers and their cognate counterparts in other multicellular m6A methyltransferase complexes.