Quantitative transcriptome N6-methyladenosine profiling reveals the mechanism of far-red regulated anthocyanin homeostasis in Arabidopsis
N6-methyladenosine (m6A) is the most abundant messenger RNA modification in higher eukaryotes. Functional studies of the RNA m6A modification in plants have been limited by mapping individual m6A-modified sites in whole transcriptomes. In this study, we introduce the method m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq) for quantitative whole-transcriptome profiling of m6A at single-nucleotide resolution under light and dark conditions in Arabidopsis. With this technology, we observed far-red but not red light, noticeably increase the m6A level. Further evidence showed that far-red light modulated mRNA stability and translation by m6A methylation. Additionally, our data uncovered that far-red light promoted m6A methylation of anthocyanin homeostasis related transcripts through the stabilization of FIONA1 (FIO1) and m6A methyltransferase complex, MTA (mRNA adenosine methylase A) and MTB, and the core component FIP37 (FKBP12 INTERACTING PROTEIN 37KD). Thus, with m6A stoichiometry information at single-base precision, we proposed a new mechanism for the regulation of anthocyanin accumulation under far-red light through m6A methylation. Overall design: PolyA samples from twelve wild type (2 input and 2 MjDim1-treated in red light, far-red light and dark conditions, respectively), four fio1 mutant (2 input and 2 MjDim1-treated in far-red light), four mta mutant (2 input and 2 MjDim1-treated in far-red light) and four phyA mutant (2 input and 2 MjDim1-treated in far-red light) were collected for high-throughput sequencing.