N6-methyladenosine (m6A) is the most ubiquitous mRNA base modification, but little is known about its precise location, temporal dynamics, and regulation. Here, we generated genomic maps of m6A sites in meiotic yeast transcripts at nearly single-nucleotide resolution, identifying 1,308 putatively methylated sites within 1,183 transcripts. We validated eight out of eight methylation sites in different genes with direct genetic analysis, demonstrated that methylated sites are significantly conserved in a related species, and built a model that predicts methylated sites directly from sequence. Sites vary in their methylation profiles along a dense meiotic time course and are regulated both locally, via predictable methylatability of each site, and globally, through the core meiotic circuitry. The methyltransferase complex components localize to the yeast nucleolus, and this localization is essential for mRNA methylation. Our data illuminate a conserved, dynamically regulated methylation program in yeast meiosis and provide an important resource for studying the function of this epitranscriptomic modification.
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The authors would like to thank Lindsey Dollard and Anna Symbor-Nagrabska for expert technical assistance; Hannah Blitzblau, Mitchell Guttman, and Dmitry Ter-Ovanesyan for fruitful discussions and technical advice; and Leslie Gaffney for making the figures beautiful. The anti-Fob1 antibody was kindly provided by Dr. Stephen Bell. G.R.F. is an American Cancer Society Professor of Genetics. This work was supported by National Institutes of Health Grants GM035010 (G.R.F) and U54 HG003067 (E.S.L.) and Broad Institute Funds. A.R. was supported by an NHGRI Pioneer Award and HHMI. S.S. was supported by an HFSP fellowship.