Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

Methylation of the N6 position of adenosine (m6 A) is a posttranscriptional modification of RNA with poorly understood prevalence and physiological relevance. The recent discovery that FTO, an obesity risk gene, encodes an m6 A demethylase implicates m6 A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m6 A localization, which combines m6 A-specific methylated RNA immunoprecipitation with nextgeneration sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m6 A, indicating that m6 A is a common base modification of mRNA. The m6 A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m6 A sites are enriched near stop codons and in 30 UTRs, and we uncover an association between m6 A residues and microRNA-binding sites within 30 UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome.