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

Abstract

SUMMARY Methylation of the N6 position of adenosine (m6A) is a post-transcriptional modification of RNA whose prevalence and physiological relevance is poorly understood. The recent discovery that FTO, an obesity risk gene, encodes an m6A demethylase implicates m6A as an important regulator of physiological processes. Here we present a method for transcriptome-wide m6A localization, which combines m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m6A, indicating that m6A is a common base modification of mRNA. The m6A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m6A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m6A residues and microRNA binding sites within 3' 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.

Profiling of m6A RNA modifications identified an age‐associated regulation of AGO2 mRNA stability

“…m6A RNA predominantly occurs in protein‐coding RNAs found in both the young and old PBMCs (Figure 1c), which support earlier observations that m6A methylation occurs primarily in protein‐coding transcripts (Dominissini et al., 2012; Meyer Kate et al., 2012). However, methylation events occur at a low rate, less than 1% of the total number of transcripts.…”

Control of box C/D snoRNP assembly by N 6 ‐methylation of adenine

“…Analysis of the targets for methylation by the METTL3–METTL14 methyl transferase complex in eukaryotes shows the preferred sequence to be DRACH (where D denotes A, G, or U; R is A or G; and H is A, C, or U), with GAC as the most common site of methylation 4, 5. The box C/D and C’/D’ sequences adopt the k‐turn conformation on binding the 15.5‐kDa protein (15.5k), with the unbulged strand having GA at the 2n,1n sequence.…”

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

“…In plants and mammals, mRNA methylation amounts vary between different developmental stages or organ types (Zhong et al ., 2008; Meyer et al ., 2012), indicating that regulation in these multicellular organisms is likely to be more subtle than a simple on or off state. It seems that variations of the writer complex evolved in other eukaryotes.…”

“…m 6 A is found within a conserved consensus sequence (G/A)(G/A) A CU (with a preference for (G/A)G A CU) in different eukaryotes (Horowitz et al ., 1984; Narayan & Rottman, 1988; Dominissini et al ., 2012; Meyer et al ., 2012; Luo et al ., 2014; Wan et al ., 2015). However, only a subset of potential sites is actually modified and the mechanisms underlying the specificity of writing are not yet understood.…”