Article

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

Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA.
Cell (Impact Factor: 32.24). 05/2012; 149(7):1635-46. DOI: 10.1016/j.cell.2012.05.003
Source: PubMed

ABSTRACT

Methylation of the N(6) position of adenosine (m(6)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 m(6)A demethylase implicates m(6)A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m(6)A localization, which combines m(6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m(6)A, indicating that m(6)A is a common base modification of mRNA. The m(6)A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A 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.

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    • "m 6 A was selected for study because it exists in most of the RNAs in a variety of organisms . The abundance of m 6 A throughout the transcriptome (about 7,000 mRNAs and over 300 ncRNAs in the mammalian genome) has been demonstrated by m 6 A profiling from two independent studies (Dominissini et al., 2012; Meyer et al., 2012). Knockdown of either METTL3 or METTL14 results in a reduction in total m 6 A levels in human cells (Dominissini et al., 2012; Liu et al., 2014). "
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    • "Transcriptome-wide approaches to map m 6 A are based on the immunoprecipitation of fragmented, poly(A)-enriched RNA using m 6 A-specific antibodies prior to NGS (MeRIP-seq or m 6 A-seq) [20] [21] (Fig. 1B). After sequencing, the reads are mapped to the reference genome. "
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    • "The m 6 A miCLIP mapping read clusters are shown in pink. To show that the m 6 A or eIF3 peaks are not an artifact of uneven RNA recovery, the RNA-Seq reads (Meyer et al., 2012) are also displayed (purple). Lastly, to determine if eIF3 binding is occurring at the related nucleotide m 6 Am, the CAGE tags (Lykke-Andersen et al., 2014) (black) are shown. "
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