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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    • ". 由于缺乏有效检测手段,相关研究多局 限于非编码 tRNA 和 rRNA,或小部分编码转录片段 [1] , 且多数 RNA 甲基化功能未知. 随着高通量测序技术发展[5]及一些 RNA 甲基化功能的发现 [6] [7] [8] [9] [10] [11] ,人们开始关注 RNA 甲基化研究. 尤 "
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    ABSTRACT: With the rapid development of high-throughput sequencing technologies, the emerging of methylated RNA immunoprecipitation sequencing (MeRIP-seq) technology makes it possible to detect RNA epigenetic modifications in a large scale, which allows transcriptome-wide profiling of RNA methylation. Mining the patterns of global mRNA methylation from these MeRIP-seq data can help reveal the potential functional roles of these mRNA methylations in regulating gene expression, splicing, RNA editing and RNA stability, effectively guiding the therapeutic intervention of cancer. Here, the principle of MeRIP-seq sequencing was first introduced. Then, the recent progress of the processing and analysis of MeRIP-seq data were comprehensively discussed. In the end, the computational problems and challenges faced in the process of MeRIP-seq data processing were also summarized.
    Progress in Biochemistry and Biophysics 06/2015; · 0.32 Impact Factor
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    • "See also Figures S1J and S1K. immunoprecipitation sequencing (RIPseq ) as described elsewhere (Dominissini et al., 2012; Meyer et al., 2012; Experimental Procedures). For each experiment , libraries were built for multiple biological replicates and concordant peaks for each experiment were used for subsequent bioinformatics analyses. "
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    ABSTRACT: N6-methyl-adenosine (m(6)A) is the most abundant modification on messenger RNAs and is linked to human diseases, but its functions in mammalian development are poorly understood. Here we reveal the evolutionary conservation and function of m(6)A by mapping the m(6)A methylome in mouse and human embryonic stem cells. Thousands of messenger and long noncoding RNAs show conserved m(6)A modification, including transcripts encoding core pluripotency transcription factors. m(6)A is enriched over 30 untranslated regions at defined sequence motifs and marks unstable transcripts, including transcripts turned over upon differentiation. Genetic inactivation or depletion of mouse and human Mettl3, one of the m(6)A methylases, led to m(6)A erasure on select target genes, prolonged Nanog expression upon differentiation, and impaired ESC exit from self-renewal toward differentiation into several lineages in vitro and in vivo. Thus, m(6)A is a mark of transcriptome flexibility required for stem cells to differentiate to specific lineages.
    Cell Stem Cell 12/2014; 15(6):707-719. DOI:10.1016/j.stem.2014.09.019 · 22.27 Impact Factor
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    • "In contrast to the well-documented role of posttranslational chemical modifi cations of amino acids for modulating protein function, the extent to which nucleotides are chemically modifi ed remains largely unknown. Nevertheless, studies have already started to document the prevalence of modifi cations such as adenosine-to-inosine conversion (RNA editing), and adenosine or cytosine methylation for the entire transcriptome (Meyer et al. 2012 ; Peng et al. 2012 ; Squires et al. 2012 ). It will be interesting to learn how these modifi cations affect the activity of ASOs. "
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    ABSTRACT: Before a messenger RNA (mRNA) is translated into a protein in the cytoplasm, its pre-mRNA precursor is extensively processed through capping, splicing and polyadenylation in the nucleus. Defects in the processing of pre-mRNAs due to mutations in RNA sequences often cause disease. Traditional small molecules or protein-based therapeutics are not well suited for correcting processing defects by targeting RNA. However, antisense oligonucleotides (ASOs) designed to bind RNA by Watson-Crick base pairing can target most RNA transcripts and have emerged as the ideal therapeutic agents for diseases that are caused by pre-mRNA processing defects. Here we review the diverse ASO-based mechanisms that can be exploited to modulate the expression of RNA. We also discuss how advancements in medicinal chemistry and a deeper understanding of the pharmacokinetic and toxicological properties of ASOs have enabled their use as therapeutic agents. We end by describing how ASOs have been used successfully to treat various pre-mRNA processing diseases in animal models.
    Advances in Experimental Medicine and Biology 09/2014; 825:303-52. DOI:10.1007/978-1-4939-1221-6_9 · 1.96 Impact Factor
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