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      The birth of the Epitranscriptome: deciphering the function of RNA modifications

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          Abstract

          Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3' UTR. We present a perspective on current work and new single-molecule sequencing methods for detecting RNA base modifications.

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          Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells.

          R Desrosiers, K Friderici, F Rottman (1974)
          The poly(A) tract found in eukaryotic mRNA was used to study methylation in mRNA obtained from Novikoff hepatoma cells. Methyl labeling of RNA was achieved with L-[methyl-(3)H]methionine under conditions that suppress radioactive incorporation into the purine ring. RNA that contains a poly(A) segment was obtained from polysomal RNA by chromatography on oligo(dT)-cellulose. Sucrose density gradient centrifugation of this RNA revealed a pattern expected for mRNA. The composition of the methyl-labeled nucleosides in the RNA was analyzed after complete enzymatic degradation to nucleosides. By use of DEAE-cellulose (borate) chromatography, which separates 2'-O-methylnucleosides from normal and base-methylated nucleosides, about 50% of the radioactivity was recovered in the 2'-O-methylnucleoside fraction and 50% in the base-methylnucleoside fraction. High-speed liquid chromatography (Aminex A-5) of the 2'-O-methylnucleoside fraction produced four peaks coincident with the four 2'-O-methylnucleoside standards. Analysis of the base-methylnucleoside fraction revealed a unique pattern. While ribosomal RNA and tRNA possessed complex base-methylnucleoside patterns, the distribution in mRNA was quite simple, consisting predominantly of N(6)-methyladenosine. These results demonstrate a unique distribution of methylated nucleosides in mRNA. By analogy to ribosomal RNA synthesis, the presence of methylnucleosides in mRNA may reflect a cellular mechanism for the selective processing of certain mRNA sequences.
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            RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage.

            Matthias Schaefer, Tim Pollex, Katharina Hanna … (2010)
            Dnmt2 proteins are the most conserved members of the DNA methyltransferase enzyme family, but their substrate specificity and biological functions have been a subject of controversy. We show here that, in addition to tRNA(Asp-GTC), tRNA(Val-AAC) and tRNA(Gly-GCC) are also methylated by Dnmt2. Drosophila Dnmt2 mutants showed reduced viability under stress conditions, and Dnmt2 relocalized to stress granules following heat shock. Strikingly, stress-induced cleavage of tRNAs was Dnmt2-dependent, and Dnmt2-mediated methylation protected tRNAs against ribonuclease cleavage. These results uncover a novel biological function of Dnmt2-mediated tRNA methylation, and suggest a role for Dnmt2 enzymes during the biogenesis of tRNA-derived small RNAs.
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              Biases in Illumina transcriptome sequencing caused by random hexamer priming

              Kasper D Hansen, Steven Brenner, Sandrine Dudoit (2010)
              Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Journal ID (iso-abbrev): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2012
                Publication date (Electronic): 31 October 2012
                Publication date PMC-release: 31 October 2013
                Volume: 13
                Issue: 10
                Page: 175
                Affiliations
                [1 ]Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
                [2 ]The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
                [3 ]Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY10065, USA
                [4 ]Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
                [5 ]Pacific Biosciences, 1380 Willow Rd, Menlo Park, CA 94025, USA
                Article
                Publisher ID: gb-2012-13-10-175
                DOI: 10.1186/gb-2012-13-10-175
                PMC ID: 3491402
                PubMed ID: 23113984
                SO-VID: 51b122db-5850-476f-9a5e-b782bf865f19
                Copyright © Copyright ©2012 BioMed Central Ltd
                History
                Date accepted : 31 October 2012
                Categories
                Subject: Opinion

                ScienceOpen disciplines: Genetics
                Keywords: epigenetics,epigenomics,epitranscriptome,m6a,methyl-6-adenosine,methyladenosine,n6-methyladenosine,rna modifications
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: epigenetics, epigenomics, epitranscriptome, m6a, methyl-6-adenosine, methyladenosine, n6-methyladenosine, rna modifications

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