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      Unique Features of the m 6A Methylome in Arabidopsis thaliana

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          Abstract

          Recent discoveries of reversible N 6-methyladenosine (m 6A) methylation on messenger RNA (mRNA) and mapping of m 6A methylomes in mammals and yeast have revealed potential regulatory functions of this RNA modification. In plants, defects in m 6A methyltransferase cause an embryo-lethal phenotype, suggesting a critical role of m 6A in plant development. Here, we profile m 6A transcriptome-wide in two accessions of Arabidopsis thaliana and reveal that m 6A is a highly conserved modification of mRNA in plants. Distinct from mammals, m 6A in A. thaliana is enriched not only around the stop codon and within 3′ untranslated regions (3′ UTRs), but also around the start codon. Gene ontology analysis indicates that the unique distribution pattern of m 6A in A. thaliana is associated with plant-specific pathways involving the chloroplast. We also discover a positive correlation between m 6A deposition and the mRNA abundance, suggesting a regulatory role of m 6A in plant gene expression.

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          Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution.

          Alexander Stark, Julius Brennecke, Natascha Bushati … (2005)
          MicroRNAs are small noncoding RNAs that serve as posttranscriptional regulators of gene expression in higher eukaryotes. Their widespread and important role in animals is highlighted by recent estimates that 20%-30% of all genes are microRNA targets. Here, we report that a large set of genes involved in basic cellular processes avoid microRNA regulation due to short 3'UTRs that are specifically depleted of microRNA binding sites. For individual microRNAs, we find that coexpressed genes avoid microRNA sites, whereas target genes and microRNAs are preferentially expressed in neighboring tissues. This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions.
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            Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing.

            Dan Dominissini, Sharon Moshitch-Moshkovitz, Mali Salmon-Divon … (2013)
            N(6)-methyladenosine-sequencing (m(6)A-seq) is an immunocapturing approach for the unbiased transcriptome-wide localization of m(6)A in high resolution. To our knowledge, this is the first protocol to allow a global view of this ubiquitous RNA modification, and it is based on antibody-mediated enrichment of methylated RNA fragments followed by massively parallel sequencing. Building on principles of chromatin immunoprecipitation-sequencing (ChIP-seq) and methylated DNA immunoprecipitation (MeDIP), read densities of immunoprecipitated RNA relative to untreated input control are used to identify methylated sites. A consensus motif is deduced, and its distance to the point of maximal enrichment is assessed; these measures further corroborate the success of the protocol. Identified locations are intersected in turn with gene architecture to draw conclusions regarding the distribution of m(6)A between and within gene transcripts. When applied to human and mouse transcriptomes, m(6)A-seq generated comprehensive methylation profiles revealing, for the first time, tenets governing the nonrandom distribution of m(6)A. The protocol can be completed within ~9 d for four different sample pairs (each consists of an immunoprecipitation and corresponding input).
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              Methylated nucleotides block 5' terminus of HeLa cell messenger RNA.

              C. Wei, A Gershowitz, B. Moss (1975)
              Polyadenylylated [poly(A)+] mRNA from HeLa cells that were labeled with [3H-methyl]-methionine and 14C-uridine was isolated by poly(U)-Sepharose chromatography. The presence of approximately two methyl groups per 1000 nucleotides of poly(A)+ RNA was calculated from the 3H/14C ratios and known degrees of methylation of 18S and 28S ribosomal RNAs. All four 2'-O-methylribonucleosides, but only two base-methylated derivatives, 7-methylguanosine (7MeG) and 6-methyladenosine (6MeA), were identified. 6MeA was the major component accounting for approximately 50% of the total methyl-labeled ribonucleosides. 7MeG, comprising about 10% of the total, was present exclusively at the 5' terminus of the poly(A)+ RNA and could be removed by periodate oxidation and beta elimination. Evidence for a 5' to 5' linkage of 7MeG to adjacent 2'-O-methylribonucleosides through at least two and probably three phosphates to give structures of the type 7MeG5'ppp5pNMep- and 7MeG5'ppp5'NMepNmep- was presented. The previous finding of similar sequences of methylated nucleotides in mRNA synthesized in vitro by enzymes associated with virus cores indicates that blocked 5' termini may be a characteristic feature of mRNAs that function in eucaryotic cells.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101528555
                Journal ID (pubmed-jr-id): 37539
                Journal ID (nlm-ta): Nat Commun
                Journal ID (iso-abbrev): Nat Commun
                Title: Nature communications
                ISSN (Electronic): 2041-1723
                Publication date Nihms-submitted: 24 October 2014
                Publication date (Electronic): 28 November 2014
                Publication date Collection: 2014
                Publication date PMC-release: 28 May 2015
                Volume: 5
                Page: 5630
                Affiliations
                [1 ]Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
                [2 ]Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
                [3 ]Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
                [4 ]Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
                Author notes
                [* ]To whom correspondence should be addressed. guifangjia@ 123456pku.edu.cn (G. J.) or jbergels@ 123456uchicago.edu (J. B.) or chuanhe@ 123456uchicago.edu (C. H.)
                Article
                Manuscript ID: NIHMS637128
                DOI: 10.1038/ncomms6630
                PMC ID: 4248235
                PubMed ID: 25430002
                SO-VID: 93e11885-f266-43aa-b978-92fa3efea570
                History
                Categories
                Subject: Article

                ScienceOpen disciplines: Uncategorized
                Keywords: n6-methyladenosine (m6a),rna methylation,plant mrna methylome,chloroplast,gene expression
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                ScienceOpen disciplines: Uncategorized
                Keywords: n6-methyladenosine (m6a), rna methylation, plant mrna methylome, chloroplast, gene expression

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