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      Regulatory Mechanisms of the RNA Modification m 6A and Significance in Brain Function in Health and Disease

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          Abstract

          RNA modifications have emerged as an additional layer of regulatory complexity governing the function of almost all species of RNA. N 6-methyladenosine (m 6A), the addition of methyl groups to adenine residues, is the most abundant and well understood RNA modification. The current review discusses the regulatory mechanisms governing m 6A, how this influences neuronal development and function and how aberrant m 6A signaling may contribute to neurological disease. M 6A is known to regulate the stability of mRNA, the processing of microRNAs and function/processing of tRNAs among other roles. The development of antibodies against m 6A has facilitated the application of next generation sequencing to profile methylated RNAs in both health and disease contexts, revealing the extent of this transcriptomic modification. The mechanisms by which m 6A is deposited, processed, and potentially removed are increasingly understood. Writer enzymes include METTL3 and METTL14 while YTHDC1 and YTHDF1 are key reader proteins, which recognize and bind the m 6A mark. Finally, FTO and ALKBH5 have been identified as potential erasers of m 6A, although there in vivo activity and the dynamic nature of this modification requires further study. M 6A is enriched in the brain and has emerged as a key regulator of neuronal activity and function in processes including neurodevelopment, learning and memory, synaptic plasticity, and the stress response. Changes to m 6A have recently been linked with Schizophrenia and Alzheimer disease. Elucidating the functional consequences of m 6A changes in these and other brain diseases may lead to novel insight into disease pathomechanisms, molecular biomarkers and novel therapeutic targets.

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          Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.

          An extensive repertoire of modifications is known to underlie the versatile coding, structural and catalytic functions of RNA, but it remains largely uncharted territory. Although biochemical studies indicate that N(6)-methyladenosine (m(6)A) is the most prevalent internal modification in messenger RNA, an in-depth study of its distribution and functions has been impeded by a lack of robust analytical methods. Here we present the human and mouse m(6)A modification landscape in a transcriptome-wide manner, using a novel approach, m(6)A-seq, based on antibody-mediated capture and massively parallel sequencing. We identify over 12,000 m(6)A sites characterized by a typical consensus in the transcripts of more than 7,000 human genes. Sites preferentially appear in two distinct landmarks--around stop codons and within long internal exons--and are highly conserved between human and mouse. Although most sites are well preserved across normal and cancerous tissues and in response to various stimuli, a subset of stimulus-dependent, dynamically modulated sites is identified. Silencing the m(6)A methyltransferase significantly affects gene expression and alternative splicing patterns, resulting in modulation of the p53 (also known as TP53) signalling pathway and apoptosis. Our findings therefore suggest that RNA decoration by m(6)A has a fundamental role in regulation of gene expression.
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            m6A-dependent regulation of messenger RNA stability

            N6 -methyladenosine (m6A) is the most prevalent internal (non-cap) modification present in the messenger RNA (mRNA) of all higher eukaryotes 1,2 . Although essential to cell viability and development 3–5 , the exact role of m6A modification remains to be determined. The recent discovery of two m6A demethylases in mammalian cells highlighted the importance of m6A in basic biological functions and disease 6–8 . Here we show that m6A is selectively recognized by the human YTH domain family 2 (YTHDF2) protein to regulate mRNA degradation. We identified over 3,000 cellular RNA targets of YTHDF2, most of which are mRNAs, but which also include non-coding RNAs, with a conserved core motif of G(m6A)C. We further establish the role of YTHDF2 in RNA metabolism, showing that binding of YTHDF2 results in the localization of bound mRNA from the translatable pool to mRNA decay sites, such as processing bodies 9 . The C-terminal domain of YTHDF2 selectively binds to m6A-containing mRNA whereas the N-terminal domain is responsible for the localization of the YTHDF2-mRNA complex to cellular RNA decay sites. Our results indicate that the dynamic m6A modification is recognized by selective-binding proteins to affect the translation status and lifetime of mRNA.
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              Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.

              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. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Journal
                Front Cell Neurosci
                Front Cell Neurosci
                Front. Cell. Neurosci.
                Frontiers in Cellular Neuroscience
                Frontiers Media S.A.
                1662-5102
                19 May 2021
                2021
                : 15
                : 671932
                Affiliations
                [1] 1Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences , Dublin, Ireland
                [2] 2FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences , Dublin, Ireland
                [3] 3UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin , Dublin, Ireland
                Author notes

                Edited by: Daniela Tropea, Trinity College Dublin, Ireland

                Reviewed by: Francesca Ruberti, Institute of Biochemistry and Cell Biology, National Research Council, Consiglio Nazionale delle Ricerche, Italy; Christina Gross, Cincinnati Children’s Hospital Medical Center, United States

                *Correspondence: Gary P. Brennan, gary.brennan@ 123456ucd.ie

                This article was submitted to Cellular Neuropathology, a section of the journal Frontiers in Cellular Neuroscience

                Article
                10.3389/fncel.2021.671932
                8170084
                34093133
                c6b4eb05-2acc-4743-b297-19082f9ace1f
                Copyright © 2021 Mathoux, Henshall and Brennan.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 24 February 2021
                : 19 April 2021
                Page count
                Figures: 1, Tables: 2, Equations: 0, References: 130, Pages: 14, Words: 0
                Categories
                Cellular Neuroscience
                Review

                Neurosciences
                m6a (n6-methyladenosine),brain function and brain diseases,brain development,epitranscriptomics,mettl3

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