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      The Role of m 6A/m-RNA Methylation in Stress Response Regulation

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          Summary

          N 6-methyladenosine (m 6A) and N 6,2′-O-dimethyladenosine (m 6Am) are abundant mRNA modifications that regulate transcript processing and translation. The role of both, here termed m 6A/m, in the stress response in the adult brain in vivo is currently unknown. Here, we provide a detailed analysis of the stress epitranscriptome using m 6A/m-seq, global and gene-specific m 6A/m measurements. We show that stress exposure and glucocorticoids region and time specifically alter m 6A/m and its regulatory network. We demonstrate that deletion of the methyltransferase Mettl3 or the demethylase Fto in adult neurons alters the m 6A/m epitranscriptome, increases fear memory, and changes the transcriptome response to fear and synaptic plasticity. Moreover, we report that regulation of m 6A/m is impaired in major depressive disorder patients following glucocorticoid stimulation. Our findings indicate that brain m 6A/m represents a novel layer of complexity in gene expression regulation after stress and that dysregulation of the m 6A/m response may contribute to the pathophysiology of stress-related psychiatric disorders.

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          Highlights

          • m 6A/m mRNA methylation in the adult mouse brain is regulated by stress

          • m 6A/m mRNA regulation is brain region, time, and gene specific

          • Mettl3 and Fto cKO alter m 6A/m, fear memory, expression, and synaptic plasticity

          • The m 6A/m glucocorticoid response is impaired in major depressive disorder patients

          Abstract

          Engel et al. demonstrate a region- and time-dependent role of brain m 6A/m methylation in stress-response regulation. Manipulating m 6A/m alters fear memory, transcriptome response, and synaptic plasticity. Altered m 6A/m dynamics in depressed patients suggest importance of m 6A/m modifications for stress-related psychiatric disorders.

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          Most cited references24

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          Transcriptome-wide mapping of N(6)-methyladenosine by m(6)A-seq based on immunocapturing and massively parallel sequencing.

          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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            Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.

            Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5' UTRs and long noncoding RNAs (lncRNAs). Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
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              N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis

              A comprehensive proteomics screen for ‘reader’ proteins that recognize m6A-modified RNA reveals that the modification both promotes and prevents the binding of factors that control mRNA homeostasis in mammalian cells.
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                Author and article information

                Contributors
                Journal
                Neuron
                Neuron
                Neuron
                Cell Press
                0896-6273
                1097-4199
                25 July 2018
                25 July 2018
                : 99
                : 2
                : 389-403.e9
                Affiliations
                [1 ]Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich 80804, Germany
                [2 ]Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
                [3 ]Clinical Laboratory, Max Planck Institute of Psychiatry, Munich 80804, Germany
                [4 ]Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
                [5 ]Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
                [6 ]Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
                [7 ]Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel
                Author notes
                []Corresponding author alon_chen@ 123456psych.mpg.de
                [8]

                Lead Contact

                Article
                S0896-6273(18)30583-X
                10.1016/j.neuron.2018.07.009
                6069762
                30048615
                47141a80-1d12-4b52-97fe-8e3b206c5617
                © 2018 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 27 September 2017
                : 4 May 2018
                : 5 July 2018
                Categories
                Article

                Neurosciences
                m6a,m6am,rna modification,stress,mettl3,fto,post-transcriptional regulation,major depressive disorder

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