m6A facilitates hippocampus-dependent learning and memory through Ythdf1

N6-methyladenosine (m6A), the most prevalent internal RNA modification on mammalian messenger RNAs, regulates the fates and functions of modified transcripts through m6A-specific binding proteins1–5. In the nervous system, m6A is abundant and modulates various neural functions6–11. Whereas m6A marks groups of mRNAs for coordinated degradation in various physiological processes12–15, the relevance of m6A for mRNA translation in vivo remains largely unknown. Here we show that, through its binding protein YTHDF1, m6A promotes protein translation of target transcripts in response to neuronal stimuli in the adult mouse hippocampus, thereby facilitating learning and memory. Mice with genetic deletion of Ythdf1 show learning and memory defects as well as impaired hippocampal synaptic transmission and long-term potentiation. Re-expression of YTHDF1 in the hippocampus of adult Ythdf1-knockout mice rescues the behavioural and synaptic defects, whereas hippocampus-specific acute knockdown of Ythdf1 or Mettl3, which encodes the catalytic component of the m6A methyltransferase complex, recapitulates the hippocampal deficiency. Transcriptome-wide mapping of YTHDF1-binding sites and m6A sites on hippocampal mRNAs identified key neuronal genes. Nascent protein labelling and tether reporter assays in hippocampal neurons showed that YTHDF1 enhances protein synthesis in a neuronal-stimulus-dependent manner. In summary, YTHDF1 facilitates translation of m6A-methylated neuronal mRNAs in response to neuronal stimulation, and this process contributes to learning and memory.Neuronal stimulation induces protein translation of m6A-methylated neuronal mRNAs facilitated by YTHDF1, and this process contributes to learning and memory.

[1]  R. Malinow,et al.  βCaMKII in Lateral Habenula Mediates Core Symptoms of Depression , 2013, Science.

[2]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[3]  M. Kupiec,et al.  Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq , 2012, Nature.

[4]  G. Ming,et al.  Neuronal Activity–Induced Gadd45b Promotes Epigenetic DNA Demethylation and Adult Neurogenesis , 2009, Science.

[5]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[6]  R. Morris,et al.  Place navigation impaired in rats with hippocampal lesions , 1982, Nature.

[7]  Joseph E LeDoux.  Emotion Circuits in the Brain , 2000 .

[8]  Ran Elkon,et al.  Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation , 2017, Cell.

[9]  E. Schuman,et al.  Dendritic Protein Synthesis, Synaptic Plasticity, and Memory , 2006, Cell.

[10]  Åsa K. Björklund,et al.  Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.

[11]  O. Elemento,et al.  Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons , 2012, Cell.

[12]  R. Huganir,et al.  GRASP1 Regulates Synaptic Plasticity and Learning through Endosomal Recycling of AMPA Receptors , 2017, Neuron.

[13]  Simon Hess,et al.  The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry , 2013, Nature Neuroscience.

[14]  Tianlei Xu,et al.  Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis. , 2017, Human molecular genetics.

[15]  Chuan He,et al.  YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs , 2017, eLife.

[16]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[17]  Chuan He,et al.  m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition , 2016, Nature.

[18]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[19]  Matthew L. K. Yip,et al.  The Role of The RNA Demethylase FTO (Fat Mass and Obesity-Associated) and mRNA Methylation in Hippocampal Memory Formation , 2017, Neuropsychopharmacology.

[20]  Anton J. Enright,et al.  The RNA m6A Reader YTHDF2 Is Essential for the Post-transcriptional Regulation of the Maternal Transcriptome and Oocyte Competence , 2017, Molecular cell.

[21]  Tao Pan,et al.  Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.

[22]  Stefan Canzar,et al.  Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation , 2017, Cell.

[23]  Samir Adhikari,et al.  Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Molecular cell.

[24]  K. Fukunaga,et al.  Aberrant Calcium/Calmodulin-Dependent Protein Kinase II (CaMKII) Activity Is Associated with Abnormal Dendritic Spine Morphology in the ATRX Mutant Mouse Brain , 2011, The Journal of Neuroscience.

[25]  T. Bredy,et al.  Experience-Dependent Accumulation of N6-Methyladenosine in the Prefrontal Cortex Is Associated with Memory Processes in Mice , 2016, The Journal of Neuroscience.

[26]  G. Ming,et al.  Neuronal activity modifies the chromatin accessibility landscape in the adult brain , 2017, Nature Neuroscience.

[27]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[28]  Yuval Kluger,et al.  m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT5/SOCS pathway , 2017, Nature.

[29]  George Paxinos,et al.  The Mouse Brain in Stereotaxic Coordinates , 2001 .

[30]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[31]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[32]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[33]  Allan R. Jones,et al.  Genome-wide atlas of gene expression in the adult mouse brain , 2007, Nature.

[34]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[35]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[36]  Jing Liu,et al.  Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin , 2011, Proceedings of the National Academy of Sciences.

[37]  V. Iyer,et al.  Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects , 2014, Nature Methods.

[38]  K. Krnjević,et al.  mTORC2 controls actin polymerization required for consolidation of long-term memory , 2013, Nature Neuroscience.

[39]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[40]  Miguel A. Andrade-Navarro,et al.  m6A modulates neuronal functions and sex determination in Drosophila , 2016, Nature.

[41]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[42]  G. Ming,et al.  Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain , 2011, Cell.

[43]  Chengqi Yi,et al.  N6-Methyladenosine in Nuclear RNA is a Major Substrate of the Obesity-Associated FTO , 2011, Nature chemical biology.

[44]  Arne Klungland,et al.  ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. , 2013, Molecular cell.

[45]  Wei Zheng,et al.  Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System , 2018, Neuron.

[46]  Uwe Ohler,et al.  PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data , 2011, Genome Biology.