Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers.

Cellular RNAs are naturally decorated with a variety of chemical modifications. The structural diversity of the modified nucleosides provides regulatory potential to sort groups of RNAs for organized metabolism and functions, thus affecting gene expression. Recent years have witnessed a burst of interest in and understanding of RNA modification biology, thanks to the emerging transcriptome-wide sequencing methods for mapping modified sites, highly sensitive mass spectrometry for precise modification detection and quantification, and extensive characterization of the modification "effectors," including enzymes ("writers" and "erasers") that alter the modification level and binding proteins ("readers") that recognize the chemical marks. However, challenges remain due to the vast heterogeneity in expression abundance of different RNA species, further complicated by divergent cell-type-specific and tissue-specific expression and localization of the effectors as well as modifications. In this review, we highlight recent progress in understanding the function of N6-methyladenosine (m6A), the most abundant internal mark on eukaryotic mRNA, in light of the specific biological contexts of m6A effectors. We emphasize the importance of context for RNA modification regulation and function.

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

[2]  Qiang Wang,et al.  Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex , 2016, Nature.

[3]  Hailing Shi,et al.  Epitranscriptomic influences on development and disease , 2017, Genome Biology.

[4]  Jun Liu,et al.  VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation , 2018, Cell Discovery.

[5]  Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway. , 2018, Molecular cell.

[6]  Mathias V. Schmidt,et al.  The Role of m6A/m-RNA Methylation in Stress Response Regulation , 2018, Neuron.

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

[8]  Chuan He,et al.  FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis , 2014, Cell Research.

[9]  B. Williams,et al.  From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing , 2014, Genome research.

[10]  Alexa B. R. McIntyre,et al.  N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection , 2016, Cell host & microbe.

[11]  Gunter Meister,et al.  Interactions, localization, and phosphorylation of the m6A generating METTL3–METTL14–WTAP complex , 2018, RNA.

[12]  Michel Herzog,et al.  MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor[W][OA] , 2008, The Plant Cell Online.

[13]  Miao Yu,et al.  A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation , 2013, Nature chemical biology.

[14]  Ligang Wu,et al.  YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex , 2016, Nature Communications.

[15]  Jaewon Park,et al.  Dynamic m6A modification regulates local translation of mRNA in axons , 2017, Nucleic acids research.

[16]  A. McCarthy,et al.  Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development , 2018, Molecular cell.

[17]  Chuan He,et al.  N6-methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis , 2017, Nature Structural &Molecular Biology.

[18]  Chuan He,et al.  Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis , 2017, Cell Research.

[19]  Jie Jin,et al.  FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N6-Methyladenosine RNA Demethylase. , 2017, Cancer cell.

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

[21]  Ping-yuan Wang,et al.  Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor. , 2018, Molecular cell.

[22]  Suzanne Cory,et al.  Modified nucleosides and bizarre 5′-termini in mouse myeloma mRNA , 1975, Nature.

[23]  H. Nishimasu,et al.  Cap-specific terminal N6-methylation of RNA by an RNA polymerase II–associated methyltransferase , 2019, Science.

[24]  Yang Shi,et al.  m6A RNA methylation regulates the UV-induced DNA damage response , 2016, Nature.

[25]  U. Schibler,et al.  Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells. , 1977, Journal of molecular biology.

[26]  R. Desrosiers,et al.  Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Yang Xie,et al.  The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention , 2017, Cell.

[28]  Eric L Van Nostrand,et al.  Sequence, Structure and Context Preferences of Human RNA Binding Proteins , 2017, bioRxiv.

[29]  Olivier Elemento,et al.  Reversible methylation of m6Am in the 5′ cap controls mRNA stability , 2016, Nature.

[30]  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.

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

[32]  Anthony Barsic,et al.  ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure , 2016, Cell.

[33]  Jernej Ule,et al.  The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency , 2018, Nature.

[34]  Gene W. Yeo,et al.  Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP) , 2016, Nature Methods.

[35]  Wolfram Tempel,et al.  Structures of Human ALKBH5 Demethylase Reveal a Unique Binding Mode for Specific Single-stranded N6-Methyladenosine RNA Demethylation* , 2014, The Journal of Biological Chemistry.

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

[37]  Michaela Frye,et al.  RNA modifications modulate gene expression during development , 2018, Science.

[38]  Ping Wang,et al.  Structural Basis for Cooperative Function of Mettl3 and Mettl14 Methyltransferases. , 2016, Molecular cell.

[39]  R. Deng,et al.  SUMOylation of the m6A-RNA methyltransferase METTL3 modulates its function , 2018, Nucleic acids research.

[40]  L. Sánchez-Pulido,et al.  The FTO (fat mass and obesity associated) gene codes for a novel member of the non-heme dioxygenase superfamily , 2007, BMC Biochemistry.

[41]  Chuanzhao Zhang,et al.  Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA , 2016, Proceedings of the National Academy of Sciences.

[42]  S. Tavazoie,et al.  N6-methyladenosine marks primary microRNAs for processing , 2015, Nature.

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

[44]  Jun Liu,et al.  Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates , 2019, Proceedings of the National Academy of Sciences.

[45]  Zhike Lu,et al.  Ythdf2-mediated m6A mRNA clearance modulates neural development in mice , 2018, Genome Biology.

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

[47]  Paul Lehner,et al.  Fat mass and obesity-related (FTO) shuttles between the nucleus and cytoplasm , 2014, Bioscience reports.

[48]  James E. Bradner,et al.  R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m6A/MYC/CEBPA Signaling , 2018, Cell.

[49]  Chuan He,et al.  N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions , 2015, Nature.

[50]  Yang Shi,et al.  Zc3h13 Regulates Nuclear RNA m6A Methylation and Mouse Embryonic Stem Cell Self-Renewal. , 2018, Molecular cell.

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

[52]  B. Moss,et al.  5'-Terminal and internal methylated nucleotide sequences in HeLa cell mRNA. , 1976, Biochemistry.

[53]  M. Bohnsack,et al.  NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs , 2015, RNA.

[54]  E. Ntini,et al.  Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency. , 2018, Cell reports.

[55]  Ji Wan,et al.  N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response. , 2018, Molecular cell.

[56]  Qi Zhou,et al.  m(6)A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. , 2015, Cell stem cell.

[57]  Mark Helm,et al.  Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d , 2018, Genes & development.

[58]  Yinyin Yuan,et al.  Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions , 2015, Developmental cell.

[59]  Yang Shi,et al.  PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression , 2018, bioRxiv.

[60]  Samie R. Jaffrey,et al.  m6A RNA methylation promotes XIST-mediated transcriptional repression , 2016, Nature.

[61]  R. Perry,et al.  Existence of Methylated Messenger RNA in Mouse L Cells , 1974 .

[62]  Kai Li,et al.  Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase , 2018, Cell Research.

[63]  Shu-Bing Qian,et al.  Dynamic m6A mRNA methylation directs translational control of heat shock response , 2015, Nature.

[64]  Yousheng Shu,et al.  A novel m6A reader Prrc2a controls oligodendroglial specification and myelination , 2018, Cell Research.

[65]  Yu Zhang,et al.  m6A facilitates hippocampus-dependent learning and memory through Ythdf1 , 2018, Nature.

[66]  Ye Fu Dynamic regulation of rna modifications by AlkB family dioxygenases , 2012 .

[67]  Tsutomu Suzuki,et al.  S-Adenosylmethionine Synthesis Is Regulated by Selective N6-Adenosine Methylation and mRNA Degradation Involving METTL16 and YTHDC1. , 2017, Cell reports.

[68]  Zhike Lu,et al.  Differential m6A, m6Am, and m1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. , 2018, Molecular cell.

[69]  F. Rottman,et al.  Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. , 1997, RNA.

[70]  A. Gingras,et al.  Cocrystal Structure of the Messenger RNA 5′ Cap-Binding Protein (eIF4E) Bound to 7-methyl-GDP , 1997, Cell.

[71]  B. Moss,et al.  Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. , 1977, Biochemistry.

[72]  C. Niehrs,et al.  RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding , 2017, Nature Structural &Molecular Biology.

[73]  Chuan He,et al.  m6A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-like Cells by Sustaining FOXM1 Expression and Cell Proliferation Program. , 2017, Cancer cell.

[74]  Samie R Jaffrey,et al.  Rethinking m6A Readers, Writers, and Erasers. , 2017, Annual review of cell and developmental biology.

[75]  Stepanka Vanacova,et al.  N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing , 2017, Nucleic acids research.

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

[77]  Samir Adhikari,et al.  Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase , 2014, Cell Research.

[78]  Hongjun Song,et al.  Fragile X mental retardation protein modulates the stability of its m6A‐marked messenger RNA targets , 2018, Human molecular genetics.

[79]  Stefan Hüttelmaier,et al.  Recognition of RNA N6-methyladenosine by IGF2BP Proteins Enhances mRNA Stability and Translation , 2018, Nature Cell Biology.

[80]  K. Martin,et al.  Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts , 2018, Nature Neuroscience.

[81]  Saeed Tavazoie,et al.  HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events , 2015, Cell.

[82]  B. Moss,et al.  Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA , 1975, Cell.

[83]  Samie R Jaffrey,et al.  Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1 , 2017, Nature Communications.

[84]  Nian Liu,et al.  N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein , 2017, Nucleic acids research.

[85]  Kwok-Kin Wong,et al.  mRNA circularization by METTL3-eIF3h enhances translation and promotes oncogenesis , 2018, Nature.

[86]  Chuan He,et al.  m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer , 2018, Nature Cell Biology.

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

[88]  Chuan He,et al.  FTO-Mediated Formation of N6-Hydroxymethyladenosine and N6-Formyladenosine in Mammalian RNA , 2013, Nature Communications.

[89]  Chuan He,et al.  A dynamic N6-methyladenosine methylome regulates intrinsic and acquired resistance to tyrosine kinase inhibitors , 2018, Cell Research.

[90]  Chuan He,et al.  Targeted m6A Reader Proteins To Study Epitranscriptomic Regulation of Single RNAs. , 2018, Journal of the American Chemical Society.

[91]  V. Anggono,et al.  Ubiquitination Regulates the Proteasomal Degradation and Nuclear Translocation of the Fat Mass and Obesity-Associated (FTO) Protein. , 2017, Journal of molecular biology.

[92]  Uwe Ohler,et al.  FMR1 targets distinct mRNA sequence elements to regulate protein expression , 2012, Nature.

[93]  J. Qiu,et al.  N 6-methyladenosine modification and METTL3 modulate enterovirus 71 replication , 2018, Nucleic acids research.

[94]  R. Gregory,et al.  The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. , 2016, Molecular cell.

[95]  Gang Xiao,et al.  Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally , 2019, Nature.

[96]  Junwei Shi,et al.  Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control , 2017, Nature.

[97]  Wei Yan,et al.  ALKBH5-dependent m6A demethylation controls splicing and stability of long 3′-UTR mRNAs in male germ cells , 2017, Proceedings of the National Academy of Sciences.

[98]  L. Aravind,et al.  Identification of the m6Am methyltransferase PCIF1 reveals the location and functions of m6Am in the transcriptome , 2018, bioRxiv.

[99]  A. Klungland,et al.  Nucleocytoplasmic Shuttling of FTO Does Not Affect Starvation-Induced Autophagy , 2017, PloS one.

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

[101]  Zhike Lu,et al.  N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation , 2018, Nature Chemical Biology.

[102]  Chuan He,et al.  YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA , 2017, Cell Research.

[103]  Zhike Lu,et al.  m6A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells , 2017, Cell reports.

[104]  WALDO E. COHN,et al.  Nucleoside-5′-Phosphates from Ribonucleic Acid , 1951, Nature.