Genome-Wide Identification, Classification and Expression Analysis of m6A Gene Family in Solanum lycopersicum

Advanced knowledge of messenger RNA (mRNA) N6-methyladenosine (m6A) and DNA N6-methyldeoxyadenosine (6 mA) redefine our understanding of these epigenetic modifications. Both m6A and 6mA carry important information for gene regulation, and the corresponding catalytic enzymes sometimes belong to the same gene family and need to be distinguished. However, a comprehensive analysis of the m6A gene family in tomato remains obscure. Here, 24 putative m6A genes and their family genes in tomato were identified and renamed according to BLASTP and phylogenetic analysis. Chromosomal location, synteny, phylogenetic, and structural analyses were performed, unravelling distinct evolutionary relationships between the MT-A70, ALKBH, and YTH protein families, respectively. Most of the 24 genes had extensive tissue expression, and 9 genes could be clustered in a similar expression trend. Besides, SlYTH1 and SlYTH3A showed a different expression pattern in leaf and fruit development. Additionally, qPCR data revealed the expression variation under multiple abiotic stresses, and LC-MS/MS determination exhibited that the cold stress decreased the level of N6 2′-O dimethyladenosine (m6Am). Notably, the orthologs of newly identified single-strand DNA (ssDNA) 6mA writer–eraser–reader also existed in the tomato genome. Our study provides comprehensive information on m6A components and their family proteins in tomato and will facilitate further functional analysis of the tomato N6-methyladenosine modification genes.

[1]  Xiangyang Xu,et al.  RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers , 2021, Frontiers in Plant Science.

[2]  Yingwu Yang,et al.  Genome-wide identification and characterization of YTH domain-containing genes, encoding the m6A readers, and their expression in tomato , 2021, Plant Cell Reports.

[3]  G. Qin,et al.  N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner , 2021, Genome Biology.

[4]  Lisha Shen,et al.  N6-methyladenosine modification underlies messenger RNA metabolism and plant development. , 2021, Current opinion in plant biology.

[5]  Sudhir Kumar,et al.  MEGA11: Molecular Evolutionary Genetics Analysis Version 11 , 2021, Molecular biology and evolution.

[6]  Jae-Young Yun,et al.  n6 -methyladenosine mrna methylation is important for salt stress tolerance in arabidopsis. , 2021, The Plant journal : for cell and molecular biology.

[7]  Y. Ohkuma,et al.  The cap-specific m6A methyltransferase, PCIF1/CAPAM, is dynamically recruited to the gene promoter in a transcription-dependent manner. , 2021, Journal of biochemistry.

[8]  F. Wang,et al.  Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sweet sorghum. , 2020, Plant science : an international journal of experimental plant biology.

[9]  Hunseung Kang,et al.  Functional Characterization of a Putative RNA Demethylase ALKBH6 in Arabidopsis Growth and Abiotic Stress Responses , 2020, International journal of molecular sciences.

[10]  R. Blumenthal,et al.  Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA , 2020, Nucleic acids research.

[11]  X. Zhang,et al.  Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat , 2020, BMC Plant Biology.

[12]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[13]  E. Grzesiuk,et al.  Human and Arabidopsis alpha‐ketoglutarate‐dependent dioxygenase homolog proteins—New players in important regulatory processes , 2020, IUBMB life.

[14]  Zhongzhou Chen,et al.  Structural basis of nucleic acid recognition and 6mA demethylation by human ALKBH1 , 2020, Cell Research.

[15]  A. Xiao,et al.  Mammalian ALKBH1 serves as an N6-mA demethylase of unpairing DNA , 2020, Cell Research.

[16]  Zhe Liang,et al.  Epigenetic Modifications of mRNA and DNA in Plants. , 2019, Molecular plant.

[17]  Xiaodong Cheng,et al.  Human MettL3–MettL14 complex is a sequence-specific DNA adenine methyltransferase active on single-strand and unpaired DNA in vitro , 2019, Cell Discovery.

[18]  Chuang Ma,et al.  Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication1[OPEN] , 2019, Plant Physiology.

[19]  Guozheng Qin,et al.  RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening , 2019, Genome Biology.

[20]  Xiaojun Nie,et al.  N6‐methyladenosine regulatory machinery in plants: composition, function and evolution , 2019, Plant biotechnology journal.

[21]  Jian-You Liao,et al.  The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice , 2019, PLoS genetics.

[22]  Zhang Zhang,et al.  Single-base mapping of m6A by an antibody-independent method , 2019, Science Advances.

[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.  PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression , 2018, bioRxiv.

[25]  Hongkun Zheng,et al.  N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses. , 2018, Molecular plant.

[26]  B. Gregory,et al.  N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis. , 2018, Cell reports.

[27]  Yuke Geng,et al.  Adenine Methylation: New Epigenetic Marker of DNA and mRNA. , 2018, Molecular plant.

[28]  Fan Liang,et al.  DNA N6-Adenine Methylation in Arabidopsis thaliana. , 2018, Developmental cell.

[29]  Zhike Lu,et al.  The m6A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis[OPEN] , 2018, Plant Cell.

[30]  C. Poulsen,et al.  An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis[OPEN] , 2018, Plant Cell.

[31]  C. Raynaud,et al.  The YTH Domain Protein ECT2 Is an m6A Reader Required for Normal Trichome Branching in Arabidopsis[OPEN] , 2018, Plant Cell.

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

[33]  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.

[34]  Zhike Lu,et al.  ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition[OPEN] , 2017, Plant Cell.

[35]  Kazutaka Katoh,et al.  MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization , 2017, Briefings Bioinform..

[36]  Fan Liang,et al.  DNA N6-adenine methylation in Arabidopsis thaliana , 2017, Mechanisms of Development.

[37]  Zhe Liang,et al.  N6-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis , 2017, Mechanisms of Development.

[38]  Zhe Liang,et al.  N(6)-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis. , 2016, Developmental cell.

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

[40]  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.

[41]  L. Aravind,et al.  Adenine methylation in eukaryotes: Apprehending the complex evolutionary history and functional potential of an epigenetic modification , 2015, BioEssays : news and reviews in molecular, cellular and developmental biology.

[42]  Christopher E. Mason,et al.  Single-nucleotide resolution mapping of m6A and m6Am throughout the transcriptome , 2015, Nature Methods.

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

[44]  L. Aravind,et al.  DNA Methylation on N6-Adenine in C. elegans , 2015, Cell.

[45]  Howard Y. Chang,et al.  m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. , 2014, Cell stem cell.

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

[47]  Zhike Lu,et al.  Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. , 2014, Nature chemical biology.

[48]  Xavier Robert,et al.  Deciphering key features in protein structures with the new ENDscript server , 2014, Nucleic Acids Res..

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

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

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

[52]  Minoru Yoshida,et al.  RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock , 2013, Cell.

[53]  Guifang Jia,et al.  Reversible RNA adenosine methylation in biological regulation. , 2013, Trends in genetics : TIG.

[54]  Zhike Lu,et al.  ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. , 2013, Molecular cell.

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

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

[57]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[58]  S. Zhong,et al.  Adenosine Methylation in Arabidopsis mRNA is Associated with the 3′ End and Reduced Levels Cause Developmental Defects , 2012, Front. Plant Sci..

[59]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

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

[61]  A. A. Borges,et al.  Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process , 2008, BMC Plant Biology.

[62]  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.

[63]  J. Leebens-Mack,et al.  Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. , 2007, The Plant journal : for cell and molecular biology.

[64]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[65]  Ziv Bar-Joseph,et al.  STEM: a tool for the analysis of short time series gene expression data , 2006, BMC Bioinformatics.

[66]  Richard C. Moore,et al.  The early stages of duplicate gene evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[68]  M. A. Koch,et al.  Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). , 2000, Molecular biology and evolution.

[69]  M. Tuck.  The formation of internal 6-methyladenine residues in eucaryotic messenger RNA. , 1992, The International journal of biochemistry.

[70]  OUP accepted manuscript , 2021, Plant Physiology.

[71]  M. Helm,et al.  LC-MS Analysis of Methylated RNA. , 2017, Methods in molecular biology.

[72]  R. Voorrips.  MapChart: software for the graphical presentation of linkage maps and QTLs. , 2002, The Journal of heredity.