Identification of epitranscriptomic methylation marker genes in Arabidopsis and their expression profiling in response to developmental, anatomical, and environmental modulations
Tài liệu tham khảo
Fu, 2014, Gene expression regulation mediated through reversible m6A RNA methylation, Nat. Rev. Genet., 15, 293, 10.1038/nrg3724
Yue, 2015, RNA N 6 -methyladenosine methylation in post-transcriptional gene expression regulation, Genes Dev., 29, 1343, 10.1101/gad.262766.115
Fang, 2020, Reversible N6-methyladenosine of RNA: the regulatory mechanisms on gene expression and implications in physiology and pathology, Genes Dis., 7, 585, 10.1016/j.gendis.2020.06.011
Wang, 2014, Reading RNA methylation codes through methyl-specific binding proteins, RNA Biol., 11, 669, 10.4161/rna.28829
Zhen, 2020, m6A reader: epitranscriptome target prediction and functional characterization of N6-methyladenosine (m6A) readers, Front. Cell Dev. Biol., 8, 741, 10.3389/fcell.2020.00741
Wang, 2021, The m 6 A consensus motif provides a paradigm of epitranscriptomic studies, Biochemistry, 60, 3410, 10.1021/acs.biochem.1c00254
Dominissini, 2012, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, 485, 201, 10.1038/nature11112
Linder, 2015, Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome, Nat. Methods, 12, 767, 10.1038/nmeth.3453
Wang, 2016, Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex, Nature, 534, 575, 10.1038/nature18298
Ping, 2014, Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase, Cell Res., 24, 177, 10.1038/cr.2014.3
Yue, 2018, VIRMA mediates preferential m6A mRNA methylation in 3′UTR and near stop codon and associates with alternative polyadenylation, Cell Disco, 4, 10, 10.1038/s41421-018-0019-0
Knuckles, 2018, Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6 A machinery component Wtap/Fl(2)d, Genes Dev., 32, 415, 10.1101/gad.309146.117
Zhong, 2008, MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor, Plant Cell, 20, 1278, 10.1105/tpc.108.058883
Růžička, 2017, Identification of factors required for m 6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI, N. Phytol., 215, 157, 10.1111/nph.14586
Reichel, 2019, Marking RNA: m6A writers, readers, and functions in Arabidopsis, J. Mol. Cell Biol., 11, 899, 10.1093/jmcb/mjz085
Gerken, 2007, The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase, Science, 318, 1469, 10.1126/science.1151710
Zheng, 2013, Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases, RNA Biol., 10, 915, 10.4161/rna.24711
Aik, 2014, Structure of human RNA N 6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation, Nucleic Acids Res., 42, 4741, 10.1093/nar/gku085
Ensfelder, 2018, ALKBH5-induced demethylation of mono- and dimethylated adenosine, Chem. Commun., 54, 8591, 10.1039/C8CC03980A
Han, 2010, Crystal structure of the FTO protein reveals basis for its substrate specificity, Nature, 464, 1205, 10.1038/nature08921
Jia, 2011, N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO, Nat. Chem. Biol., 7, 885, 10.1038/nchembio.687
Feng, 2014, Crystal structures of the human RNA demethylase Alkbh5 reveal basis for substrate recognition, J. Biol. Chem., 289, 11571, 10.1074/jbc.M113.546168
Martínez-Pérez, 2017, Arabidopsis m 6 A demethylase activity modulates viral infection of a plant virus and the m 6 A abundance in its genomic RNAs, Proc. Natl. Acad. Sci., 114, 10755, 10.1073/pnas.1703139114
Duan, 2017, ALKBH10B Is an RNA N 6 -methyladenosine demethylase affecting Arabidopsis floral transition, Plant Cell, 29, 2995, 10.1105/tpc.16.00912
Liao, 2018, YTH domain: a family of N 6 -methyladenosine (m 6 A) readers, Genom. Proteom. Bioinforma., 16, 99, 10.1016/j.gpb.2018.04.002
Alarcón, 2015, HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events, Cell, 162, 1299, 10.1016/j.cell.2015.08.011
Meyer, 2017, Rethinking m 6 A readers, writers, and erasers, Annu. Rev. Cell Dev. Biol., 33, 319, 10.1146/annurev-cellbio-100616-060758
Patil, 2018, Reading m6A in the Transcriptome: m6A-Binding Proteins, Trends Cell Biol., 28, 113, 10.1016/j.tcb.2017.10.001
Ok, 2005, Novel CIPK1-associated proteins in Arabidopsis contain an evolutionarily conserved C-terminal region that mediates nuclear localization, Plant Physiol., 139, 138, 10.1104/pp.105.065649
Zhang, 2008, A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana, PLoS One, 3, 10.1371/journal.pone.0002410
Thomas, 2012, Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis, Plant Cell, 24, 4376, 10.1105/tpc.112.096107
Batista, 2014, m6A RNA modification controls cell fate transition in mammalian embryonic stem cells, Cell Stem Cell, 15, 707, 10.1016/j.stem.2014.09.019
Widagdo, 2018, The m6A‐epitranscriptomic signature in neurobiology: from neurodevelopment to brain plasticity, J. Neurochem., 147, 137, 10.1111/jnc.14481
Zhang, 2020, Roles of N6-methyladenosine (m6A) in stem cell fate decisions and early embryonic development in mammals, Front. Cell Dev. Biol., 8, 782, 10.3389/fcell.2020.00782
Wu, 2020, m6A RNA methylation in cardiovascular diseases, Mol. Ther., 28, 2111, 10.1016/j.ymthe.2020.08.010
Lin, 2016, The m 6 A methyltransferase METTL3 promotes translation in human cancer cells, Mol. Cell., 62, 335, 10.1016/j.molcel.2016.03.021
Panneerdoss, 2018, Cross-talk among writers, readers, and erasers of m 6 A regulates cancer growth and progression, Sci. Adv., 4, eaar8263, 10.1126/sciadv.aar8263
Sun, 2019, The role of m6A RNA methylation in cancer, Biomed. Pharmacother., 112, 10.1016/j.biopha.2019.108613
Lan, 2019, The critical role of RNA m 6 A methylation in cancer, Cancer Res., 79, 1285, 10.1158/0008-5472.CAN-18-2965
Arribas-Hernández, 2018, An m 6 A-YTH module controls developmental timing and morphogenesis in Arabidopsis, Plant Cell, 30, 952, 10.1105/tpc.17.00833
Chmielowska-Bąk, 2019, In search of the mRNA modification landscape in plants, BMC Plant Biol., 19, 421, 10.1186/s12870-019-2033-2
Bodi, 2012, Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects, Front. Plant Sci., 3, 10.3389/fpls.2012.00048
Scutenaire, 2018, The YTH domain protein ECT2 is an m 6 A reader required for normal trichome branching in Arabidopsis, Plant Cell, 30, 986, 10.1105/tpc.17.00854
Goodstein, 2012, Phytozome: a comparative platform for green plant genomics, Nucleic Acids Res., 40, D1178, 10.1093/nar/gkr944
Wilkins, 1998, Protein identification and analysis tools in the ExPASy server, 531
Hooper, 2017, SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations, Nucleic Acids Res., 45, D1064, 10.1093/nar/gkw1041
Lee, 2012, PGDD: a database of gene and genome duplication in plants, Nucleic Acids Res., 41, D1152, 10.1093/nar/gks1104
Juretic, 2005, The evolutionary fate of MULE-mediated duplications of host gene fragments in rice, Genome Res., 15, 1292, 10.1101/gr.4064205
Koch, 2000, Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae), Mol. Biol. Evol., 17, 1483, 10.1093/oxfordjournals.molbev.a026248
Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340
Kumar, 2018, MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 35, 1547, 10.1093/molbev/msy096
Finn, 2014, Pfam: the protein families database, Nucleic Acids Res., 42, D222, 10.1093/nar/gkt1223
Bailey, 2015, The MEME suite, Nucleic Acids Res., 43, W39, 10.1093/nar/gkv416
Hu, 2015, GSDS 2.0: an upgraded gene feature visualization server, Bioinformatics, 31, 1296, 10.1093/bioinformatics/btu817
Hruz, 2008, Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes, Adv. Bioinform., 2008, 10.1155/2008/420747
Saeed, 2006, [9] TM4 microarray software suite, 134, 10.1016/S0076-6879(06)11009-5
Lescot, 2002, PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences, Nucleic Acids Res., 30, 325, 10.1093/nar/30.1.325
Flagel, 2009, Gene duplication and evolutionary novelty in plants, N. Phytol., 183, 557, 10.1111/j.1469-8137.2009.02923.x
Panchy, 2016, Evolution of gene duplication in plants, Plant Physiol., 171, 2294, 10.1104/pp.16.00523
Li, 1981, Pseudogenes as a paradigm of neutral evolution, Nature, 292, 237, 10.1038/292237a0
Zhu, 2021, Genome-wide investigation of N6-methyladenosine regulatory genes and their roles in tea (Camellia sinensis) leaves during withering process, Front. Plant Sci., 12, 10.3389/fpls.2021.702303
Li, 2014, Genome-wide identification, biochemical characterization, and expression analyses of the YTH domain-containing RNA-binding protein family in Arabidopsis and rice, Plant Mol. Biol. Rep., 32, 1169, 10.1007/s11105-014-0724-2
Sun, 2020, Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in common wheat, BMC Plant Biol., 20, 351, 10.1186/s12870-020-02505-1
Wang, 2011, Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent Angiosperms, PLoS One, 6
Shen, 2016, N 6 -Methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis, Dev. Cell., 38, 186, 10.1016/j.devcel.2016.06.008
Vespa, 2004, The immunophilin-interacting protein AtFIP37 from Arabidopsis is essential for plant development and is involved in trichome endoreduplication, Plant Physiol., 134, 1283, 10.1104/pp.103.028050
Wei, 2018, The m 6 A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis, Plant Cell, 30, 968, 10.1105/tpc.17.00934
Shaw, 2001, The effect of net charge on the solubility, activity, and stability of ribonuclease Sa, Protein Sci., 10, 1206, 10.1110/ps.440101