Abstract
The role of epitranscriptomics, i.e., RNA base modification, as a component of a “methylome” in disease has emerged as a result of the development of next generation sequencing and other related state-of-art technologies. Epitranscriptomic state is controlled by writing, erasing, and reading methylation, which is mediated by enzymatic reactions. More than 20 methyltransferases have been identified so far. Epitranscriptomic mechanisms are involved in the development of diseases such as cancer of mice and humans. In this review article, we discuss recent developments in epitranscriptomics for the further application of epitranscriptomic knowledge for use as diagnostic tools and therapeutic approaches.
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References
Alarcón RC, Goodarzi H, Lee H et al (2015a) HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events. Cell 162:1299–1308
Alarcón RC, Lee H, Goodarzi H et al (2015b) N6-methyladenosine marks primary microRNAs for processing. Nature 519:482–485
Alexandrov A, Martzen RM, Phizicky ME (2002) Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8:1253–1266
Arguello AE, DeLiberto AN, Kleiner RE (2017) RNA chemical proteomics reveals the N6-methyladenosine (m6A)-regulated protein-RNA interactome. J Am Chem Soc 139:17249–17252
Aschenbrenne J, Werner S, Marchand V et al (2018) Engineering of a DNA polymerase for direct m6 A sequencing. Angew Chem Int Ed Engl 57:417–421
Auxilien S, Guérineau V, Szweykowska-Kulińska Z et al (2012) The human tRNA m(5)C methyltransferase misu is multisite-specific. RNA Biol 9:1331–1338
Baser A, Skabkin M, Kleber S, Dang Y et al (2019) Onset of differentiation is post-transcriptionally controlled in adult neural stem cells. Nature 566:100–104
Batista PJ, Molinie B, Wang J et al (2014) m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15:707–719
Beemon K, Keith J (1977) Localization of N6-methyladenosine in the Rous sarcoma virus genome. J Mol Biol 113:165–179
Bertero A, Brown S, Madrigal P et al (2018) The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency. Nature 555:256–259
Boles NC, Temple S (2017) Epimetronomics: m6A marks the tempo of corticogenesis. Neuron 96:718–720
Brown AJ, Kinzig GC, DeGregorio JS et al (2016) Methyltransferase-like protein 16 binds the 3′-terminal triple helix of MALAT1 long noncoding RNA. Proc Natl Acad Sci USA 113:14013–14018
Brzezniak KL, Bijata M, Szczesny JR et al (2011) Involvement of human ELAC2 gene product in 3′ end processing of mitochondrial tRNAs. RNA Biol 8:616–626
Chen X, Li X, Guo J et al (2017) The roles of microRNAs in regulation of mammalian spermatogenesis. J Anim Sci Biotechnol 8:35
Chen X, Li A, Sun BF et al (2019) 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nat Cell Biol 21:978–990
Chen H, Gu L, Orellana EA et al (2020) METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing. Cell Res 30:544–547
Coker H, Wei G, Brockdorff N (2019) m6A modification of non-coding RNA and the control of mammalian gene expression. Biochim Biophys Acta Gene Regul Mech 1862:310–318
Courtney DG, Kennedy EM, Dumm RE et al (2017) Epitranscriptomic enhancement of influenza a virus gene expression and replication. Cell Host Microbe 22:377–386
Cui Q, Shi H, Ye P et al (2017) m6A RNA methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep 18:2622–2634
Dominissini D, Moshitch-Moshkovitz S, Schwartz S et al (2012) Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485:201–206
Doxtader AK, Wang P, Scarborough MA et al (2018) Structural basis for regulation of METTL16, an S-adenosylmethionine homeostasis factor. Mol Cell 71:1001–1011
Ellis SR, Morales MJ, Li JM et al (1986) Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J Biol Chem 261:9703–9709
Flores JV, Cordero-Espinoza L, Oeztuerk-Winder F et al (2017) Cytosine-5 RNA methylation regulates neural stem cell differentiation and motility. Stem Cell Rep 8:112–124
Frye M, Harada BT, Behm M et al (2018) RNA modifications modulate gene expression during development. Science 361:1346–1349
Fustin JM, Doi M, Yamaguchi Y et al (2013) RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155:793–806
Geula S, Moshitch-Moshkovitz S, Dominissini D et al (2015) Stem cells. m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation. Science 347:1002–1006
Gillis D, Krishnamohan A, Yaacov B et al (2014) TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. J Med Genet 51:581–586
Gkatza AN, Castro C, Harvey FR et al (2019) Cytosine-5 RNA methylation links protein synthesis to cell metabolism. PLoS Biol 17:e3000297
Gokhale NS, McIntyre ABR, McFadden MJ et al (2016) N6-Methyladenosine in Flaviviridae viral RNA genomes regulates infection. Cell Host Microbe 20:654–665
Goll MG, Kirpekar F, Maggert KA et al (2006) Methylation of tRNA Asp by the DNA methyltransferase homolog Dnmt2. Science 311:395–398
Golovina AY, Dzama MM, Petriukov KS et al (2014) Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis. Nucleic Acids Res 42:e27
Hafner M, Landthaler M, Burger L et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129–141
Haute VL, Lee SY, McCann JB et al (2019) NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res 47:8720–8733
Hess ME, Hess S, Meyer KD et al (2013) The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nat Neurosci 16:1042–1048
Hesser CR, Karijolich J, Dominissini D et al (2018) N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi’s sarcoma-associated herpesvirus infection. PLoS Pathog 14:e1006995
Holzmann J, Frank P, Löffler E et al (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135:462–474
Huang X, Zhao J, Yang M et al (2017) Association between FTO gene polymorphism (rs9939609 T/A) and cancer risk: a meta-analysis. Eur J Cancer Care 26
Imanishi M, Tsuji S, Suda A et al (2017) Detection of N6-methyladenosine based on the methyl-sensitivity of MazF RNA endonuclease. Chem Commun 53:12930–12933
Jia G, Fu Y, Zhao X et al (2011) N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol 7:885–887
Ke S, Pandya-Jones A, Saito Y et al (2017) M 6 A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. Genes Dev 31:990–1006
Khella MS, Salem AM, Abdel-Rahman O et al (2018) The association between the FTO rs9939609 variant and malignant pleural mesothelioma risk: a case-control study. Genet Test Mol Biomarkers 22:79–84
Konno M, Taniguchi M, Ishii H (2019a) Significant epitranscriptomes in heterogeneous cancer. Cancer Sci 110:2318–2327
Konno M, Koseki J, Asai A et al (2019b) Distinct methylation levels of mature microRNAs in gastrointestinal cancers. Nat Commun 10:3888
Kweon SM, Chen Y, Moon E et al (2019) An adversarial DNA N(6)-methyladenine-sensor network preserves polycomb silencing. Mol Cell 74:1138–1147
Lee KW, Bogenhagen DF (2014) Assignment of 2′-O-methyltransferases to modification sites on the mammalian mitochondrial large subunit 16S rRNA. J Biol Chem 289:24936–24942
Lence T, Akhtar J, Bayer M et al (2016) m6A modulates neuronal functions and sex determination in Drosophila. Nature 540:242–247
Li HB, Tong J, Zhu S et al (2017a) M6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 548:338–342
Li Z, Weng H, Su R et al (2017b) FTO plays an oncogenic role in acute myeloid leukemia as a N6-methyladenosine RNA demethylase. Cancer Cell 31:127–141
Li X, Xiong X, Zhang M et al (2017c) Base-resolution mapping reveals distinct M1A methylome in nuclear- and mitochondrial-encoded transcripts. Mol Cell 68:993–1005
Li Z, Shi J, Yu L et al (2018) N6-methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus. Virol J 15:87
Li X, Liang QX, Lin JR et al (2020) Epitranscriptomic technologies and analyses. Sci China Life Sci 63:501–515
Lichinchi G, Zhao BS, Wu Y et al (2016a) Dynamics of human and viral RNA methylation during Zika virus infection. Cell Host Microbe 20:666–673
Lichinchi G, Gao S, Saletore Y et al (2016b) Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells. Nat Microbiol 1:16011
Lin Y, Ueda J, Yagyu K et al (2013) Association between variations in the fat mass and obesity-associated gene and pancreatic cancer risk: a case-control study in Japan. BMC Cancer 13:337
Lin S, Choe J, Du P et al (2016) The m(6)A methyltransferase METTL3 promotes translation in human cancer cells. Mol Cell 62:335–345
Linder B, Grozhik AV, Olarerin-George AO et al (2015) Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods 12:767–772
Liu N, Parisien M, Dai Q et al (2013) Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19:1848–1856
Liu J, Yue Y, Han D et al (2014) A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol 10:93–95
Liu N, Dai Q, Zheng G et al (2015) N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518:560–564
Llorens-Bobadilla E, Zhao S, Baser A et al (2015) Single-cell transcriptomics reveals a population of dormant neural stem cells that become activated upon brain injury. Cell Stem Cell 17:329–340
Ma Y, Wu L, Shaw N et al (2015) Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex. Proc Natl Acad Sci USA 112:9436–9441
Mendel M, Chen KM, Homolka D et al (2018) Methylation of structured RNA by the m6A writer METTL16 is essential for mouse embryonic development. Mol Cell 71:986–1000
Meyer KD, Jaffrey SR (2014) The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol 15:313–326
Meyer KD, Jaffrey SR (2017) Rethinking m6A readers, writers, and erasers. Annu Rev Cell Dev Biol 33:319–342
Meyer KD, Saletore Y, Zumbo P et al (2012) Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149:1635–1646
Meyer KD, Patil PD, Zhou J et al (2015) 5’ UTR m(6)A promotes cap-independent translation. Cell 163:999–1010
Mishima E, Jinno D, Akiyama Y et al (2015) Immuno-northern blotting: detection of RNA modifications by using antibodies against modified nucleosides. PLoS One 10:e0143756
Molinie B, Wang J, Lim KS et al (2016) m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nat Methods 13:692–698
Nishizawa Y, Konno M, Asai A et al (2017) Oncogene c-Myc promotes epitranscriptome m6A reader YTHDF1 expression in colorectal cancer. Oncotarget 9:7476–7486
Ontiveros RJ, Stoute J, Liu KF (2019) The chemical diversity of RNA modifications. Biochem J 476:1227–1245
Ozanick S, Krecic A, Andersland J et al (2005) The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11:1281–1290
Pandolfini L, Barbieri I, Bannister JA et al (2019) METTL1 promotes let-7 microRNA processing via m7G methylation. Mol Cell 74:1278–1290
Patil PD, Chen CK, Pickering FB et al (2016) m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature 537:369–373
Pendleton EK, Chen B, Liu K et al (2017) The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169:824–835
Perveen S, Yazdi KA, Devkota K et al (2021) A high-throughput RNA displacement assay for screening SARS-CoV-2 nsp10-nsp16 complex toward developing therapeutics for COVID-19. SLAS Discov 10:2472555220985040
Reinhard L, Sridhara S, Hällberg BM (2017) The MRPP1/MRPP2 complex is a tRNA-maturation platform in human mitochondria. Nucleic Acids Res 45:12469–12480
Safra M, Sas-Chen A, Nir R et al (2017) The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551:251–255
Shi Z, Xu S, Xing S et al (2019) Mettl17, a regulator of mitochondrial ribosomal RNA modifications, is required for the translation of mitochondrial coding genes. FASEB J 33:13040–13050
Signer RA, Magee JA, Salic A et al (2014) Haematopoietic stem cells require a highly regulated protein synthesis rate. Nature 509:49–54
Śledź P, Jinek M (2016) Structural insights into the molecular mechanism of the m(6)a writer complex. elife 5:e18434
Taketo K, Konno M, Asai A et al (2018) The epitranscriptome m6A writer METTL3 promotes chemo- and radioresistance in pancreatic cancer cells. Int J Oncol 52:621–629
van Haute L, Hendrick AG, D’Souza AR et al (2019) METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis. Nucleic Acids Res 47:10267–10281
van Tran N, Ernst FGM, Hawley BR et al (2019) The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res 47:7719–7733
Vilardo E, Nachbagauer C, Buzet A et al (2012) A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase—extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res 40:11583–11593
Walters BJ, Mercaldo V, Gillon CJ et al (2017) The role of the RNA demethylase FTO (fat mass and obesity-associated) and mRNA methylation in hippocampal memory formation. Neuropsychopharmacology 42:1502–1510
Wang X, He C (2014) Dynamic RNA modifications in posttranscriptional regulation. Mol Cell 56:5–12
Wang X, Lu Z, Gomez A et al (2014) N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505:117–120
Wang P, Doxtader AK, Nam Y (2016a) Structural basis for cooperative function of Mettl3 and Mettl14 methyltransferases. Mol Cell 63:306–317
Wang X, Feng J, Xue Y et al (2016b) Structural basis of N(6)-adenosine methylation by the METTL3-METTL14 complex. Nature 534:575–578
Wang Y, Li Y, Yue M et al (2018) N(6)-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nat Neurosci 21:195–206
Warda SA, Kretschmer J, Hackert P et al (2017) Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep 18:2004–2014
Widagdo J, Zhao QY, Kempen MJ et al (2016) Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice. J Neurosc 36:6771–6777
Xiang Y, Laurent B, Hsu CH et al (2017) RNA m6A methylation regulates the ultraviolet-induced DNA damage response. Nature 543:573–576
Xu L, Liu X, Sheng N et al (2017a) Three distinct 3-methylcytidine (m3C) methyltransferases modify tRNA and mRNA in mice and humans. J Biol Chem 292:14695–14703
Xu K, Yang Y, Feng GH et al (2017b) Mettl3-mediated m(6)A regulates spermatogonial differentiation and meiosis initiation. Cell Res 27:1100–1114
Yang X, Yang Y, Sun BF et al (2017) 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an M5C reader. Cell Res 27:606–625
Ye F, Chen ER, Nilsen TW (2017) Kaposi’s sarcoma-associated herpesvirus utilizes and manipulates RNA N6-adenosine methylation to promote lytic replication. J Virol 91:e00466–e00417
Yin H, Wang H, Jiang W et al (2017) Electrochemical immunosensor for N6-methyladenosine detection in human cell lines based on biotin-streptavidin system and silver-SiO2 signal amplification. Biosens Bioelectron 90:494–500
Yoon KJ, Ringeling FR, Vissers C et al (2017) Temporal control of mammalian cortical neurogenesis by m6A methylation. Cell 171:877–889
Zhang X, Liu Z, Yi J et al (2012) The tRNA methyltransferase NSun2 stabilizes p16INK4 mRNA by methylating the 3′-untranslated region of p16. Nat Commun 3:712
Zhang C, Samanta D, Lu H et al (2016a) Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA. Proc Natl Acad Sci USA 113:E2047–E2056
Zhang C, Zhi WI, Lu H et al (2016b) Hypoxia-inducible factors regulate pluripotency factor expression by ZNF217- and ALKBH5-mediated modulation of RNA methylation in breast cancer cells. Oncotarget 7:64527–64542
Zhang L, Liu C, Ma H et al (2019) Transcriptome-wide mapping of internal N 7-methylguanosine methylome in mammalian mRNA. Mol Cell 74:1304–1316
Zheng G, Dahl JA, Niu Y et al (2013) ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell 49:18–29
Zhong X, Yu J, Frazier K et al (2018) Circadian clock regulation of hepatic lipid metabolism by modulation of m6A mRNA methylation. Cell Rep 25:1816–1828
Zhou H, Wang F, Wang H et al (2017) The conformational changes of Zika virus methyltransferase upon converting SAM to SAH. Oncotarget 8:14830–14834
Acknowledgments
We wish to thank the members of our laboratories. This work was supported in part by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (17H04282, 17K19698, 18K16356, and 18K16355); and Japan Agency for Medical Research and Development (AMED) (16cm0106414h0001 and 17cm0106414h0002). Partial support was received from the Princess Takamatsu Cancer Research Fund. Partial institutional endowments were received from Hirotsu Bio Science Inc. (Tokyo, Japan); Kinshu-kai Medical Corporation (Osaka, Japan); Kyowa-kai Medical Corporation (Osaka, Japan); IDEA Consultants Inc. (Tokyo, Japan); and Unitech Co. Ltd. (Chiba, Japan).
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Konno, M., Ishii, H. (2021). Epitranscriptomics and Diseases. In: Jurga, S., Barciszewski, J. (eds) Epitranscriptomics. RNA Technologies, vol 12. Springer, Cham. https://doi.org/10.1007/978-3-030-71612-7_4
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