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  • Review Article
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Biological roles of adenine methylation in RNA

Nature Reviews Genetics volume 24, pages 143–160 (2023)Cite this article

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Abstract

N6-Methyladenosine (m6A) is one of the most abundant modifications of the epitranscriptome and is found in cellular RNAs across all kingdoms of life. Advances in detection and mapping methods have improved our understanding of the effects of m6A on mRNA fate and ribosomal RNA function, and have uncovered novel functional roles in virtually every species of RNA. In this Review, we explore the latest studies revealing roles for m6A-modified RNAs in chromatin architecture, transcriptional regulation and genome stability. We also summarize m6A functions in biological processes such as stem-cell renewal and differentiation, brain function, immunity and cancer progression.

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Fig. 1: Molecular consequences of m6A modification of mRNA.
Fig. 2: Molecular consequences of m6A modification of non-coding RNAs.
Fig. 3: Genomic consequences of m6A.
Fig. 4: m6A is a critical modification during early development and embryogenesis.
Fig. 5: m6A function in adult cell homeostasis in the nervous system and immune reactions.

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Change history

  • 27 October 2022

    In the version of this article initially published, abbreviations but not full names were listed for the adenosines in the Box 1 figure, which have now been restored in the HTML and PDF versions of the article.

References

  1. Wei, C. M., Gershowitz, A. & Moss, B. Methylated nucleotides block 5′ terminus of HeLa cell messenger RNA. Cell 4, 379–386 (1975).

    Article  CAS  PubMed  Google Scholar 

  2. Sommer, S., Lavi, U. & Darnell, J. E. Jr. The absolute frequency of labeled N-6-methyladenosine in HeLa cell messenger RNA decreases with label time. J. Mol. Biol. 124, 487–499 (1978).

    Article  CAS  PubMed  Google Scholar 

  3. Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012). Together with Meyer et al. (2012), this paper reports the mapping of m6A in the human and mouse transcriptome.

    Article  CAS  PubMed  Google Scholar 

  5. Tegowski, M., Flamand, M. N. & Meyer, K. D. scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells. Mol. Cell 82, 868–878.e10 (2022).

    Article  CAS  PubMed  Google Scholar 

  6. Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014). This paper reports that the METTL3–METTL14–WTAP complex mediates N6-adenosine methylation.

    Article  CAS  PubMed  Google Scholar 

  7. Wei, C. M. & Moss, B. Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. Biochemistry 16, 1672–1676 (1977).

    Article  CAS  PubMed  Google Scholar 

  8. Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12, 767–772 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013). This study identifies and characterizes ALKBH5 as an m6A demethylase, demonstrating that m6A is a dynamic reversible modification in mRNA.

    Article  CAS  PubMed  Google Scholar 

  10. Jia, G. et al. N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat. Chem. Biol. 7, 885–887 (2011). This study identifies and characterizes FTO as an m6A demethylase, suggesting that m6A is a dynamic reversible modification in mRNA; it should be read in conjunction with Mauer et al. (2017), which suggests that FTO is an m6Am demethylase.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Piekna-Przybylska, D., Decatur, W. A. & Fournier, M. J. The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res. 36, D178–D183 (2008).

    Article  CAS  PubMed  Google Scholar 

  12. Sergiev, P. V., Aleksashin, N. A., Chugunova, A. A., Polikanov, Y. S. & Dontsova, O. A. Structural and evolutionary insights into ribosomal RNA methylation. Nat. Chem. Biol. 14, 226–235 (2018).

    Article  CAS  PubMed  Google Scholar 

  13. Ma, H. et al. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat. Chem. Biol. 15, 88–94 (2019).

    Article  CAS  PubMed  Google Scholar 

  14. Ren, W. et al. Structure and regulation of ZCCHC4 in m6A-methylation of 28S rRNA. Nat. Commun. 10, 5042 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  15. Pinto, R. et al. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Nucleic Acids Res. 48, 830–846 (2020).

    Article  CAS  PubMed  Google Scholar 

  16. van Tran, N. et al. The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. Nucleic Acids Res. 47, 7719–7733 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Liberman, N. et al. N6-Adenosine methylation of ribosomal RNA affects lipid oxidation and stress resistance. Sci. Adv. 6, eaaz4370 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Xing, M. et al. The 18S rRNA m6A methyltransferase METTL5 promotes mouse embryonic stem cell differentiation. EMBO Rep. 21, e49863 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Rong, B. et al. Ribosome 18S m6A methyltransferase METTL5 promotes translation initiation and breast cancer cell growth. Cell Rep. 33, 108544 (2020).

    Article  CAS  PubMed  Google Scholar 

  20. Leismann, J. et al. The 18S ribosomal RNA m6A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep. 21, e49443 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ignatova, V. V. et al. The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev. 34, 715–729 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Sendinc, E., Valle-Garcia, D., Jiao, A. & Shi, Y. Analysis of m6A RNA methylation in Caenorhabditis elegans. Cell Discov. 6, 47 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Sepich-Poore, C. et al. The METTL5–TRMT112 N6-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation. J. Biol. Chem. 298, 101590 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Kierzek, E. & Kierzek, R. The thermodynamic stability of RNA duplexes and hairpins containing N6-alkyladenosines and 2-methylthio-N6-alkyladenosines. Nucleic Acids Res. 31, 4472–4480 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Meyer, K. D. & Jaffrey, S. R. The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat. Rev. 15, 313–326 (2014).

    Article  CAS  Google Scholar 

  26. Liu, N. et al. N6-Methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nature 518, 560–564 (2015). This paper describes a mechanism by which m6A affects RNA folding to indirectly have an impact on the binding of proteins to RNA.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Wang, S. et al. The m6A methylation perturbs the Hoogsteen pairing-guided incorporation of an oxidized nucleotide. Chem. Sci. 8, 6380–6388 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Ashraf, S., Huang, L. & Lilley, D. M. J. Effect of methylation of adenine N6 on kink turn structure depends on location. RNA Biol. 16, 1377–1385 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Ogawa, A. et al. N6-Methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand. Mol. Cell 81, 659–674.e7 (2021).

    Article  CAS  PubMed  Google Scholar 

  30. Patil, D. P., Pickering, B. F. & Jaffrey, S. R. Reading m6A in the transcriptome: m6A-binding proteins. Trends Cell Biol. 28, 113–127 (2018).

    Article  CAS  PubMed  Google Scholar 

  31. Shi, H., Wei, J. & He, C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol. Cell 74, 640–650 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Zaccara, S., Ries, R. J. & Jaffrey, S. R. Reading, writing and erasing mRNA methylation. Nat. Rev. 20, 608–624 (2019).

    Article  CAS  Google Scholar 

  33. Huang, H. et al. Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat. Cell Biol. 20, 285–295 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Edupuganti, R. R. et al. N6-Methyladenosine (m6A) recruits and repels proteins to regulate mRNA homeostasis. Nat. Struct. Mol. Biol. 24, 870–878 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ping, X. L. et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fustin, J. M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013).

    Article  CAS  PubMed  Google Scholar 

  37. Meyer, K. D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Wang, X. et al. N6-Methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015). Together with Meyer et al. (2015), this paper establishes a role for m6A in regulating mRNA translation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Li, A. et al. Cytoplasmic m6A reader YTHDF3 promotes mRNA translation. Cell Res. 27, 444–447 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Wang, X. et al. N6-Methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014). This paper establishes a role for m6A in modulating mRNA stability.

    Article  PubMed  Google Scholar 

  42. Viegas, I. J. et al. N6-Methyladenosine in poly(A) tails stabilize VSG transcripts. Nature 604, 362–370 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Alarcon, C. R., Lee, H., Goodarzi, H., Halberg, N. & Tavazoie, S. F. N6-Methyladenosine marks primary microRNAs for processing. Nature 519, 482–485 (2015). This paper establishes a role for m6A in modulating miRNA processing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Alarcon, C. R. et al. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Lence, T. et al. m6A modulates neuronal functions and sex determination in Drosophila. Nature 540, 242–247 (2016).

    Article  CAS  PubMed  Google Scholar 

  46. Haussmann, I. U. et al. m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature 540, 301–304 (2016).

    Article  CAS  PubMed  Google Scholar 

  47. Xiao, W. et al. Nuclear m6A reader YTHDC1 regulates mRNA splicing. Mol. Cell 61, 507–519 (2016). This study establishes a role for m6A in modulating splicing.

    Article  CAS  PubMed  Google Scholar 

  48. Roundtree, I. A. et al. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. eLife 6, e31311 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  49. Edens, B. M. et al. FMRP modulates neural differentiation through m6A-dependent mRNA nuclear export. Cell Rep. 28, 845–854.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Hsu, P. J. et al. The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine-containing mRNAs. J. Biol. Chem. 294, 19889–19895 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wang, Y. et al. N6-Methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat. Cell Biol. 16, 191–198 (2014). This study establishes a role for METTL3 and METTL14 in stemcell renewal via reduced stability of m6A-modified transcripts.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Du, H. et al. YTHDF2 destabilizes m6A-containing RNA through direct recruitment of the CCR4–NOT deadenylase complex. Nat. Commun. 7, 12626 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Park, O. H. et al. Endoribonucleolytic cleavage of m6A-containing RNAs by RNase P/MRP complex. Mol. Cell 74, 494–507.e8 (2019).

    Article  CAS  PubMed  Google Scholar 

  54. Shi, H. et al. YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA. Cell Res. 27, 315–328 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Choi, J. et al. N6-Methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat. Struct. Mol. Biol. 23, 110–115 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Taoka, M. et al. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res. 46, 9289–9298 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Chen, T. et al. m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell 16, 289–301 (2015).

    Article  CAS  PubMed  Google Scholar 

  58. Das Mandal, S. & Ray, P. S. Transcriptome-wide analysis reveals spatial correlation between N6-methyladenosine and binding sites of microRNAs and RNA-binding proteins. Genomics 113, 205–216 (2021).

    Article  PubMed  Google Scholar 

  59. Kanoria, S., Rennie, W. A., Carmack, C. S., Lu, J. & Ding, Y. N6-Methyladenosine enhances post-transcriptional gene regulation by microRNAs. Bioinform Adv. 2, vbab046 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Chen, L. L. The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat. Rev. 21, 475–490 (2020).

    Article  CAS  Google Scholar 

  61. Memczak, S. et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495, 333–338 (2013).

    Article  CAS  PubMed  Google Scholar 

  62. Hansen, T. B. et al. Natural RNA circles function as efficient microRNA sponges. Nature 495, 384–388 (2013).

    Article  CAS  PubMed  Google Scholar 

  63. Yang, Y. et al. Extensive translation of circular RNAs driven by N6-methyladenosine. Cell Res. 27, 626–641 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Di Timoteo, G. et al. Modulation of circRNA metabolism by m6A modification. Cell Rep. 31, 107641 (2020).

    Article  PubMed  Google Scholar 

  65. Pendleton, K. E. et al. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169, 824–835.e14 (2017). This study shows that METTL16 m6A methyltransferase regulates SAM synthetase mRNA splicing, modulating SAM levels and, thereby, indirectly regulating the methylation of proteins and nucleic acids.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Warda, A. S. et al. Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 18, 2004–2014 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Huang, H. et al. Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally. Nature 567, 414–419 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Li, Y. et al. N6-Methyladenosine co-transcriptionally directs the demethylation of histone H3K9me2. Nat. Genet. 52, 870–877 (2020).

    Article  CAS  PubMed  Google Scholar 

  69. Akhtar, J. et al. m6A RNA methylation regulates promoter-proximal pausing of RNA polymerase II. Mol. Cell 81, 3356–3367.e6 (2021).

    Article  CAS  PubMed  Google Scholar 

  70. Xu, W. et al. Dynamic control of chromatin-associated m6A methylation regulates nascent RNA synthesis. Mol. Cell 82, 1156–1168.e7 (2022).

    Article  CAS  PubMed  Google Scholar 

  71. Mendel, M. et al. Methylation of structured RNA by the m6A writer METTL16 is essential for mouse embryonic development. Mol. Cell 71, 986–1000.e11 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Mendel, M. et al. Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell 184, 3125–3142.e25 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Yang, L., Froberg, J. E. & Lee, J. T. Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem. Sci. 39, 35–43 (2014).

    Article  PubMed  Google Scholar 

  74. Patil, D. P. et al. m6A RNA methylation promotes XIST-mediated transcriptional repression. Nature 537, 369–373 (2016). This paper establishes a role for m6A in Xist-mediated silencing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Nesterova, T. B. et al. Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation. Nat. Commun. 10, 3129 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  76. Kopp, F. & Mendell, J. T. Functional classification and experimental dissection of long noncoding RNAs. Cell 172, 393–407 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Wang, X. et al. N6-Methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles. Dev. Cell 56, 702–715.e8 (2021).

    Article  CAS  PubMed  Google Scholar 

  78. Andergassen, D. & Rinn, J. L. From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat. Rev. Genet. 23, 229–243 (2022).

    Article  CAS  PubMed  Google Scholar 

  79. Liu, J. et al. N6-Methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science 367, 580–586 (2020). This study performs targeted epigenomic editing to test the direct role of m6A on specific RNAs.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Lee, J. H. et al. Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Mol. Cell 81, 3368–3385.e9 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Romanish, M. T., Cohen, C. J. & Mager, D. L. Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer. Semin. Cancer Biol. 20, 246–253 (2010).

    Article  CAS  PubMed  Google Scholar 

  82. Chelmicki, T. et al. m6A RNA methylation regulates the fate of endogenous retroviruses. Nature 591, 312–316 (2021). This study establishes a role for m6A in suppressing ERVs to help maintain genome stability.

    Article  CAS  PubMed  Google Scholar 

  83. Xu, W. et al. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature 591, 317–321 (2021).

    Article  CAS  PubMed  Google Scholar 

  84. Niehrs, C. & Luke, B. Regulatory R-loops as facilitators of gene expression and genome stability. Nat. Rev. 21, 167–178 (2020).

    Article  CAS  Google Scholar 

  85. Abakir, A. et al. N6-Methyladenosine regulates the stability of RNA:DNA hybrids in human cells. Nat. Genet. 52, 48–55 (2020). This paper establishes a role for m6A in regulating R-loop formation.

    Article  CAS  PubMed  Google Scholar 

  86. Yang, X. et al. m6A promotes R-loop formation to facilitate transcription termination. Cell Res. 29, 1035–1038 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Zhang, C. et al. METTL3 and N6-methyladenosine promote homologous recombination-mediated repair of DSBs by modulating DNA–RNA hybrid accumulation. Mol. Cell 79, 425–442.e7 (2020).

    Article  CAS  PubMed  Google Scholar 

  88. Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science 347, 1002–1006 (2015). This paper establishes a role for METTL3 in mES cell renewal and differentiation and shows that m6A reduces pluripotency factor transcript stability to facilitate ES cell differentiation.

    Article  CAS  PubMed  Google Scholar 

  89. Meng, T. G. et al. Mettl14 is required for mouse postimplantation development by facilitating epiblast maturation. FASEB J. 33, 1179–1187 (2019).

    Article  CAS  PubMed  Google Scholar 

  90. Zhong, S. et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant. Cell 20, 1278–1288 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Batista, P. J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Aguilo, F. et al. Coordination of m6A mRNA methylation and gene transcription by ZFP217 regulates pluripotency and reprogramming. Cell Stem Cell 17, 689–704 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Wen, J. et al. Zc3h13 regulates nuclear RNA m6A methylation and mouse embryonic stem cell self-renewal. Mol. Cell 69, 1028–1038.e6 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Bertero, A. et al. The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency. Nature 555, 256–259 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Heck, A. M., Russo, J., Wilusz, J., Nishimura, E. O. & Wilusz, C. J. YTHDF2 destabilizes m6A-modified neural-specific RNAs to restrain differentiation in induced pluripotent stem cells. RNA 26, 739–755 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Zaccara, S. & Jaffrey, S. R. A unified model for the function of YTHDF proteins in regulating m6A-modified mRNA. Cell 181, 1582–1595.e18 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Yartseva, V. & Giraldez, A. J. The maternal-to-zygotic transition during vertebrate development: a model for reprogramming. Curr. Top. Dev. Biol. 113, 191–232 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Zhao, B. S. et al. m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition. Nature 542, 475–478 (2017). This study establishes a role for m6A in maternal transcript clearance during zebrafish MZT.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Kontur, C., Jeong, M., Cifuentes, D. & Giraldez, A. J. Ythdf m6A readers function redundantly during zebrafish development. Cell Rep. 33, 108598 (2020).

    Article  CAS  PubMed  Google Scholar 

  100. Wojtas, M. N. et al. Regulation of m6A transcripts by the 3′ → 5′ RNA helicase YTHDC2 is essential for a successful meiotic program in the mammalian germline. Mol. Cell 68, 374–387.e12 (2017).

    Article  CAS  PubMed  Google Scholar 

  101. Hsu, P. J. et al. Ythdc2 is an N6-methyladenosine binding protein that regulates mammalian spermatogenesis. Cell Res. 27, 1115–1127 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Bailey, A. S. et al. The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. eLife 6, e26116 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  103. Ivanova, I. et al. The RNA m6A reader YTHDF2 is essential for the post-transcriptional regulation of the maternal transcriptome and oocyte competence. Mol. Cell 67, 1059–1067.e4 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Kasowitz, S. D. et al. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 14, e1007412 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  105. Sui, X. et al. METTL3-mediated m6A is required for murine oocyte maturation and maternal-to-zygotic transition. Cell Cycle 19, 391–404 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Giraldez, A. J. et al. Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312, 75–79 (2006).

    Article  CAS  PubMed  Google Scholar 

  107. Chang, H. et al. Terminal uridylyltransferases execute programmed clearance of maternal transcriptome in vertebrate embryos. Mol. Cell 70, 72–82.e7 (2018).

    Article  CAS  PubMed  Google Scholar 

  108. Wu, Y. & Hirschi, K. K. Regulation of hemogenic endothelial cell development and function. Annu. Rev. Physiol. 83, 17–37 (2021).

    Article  CAS  PubMed  Google Scholar 

  109. Zhang, C. et al. m6A modulates haematopoietic stem and progenitor cell specification. Nature 549, 273–276 (2017).

    Article  CAS  PubMed  Google Scholar 

  110. Lv, J. et al. Endothelial-specific m6A modulates mouse hematopoietic stem and progenitor cell development via Notch signaling. Cell Res. 28, 249–252 (2018).

    Article  PubMed  Google Scholar 

  111. Lee, H. et al. Stage-specific requirement for Mettl3-dependent m6A mRNA methylation during haematopoietic stem cell differentiation. Nat. Cell Biol. 21, 700–709 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  112. Vu, L. P. et al. The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells. Nat. Med. 23, 1369–1376 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Weng, H. et al. METTL14 inhibits hematopoietic stem/progenitor differentiation and promotes leukemogenesis via mRNA m6A modification. Cell Stem Cell 22, 191–205.e9 (2018).

    Article  CAS  PubMed  Google Scholar 

  114. Yoon, K. J. et al. Temporal control of mammalian cortical neurogenesis by m6A methylation. Cell 171, 877–889.e17 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Wang, Y. et al. N6-Methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications. Nat. Neurosci. 21, 195–206 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Li, M. et al. Ythdf2-mediated m6A mRNA clearance modulates neural development in mice. Genome Biol. 19, 69 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  117. Li, L. et al. Fat mass and obesity-associated (FTO) protein regulates adult neurogenesis. Hum. Mol. Genet. 26, 2398–2411 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Liu, J., Harada, B. T. & He, C. Regulation of gene expression by N6-methyladenosine in cancer. Trends Cell Biol. 29, 487–499 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  119. Yang, C. et al. The role of m6A modification in physiology and disease. Cell Death Dis. 11, 960 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Buffington, S. A., Huang, W. & Costa-Mattioli, M. Translational control in synaptic plasticity and cognitive dysfunction. Annu. Rev. Neurosci. 37, 17–38 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Merkurjev, D. et al. Synaptic N6-methyladenosine (m6A) epitranscriptome reveals functional partitioning of localized transcripts. Nat. Neurosci. 21, 1004–1014 (2018). This paper reports the identification of subcellular synapse-specific m6A-methylated transcripts.

    Article  CAS  PubMed  Google Scholar 

  122. Yu, J. et al. Dynamic m6A modification regulates local translation of mRNA in axons. Nucleic Acids Res. 46, 1412–1423 (2018).

    Article  CAS  PubMed  Google Scholar 

  123. Widagdo, J. et al. Experience-dependent accumulation of N6-methyladenosine in the prefrontal cortex is associated with memory processes in mice. J. Neurosci. 36, 6771–6777 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Walters, B. J. et al. The role of the RNA demethylase FTO (fat mass and obesity-associated) and mRNA methylation in hippocampal memory formation. Neuropsychopharmacology 42, 1502–1510 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  125. Engel, M. et al. The role of m6A/m-RNA methylation in stress response regulation. Neuron 99, 389–403.e9 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Mauer, J. et al. Reversible methylation of m6Am in the 5′ cap controls mRNA stability. Nature 541, 371–375 (2017). This study characterizes FTO as an m6Am demethylase that regulates mRNA stability, suggesting that m6Am is a dynamic reversable modification; it should be read in conjunction with Jia et al. (2011), which suggests that FTO is a m6A demethylase.

    Article  CAS  PubMed  Google Scholar 

  127. Zhang, Z. et al. METTL3-mediated N6-methyladenosine mRNA modification enhances long-term memory consolidation. Cell Res. 28, 1050–1061 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Shi, H. et al. m6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature 563, 249–253 (2018). This study reveals a regulatory role for m6A in neurobehavioural phenotypes by promoting translation of selected transcripts.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Li, H. B. et al. m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. Nature 548, 338–342 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Winkler, R. et al. m6A modification controls the innate immune response to infection by targeting type I interferons. Nat. Immunol. 20, 173–182 (2019).

    Article  CAS  PubMed  Google Scholar 

  131. Liu, Y. et al. N6-Methyladenosine RNA modification-mediated cellular metabolism rewiring inhibits viral replication. Science 365, 1171–1176 (2019). This paper shows that m6A-marked transcripts allow a levelled response to viral infection.

    Article  CAS  PubMed  Google Scholar 

  132. Chow, K. T., Gale, M. Jr & Loo, Y. M. RIG-I and other RNA sensors in antiviral immunity. Annu. Rev. Immunol. 36, 667–694 (2018).

    Article  CAS  PubMed  Google Scholar 

  133. Lu, M. et al. N6-Methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I. Nat. Microbiol. 5, 584–598 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Qiu, W. et al. N6-Methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA. Nat. Commun. 12, 1582 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Chen, Y. G. et al. N6-Methyladenosine modification controls circular RNA immunity. Mol. Cell 76, 96–109.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Su, R. et al. R-2HG exhibits anti-tumor activity by targeting FTO/m6A/MYC/CEBPA signaling. Cell 172, 90–105.e23 (2018).

    Article  CAS  PubMed  Google Scholar 

  137. Paris, J. et al. Targeting the RNA m6A reader YTHDF2 selectively compromises cancer stem cells in acute myeloid leukemia. Cell Stem Cell 25, 137–148.e6 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Cheng, Y. et al. N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer Cell 39, 958–972.e8 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Cui, Q. et al. m6A RNA methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep. 18, 2622–2634 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Zhang, S. et al. m6A demethylase ALKBH5 maintains tumorigenicity of glioblastoma stem-like cells by sustaining FOXM1 expression and cell proliferation program. Cancer Cell 31, 591–606.e6 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Liberman, N. et al. Intergenerational hormesis is regulated by heritable 18S rRNA methylation. Preprint at bioRxiv https://doi.org/10.1101/2021/1109.1127.461965 (2021).

    Article  Google Scholar 

  142. Yankova, E. et al. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 593, 597–601 (2021). This study identifies small molecules that can effectively inhibit METTL3, raising the possibility of therapeutic options for myeloid leukaemia and other m6A-related pathologies.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Kruse, S. et al. A novel synthesis and detection method for cap-associated adenosine modifications in mouse mRNA. Sci. Rep. 1, 126 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  144. Yuki, H., Kawasaki, H., Imayuki, A. & Yajima, T. Determination of 6-methyladenine in DNA by high-performance liquid chromatography. J. Chromatogr. 168, 489–494 (1979).

    Article  CAS  PubMed  Google Scholar 

  145. Thuring, K., Schmid, K., Keller, P. & Helm, M. LC–MS analysis of methylated RNA. Methods Mol. Biol. 1562, 3–18 (2017).

    Article  CAS  PubMed  Google Scholar 

  146. Liu, N. et al. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19, 1848–1856 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Imanishi, M., Tsuji, S., Suda, A. & Futaki, S. Detection of N6-methyladenosine based on the methyl-sensitivity of MazF RNA endonuclease. Chem. Commun. 53, 12930–12933 (2017).

    Article  CAS  Google Scholar 

  148. Garcia-Campos, M. A. et al. Deciphering the “m6A code” via antibody-independent quantitative profiling. Cell 178, 731–747.e16 (2019).

    Article  CAS  PubMed  Google Scholar 

  149. Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. 12, 311–316 (2016).

    Article  CAS  PubMed  Google Scholar 

  151. Safra, M. et al. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551, 251–255 (2017).

    Article  CAS  PubMed  Google Scholar 

  152. Li, X. et al. Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Mol. Cell 68, 993–1005.e9 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Grozhik, A. V. et al. Antibody cross-reactivity accounts for widespread appearance of m1A in 5′ UTRs. Nat. Commun. 10, 5126 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  154. Harcourt, E. M., Ehrenschwender, T., Batista, P. J., Chang, H. Y. & Kool, E. T. Identification of a selective polymerase enables detection of N6-methyladenosine in RNA. J. Am. Chem. Soc. 135, 19079–19082 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Hong, T. et al. Precise antibody-independent m6A identification via 4SedTTP-involved and FTO-assisted strategy at single-nucleotide resolution. J. Am. Chem. Soc. 140, 5886–5889 (2018).

    Article  CAS  PubMed  Google Scholar 

  156. Aschenbrenner, J. et al. Engineering of a DNA polymerase for direct m6A sequencing. Angew. Chem. Int. Ed. 57, 417–421 (2018).

    Article  CAS  Google Scholar 

  157. Ke, S. et al. A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation. Genes Dev. 29, 2037–2053 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Molinie, B. et al. m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome. Nat. Methods 13, 692–698 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Bringmann, P. & Luhrmann, R. Antibodies specific for N6-methyladenosine react with intact snRNPs U2 and U4/U6. FEBS Lett. 213, 309–315 (1987).

    Article  CAS  PubMed  Google Scholar 

  160. Dai, Q. et al. NM-seq maps 2′-O-methylation sites in human mRNA with base precision. Nat. Methods 14, 695–698 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  161. Castellanos-Rubio, A. et al. A novel RT-QPCR-based assay for the relative quantification of residue specific m6A RNA methylation. Sci. Rep. 9, 4220 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  162. Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461–465 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  163. Garalde, D. R. et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat. Methods 15, 201–206 (2018).

    Article  CAS  PubMed  Google Scholar 

  164. Chen, Y. et al. Study of the whole genome, methylome and transcriptome of Cordyceps militaris. Sci. Rep. 9, 898 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Pratanwanich, P. N. et al. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nat. Biotechnol. 39, 1394–1402 (2021).

    Article  CAS  PubMed  Google Scholar 

  166. Mikutis, S. et al. meCLICK-Seq, a substrate-hijacking and RNA degradation strategy for the study of RNA microsoftethylation. ACS Cent. Sci. 6, 2196–2208 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  167. Liu, W. et al. Identification of a selective DNA ligase for accurate recognition and ultrasensitive quantification of N6-methyladenosine in RNA at one-nucleotide resolution. Chem. Sci. 9, 3354–3359 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Xiao, Y. et al. An elongation- and ligation-based qPCR amplification method for the radiolabeling-free detection of locus-specific N6-methyladenosine modification. Angew. Chem. Int. Ed. 57, 15995–16000 (2018).

    Article  CAS  Google Scholar 

  169. Bokar, J. A., Shambaugh, M. E., Polayes, D., Matera, A. G. & Rottman, F. M. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase. RNA 3, 1233–1247 (1997). This paper identifies METTL3 as the catalytic subunit of the complex that mediates N6-adenosine methylation.

    CAS  PubMed  PubMed Central  Google Scholar 

  170. Clancy, M. J., Shambaugh, M. E., Timpte, C. S. & Bokar, J. A. Induction of sporulation in Saccharomyces cerevisiae leads to the formation of N6-methyladenosine in mRNA: a potential mechanism for the activity of the IME4 gene. Nucleic Acids Res. 30, 4509–4518 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  171. Shima, H. et al. S-Adenosylmethionine synthesis is regulated by selective N6-adenosine methylation and mRNA degradation involving METTL16 and YTHDC1. Cell Rep. 21, 3354–3363 (2017).

    Article  CAS  PubMed  Google Scholar 

  172. Akichika, S. et al. Cap-specific terminal N6-methylation of RNA by an RNA polymerase II-associated methyltransferase. Science 363, eaav0080 (2019).

    Article  CAS  PubMed  Google Scholar 

  173. Sun, H., Zhang, M., Li, K., Bai, D. & Yi, C. Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase. Cell Res. 29, 80–82 (2019).

    Article  CAS  PubMed  Google Scholar 

  174. Boulias, K. et al. Identification of the m6Am methyltransferase PCIF1 reveals the location and functions of m6Am in the transcriptome. Mol. Cell 75, 631–643.e8 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  175. Sendinc, E. et al. PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression. Mol. Cell 75, 620–630.e9 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  176. Belanger, F., Stepinski, J., Darzynkiewicz, E. & Pelletier, J. Characterization of hMTr1, a human Cap1 2′-O-ribose methyltransferase. J. Biol. Chem. 285, 33037–33044 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  177. Tollervey, D., Lehtonen, H., Jansen, R., Kern, H. & Hurt, E. C. Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA methylation, and ribosome assembly. Cell 72, 443–457 (1993).

    Article  CAS  PubMed  Google Scholar 

  178. Kiss-Laszlo, Z., Henry, Y., Bachellerie, J. P., Caizergues-Ferrer, M. & Kiss, T. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077–1088 (1996).

    Article  CAS  PubMed  Google Scholar 

  179. Nicoloso, M., Qu, L. H., Michot, B. & Bachellerie, J. P. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2′-O-ribose methylation of rRNAs. J. Mol. Biol. 260, 178–195 (1996).

    Article  CAS  PubMed  Google Scholar 

  180. Tycowski, K. T., Smith, C. M., Shu, M. D. & Steitz, J. A. A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. Proc. Natl Acad. Sci. USA 93, 14480–14485 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  181. Juhling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159–D162 (2009).

    Article  PubMed  Google Scholar 

  182. Ozanick, S., Krecic, A., Andersland, J. & Anderson, J. T. The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11, 1281–1290 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  183. Chujo, T. & Suzuki, T. Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. RNA 18, 2269–2276 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  184. Vilardo, E. et al. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. Nucleic Acids Res. 48, 6157–6169 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  185. Vilardo, E. et al. A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase — extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res. 40, 11583–11593 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Lafontaine, D., Delcour, J., Glasser, A. L., Desgres, J. & Vandenhaute, J. The DIM1 gene responsible for the conserved m62Am62A dimethylation in the 3′-terminal loop of 18S rRNA is essential in yeast. J. Mol. Biol. 241, 492–497 (1994).

    Article  CAS  PubMed  Google Scholar 

  187. Suvorov, A. N., van Gemen, B. & van Knippenberg, P. H. Increased kasugamycin sensitivity in Escherichia coli caused by the presence of an inducible erythromycin resistance (erm) gene of Streptococcus pyogenes. Mol. Gen. Genet. 215, 152–155 (1988).

    Article  CAS  PubMed  Google Scholar 

  188. Shen, H., Stoute, J. & Liu, K. F. Structural and catalytic roles of the human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation. J. Biol. Chem. 295, 12058–12070 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Chen, H. et al. METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing. Cell Res. 30, 544–547 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  190. Goh, Y. T., Koh, C. W. Q., Sim, D. Y., Roca, X. & Goh, W. S. S. METTL4 catalyzes m6Am methylation in U2 snRNA to regulate pre-mRNA splicing. Nucleic Acids Res. 48, 9250–9261 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  191. Liu, F. et al. ALKBH1-mediated tRNA demethylation regulates translation. Cell 167, 816–828.e16 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  192. Kawarada, L. et al. ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. Nucleic Acids Res. 45, 7401–7415 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  193. Aas, P. A. et al. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature 421, 859–863 (2003).

    Article  CAS  PubMed  Google Scholar 

  194. Xu, C. et al. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. Nat. Chem. Biol. 10, 927–929 (2014).

    Article  CAS  PubMed  Google Scholar 

  195. Theler, D., Dominguez, C., Blatter, M., Boudet, J. & Allain, F. H. Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA. Nucleic Acids Res. 42, 13911–13919 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  196. Xu, C. et al. Structural basis for the discriminative recognition of N6-methyladenosine RNA by the human YT521-B homology domain family of proteins. J. Biol. Chem. 290, 24902–24913 (2015).

    Article  CAS  PubMed  Google Scholar 

  197. Liu, N. et al. N6-Methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 45, 6051–6063 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  198. Toh, S. M., Xiong, L., Bae, T. & Mankin, A. S. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 14, 98–106 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  199. Furuichi, Y. et al. Methylated, blocked 5 termini in HeLa cell mRNA. Proc. Natl Acad. Sci. USA 72, 1904–1908 (1975).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  200. Oerum, S., Degut, C., Barraud, P. & Tisne, C. m1A post-transcriptional modification in tRNAs. Biomolecules 7, 20 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  201. Peifer, C. et al. Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41, 1151–1163 (2013).

    Article  CAS  PubMed  Google Scholar 

  202. Waku, T. et al. NML-mediated rRNA base methylation links ribosomal subunit formation to cell proliferation in a p53-dependent manner. J. Cell Sci. 129, 2382–2393 (2016).

    CAS  PubMed  Google Scholar 

  203. Yokoyama, W. et al. rRNA adenine methylation requires T07A9.8 gene as rram-1 in Caenorhabditis elegans. J. Biochem. 163, 465–474 (2018).

    Article  CAS  PubMed  Google Scholar 

  204. Sharma, S. et al. A single N1-methyladenosine on the large ribosomal subunit rRNA impacts locally its structure and the translation of key metabolic enzymes. Sci. Rep. 8, 11904 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  205. Schwartz, S. m1A within cytoplasmic mRNAs at single nucleotide resolution: a reconciled transcriptome-wide map. RNA 24, 1427–1436 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  206. Wei, C., Gershowitz, A. & Moss, B. N6,O2′-Dimethyladenosine a novel methylated ribonucleoside next to the 5′ terminal of animal cell and virus mRNAs. Nature 257, 251–253 (1975).

    Article  CAS  PubMed  Google Scholar 

  207. Keith, J. M., Muthukrishnan, S. & Moss, B. Effect of methylation of the N6 position of the penultimate adenosine of capped mRNA on ribosome binding. J. Biol. Chem. 253, 5039–5041 (1978).

    Article  CAS  PubMed  Google Scholar 

  208. Pandey, R. R. et al. The mammalian Cap-specific m6Am RNA methyltransferase PCIF1 regulates transcript levels in mouse tissues. Cell Rep. 32, 108038 (2020).

    Article  CAS  PubMed  Google Scholar 

  209. Ben-Haim, M. S. et al. Dynamic regulation of N6,2′-O-dimethyladenosine (m6Am) in obesity. Nat. Commun. 12, 7185 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  210. Tartell, M. A. et al. Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-β. Proc. Natl Acad. Sci. USA 118, e2025769118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  211. Mauer, J. et al. FTO controls reversible m6Am RNA methylation during snRNA biogenesis. Nat. Chem. Biol. 15, 340–347 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  212. Zorbas, C. et al. The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis. Mol. Biol. Cell 26, 2080–2095 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  213. Liu, K. et al. Regulation of translation by methylation multiplicity of 18S rRNA. Cell Rep. 34, 108825 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

Work from the Greer laboratory is supported by grants from the US National Institutes of Health (NIH) (DP2AG055947 and R01AI151215). The authors apologize for literature omitted owing to space limitations.

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Authors and Affiliations

  1. Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA

    Konstantinos Boulias & Eric Lieberman Greer

  2. Department of Pediatrics, Harvard Medical School, Boston, MA, USA

    Konstantinos Boulias & Eric Lieberman Greer

  3. Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA

    Konstantinos Boulias & Eric Lieberman Greer

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Glossary

Hoogsteen base pairing

An alternative base pairing in which the purine is flipped and form different hydrogen bonds with partner bases. For adenines, the second hydrogen bond with the pyrimidine base is formed with N6 rather than N1. These alternative base pairs allow for additional structures beyond double helix including triplexes and quadruplexes.

miRNA microprocessor complex

A protein complex involved in the early stages of processing microRNA (miRNA) and RNA interference in animal cells.

Spliceosome

A large RNA–protein complex that catalyses the removal of introns from nuclear pre-mRNA.

Long non-coding RNAs

(lncRNAs). Non-coding RNAs longer than 200 nucleotides.

Chromosome-associated regulatory RNAs

(carRNAs). Regulatory RNAs associated with the chromatin.

Endogenous retrovirus RNAs

(ERVs). The prevalent endogenous viral elements that are derived from retroviruses that have become integrated into the genome.

R-loops

These RNA:DNA hybrids form three-stranded structures when nascent RNA transcripts hybridize with one strand of the DNA template.

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Boulias, K., Greer, E.L. Biological roles of adenine methylation in RNA. Nat Rev Genet 24, 143–160 (2023). https://doi.org/10.1038/s41576-022-00534-0

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