Abstract
N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic mRNA. Recent discoveries of the locations, functions and mechanisms of m6A have shed light on a new layer of gene regulation at the RNA level, giving rise to the field of m6A epitranscriptomics. In this Perspective, we provide an update on the various effects of mammalian m6A modification, which affects many different stages of the RNA life cycle.
This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
CCL3 secreted by hepatocytes promotes the metastasis of intrahepatic cholangiocarcinoma by VIRMA-mediated N6-methyladenosine (m6A) modification
Journal of Translational Medicine Open Access 23 January 2023
-
YTHDC1 is downregulated by the YY1/HDAC2 complex and controls the sensitivity of ccRCC to sunitinib by targeting the ANXA1-MAPK pathway
Journal of Experimental & Clinical Cancer Research Open Access 17 August 2022
-
Transcriptome-wide analysis of glioma stem cell specific m6A modifications in long-non-coding RNAs
Scientific Reports Open Access 31 March 2022
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout



References
Bokar, J.A. in Fine-Tuning of RNA Functions by Modification and Editing 141–177 (Springer, 2005).
Carlile, T.M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014).
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).Together with ref. 4, developed the first high-throughput method to map m6A sites across the mammalian transcriptome.
Meyer, K.D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).Together with ref. 3, mapped m6A sites across the mammalian transcriptome.
Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148–162 (2014).
Squires, J.E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023–5033 (2012).
Slotkin, W. & Nishikura, K. Adenosine-to-inosine RNA editing and human disease. Genome Med. 5, 105–117 (2013).
Desrosiers, R., Friderici, K. & Rottman, F. Identification of methylated nucleosides in messenger RNA from Novikoff hepatoma cells. Proc. Natl. Acad. Sci. USA 71, 3971–3975 (1974).
Rottman, F., Shatkin, A.J. & Perry, R.P. Sequences containing methylated nucleotides at the 5′ termini of messenger RNAs: possible implications for processing. Cell 3, 197–199 (1974).
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).Identified FTO as an m6A eraser, thus indicating that m6A modification is reversible.
Schwartz, S. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409–1421 (2013).
Chen, K. et al. High-resolution N6-methyladenosine (m6A) map using photo-crosslinking-assisted m6A sequencing. Angew. Chem. Int. Edn Engl. 54, 1587–1590 (2015).
Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12, 767–772 (2015).
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).
Wei, C.M. & Moss, B. Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. Biochemistry 16, 1672–1676 (1977).
Csepany, T., Lin, A., Baldick, C.J. Jr. & Beemon, K. Sequence specificity of mRNA N6-adenosine methyltransferase. J. Biol. Chem. 265, 20117–20122 (1990).
Harper, J.E., Miceli, S.M., Roberts, R.J. & Manley, J.L. Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res. 18, 5735–5741 (1990).
Carroll, S.M., Narayan, P. & Rottman, F.M. N6-methyladenosine residues in an intron-specific region of prolactin pre-mRNA. Mol. Cell. Biol. 10, 4456–4465 (1990).
Kane, S.E. & Beemon, K. Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol. Cell. Biol. 5, 2298–2306 (1985).
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).Probed the m6A status at single-nucleotide resolution and revealed fractional m6A modification in mRNA and lncRNA.
Yue, Y., Liu, J. & He, C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 29, 1343–1355 (2015).
Fu, Y., Dominissini, D., Rechavi, G. & He, C. Gene expression regulation mediated through reversible m6A RNA methylation. Nat. Rev. Genet. 15, 293–306 (2014).
Meyer, K.D. & Jaffrey, S.R. The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat. Rev. Mol. Cell Biol. 15, 313–326 (2014).
Liu, N. & Pan, T. RNA epigenetics. Transl. Res. 165, 28–35 (2015).
Bokar, J.A., Rath-Shambaugh, M.E., Ludwiczak, R., Narayan, P. & Rottman, F. Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei: internal mRNA methylation requires a multisubunit complex. J. Biol. Chem. 269, 17697–17704 (1994).
Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10, 93–95 (2014).
Wang, Y. et al. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat. Cell Biol. 16, 191–198 (2014).
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).
Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5′ sites. Cell Reports 8, 284–296 (2014).
Ping, X.-L. et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014).
Lamond, A.I. & Spector, D.L. Nuclear speckles: a model for nuclear organelles. Nat. Rev. Mol. Cell Biol. 4, 605–612 (2003).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Loos, R.J. & Bouchard, C. FTO: the first gene contributing to common forms of human obesity. Obes. Rev. 9, 246–250 (2008).
Smemo, S. et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature 507, 371–375 (2014).
Fu, Y. et al. FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nat. Commun. 4, 1798 (2013).
Schwartz, J.C., Wang, X., Podell, E.R. & Cech, T.R. RNA seeds higher-order assembly of FUS protein. Cell Reports 5, 918–925 (2013).
Chen, T. et al. m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell 16, 289–301 (2015).Demonstrated that miRNAs guide METTL3 and facilitate m6A methylation.
Zhou, J. et al. Dynamic m6A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).Demonstrated stress-inducible m6A methylation and showed that m6A promotes cap-independent mRNA translation.
Wang, X. et al. N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161, 1388–1399 (2015).Demonstrated that m6A-mediated recruitment of YTHDF1 promotes cap-dependent mRNA translation.
Wang, X. et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505, 117–120 (2014).Demonstrated that m6A-mediated recruitment of YTHDF2 promotes mRNA decay in P bodies.
Xu, C. et al. Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain. Nat. Chem. Biol. 10, 927–929 (2014).
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).
Li, F., Zhao, D., Wu, J. & Shi, Y. Structure of the YTH domain of human YTHDF2 in complex with an m6A mononucleotide reveals an aromatic cage for m6A recognition. Cell Res. 24, 1490–1492 (2014).
Luo, S. & Tong, L. Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain. Proc. Natl. Acad. Sci. USA 111, 13834–13839 (2014).
Kato, M. et al. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767 (2012).Described a low-complexity sequence in proteins that promotes RNA-granule formation and identified proteins associated with RNA granules.
Ramaswami, M., Taylor, J.P. & Parker, R. Altered ribostasis: RNA-protein granules in degenerative disorders. Cell 154, 727–736 (2013).
Kwon, I. et al. Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains. Cell 155, 1049–1060 (2013).
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).
Roost, C. et al. Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J. Am. Chem. Soc. 137, 2107–2115 (2015).
Sternglanz, H. & Bugg, C.E. Conformation of N6-methyladenine, a base involved in DNA modification: restriction processes. Science 182, 833–834 (1973).
Spitale, R.C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015).Demonstrated m6A-mediated destabilization of local RNA structure across the transcriptome.
Liu, N. et al. N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nature 518, 560–564 (2015).Discovered an m6A-switch mechanism regulating RNA-HNRNPC interactions and m6A-mediated pre-mRNA processing.
Zhou, K.I. et al. N(6)-Methyladenosine modification in a long noncoding RNA hairpin predisposes its conformation to protein binding. J. Mol. Biol. doi:10.1016/j.jmb.2015.08.021 (4 September 2015).
König, J. et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat. Struct. Mol. Biol. 17, 909–915 (2010).
McCloskey, A., Taniguchi, I., Shinmyozu, K. & Ohno, M. hnRNP C tetramer measures RNA length to classify RNA polymerase II transcripts for export. Science 335, 1643–1646 (2012).
Rajagopalan, L.E., Westmark, C.J., Jarzembowski, J.A. & Malter, J.S. hnRNP C increases amyloid precursor protein (APP) production by stabilizing APP mRNA. Nucleic Acids Res. 26, 3418–3423 (1998).
Zarnack, K. et al. Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 152, 453–466 (2013).
Alarcón, C.R., Lee, H., Goodarzi, H., Halberg, N. & Tavazoie, S.F. N6-methyladenosine marks primary microRNAs for processing. Nature 519, 482–485 (2015).Demonstrated the effects of m6A on miRNA biogenesis.
Alarcón, C.R. et al. HNRNPA2B1 is a mediator of m6A-dependent nuclear RNA processing events. Cell 162, 1299–1308 (2015).
Meyer, K.D. et al. 5′ UTR m6A promotes cap-independent translation. Cell 163, 999–1010 (2015).Together with ref. 38, demonstrated that m6A promotes cap-independent mRNA translation.
Hinnebusch, A.G. The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).
Choi, J. et al. N6-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. Nat. Struct. Mol. Biol. doi:10.1038/nsmb.3148 (11 January 2016). Demonstrated the effects of m6A on translation dynamics.
Batista, P.J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719 (2014).
Geula, S. et al. Stem cells. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science 347, 1002–1006 (2015).
Fustin, J.-M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013).
Gerken, T. et al. The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science 318, 1469–1472 (2007).
Fischer, J. et al. Inactivation of the Fto gene protects from obesity. Nature 458, 894–898 (2009).
Hongay, C.F. & Orr-Weaver, T.L. Drosophila inducer of meiosis 4 (IME4) is required for Notch signaling during oogenesis. Proc. Natl. Acad. Sci. USA 108, 14855–14860 (2011).
Agarwala, S.D., Blitzblau, H.G., Hochwagen, A. & Fink, G.R. RNA methylation by the MIS complex regulates a cell fate decision in yeast. PLoS Genet. 8, e1002732 (2012).
Bodi, Z. et al. Adenosine methylation in Arabidopsis mRNA is associated with the 3′ end and reduced levels cause developmental defects. Front. Plant Sci. 3, 48–57 (2012).
Acknowledgements
Research on RNA modifications in the laboratory of T.P. is supported by the US National Institutes of Health (EUREKA R01GM88599 and R01GM113194).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
Liu, N., Pan, T. N6-methyladenosine–encoded epitranscriptomics. Nat Struct Mol Biol 23, 98–102 (2016). https://doi.org/10.1038/nsmb.3162
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nsmb.3162
This article is cited by
-
CCL3 secreted by hepatocytes promotes the metastasis of intrahepatic cholangiocarcinoma by VIRMA-mediated N6-methyladenosine (m6A) modification
Journal of Translational Medicine (2023)
-
Post-transcriptional checkpoints in autoimmunity
Nature Reviews Rheumatology (2023)
-
Molecular mechanisms of environmental exposures and human disease
Nature Reviews Genetics (2023)
-
The emerging role of epitranscriptome in shaping stress responses in plants
Plant Cell Reports (2023)
-
YTHDC1 is downregulated by the YY1/HDAC2 complex and controls the sensitivity of ccRCC to sunitinib by targeting the ANXA1-MAPK pathway
Journal of Experimental & Clinical Cancer Research (2022)