Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 1,935

The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.

Gene expression regulation mediated through reversible m6A RNA methylation

Fu, Ye, Dominissini, Dan, Rechavi, Gideon, He, Chuan·2014·Nature Reviews Genetics
DOI 10.1038/nrg3724
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nrg3724

Cites

20 of 20 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 20 references

Research works printed but not linked: 102

  1. Bhutani, N., Burns, D. M. & Blau, H. M. DNA demethylation dynamics. Cell 146, 866–872 (2011). · DOI · Paper page
  2. Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000). · DOI · Paper page
  3. Shi, Y. Histone lysine demethylases: emerging roles in development, physiology and disease. Nature Rev. Genet. 8, 829–833 (2007). · DOI · Paper page
  4. Bird, A. Molecular biology. Methylation talk between histones and DNA. Science. 294, 2113–2115 (2001). · DOI · Paper page
  5. He, C. Grand challenge commentary: RNA epigenetics? Nature Chem. Biol. 6, 863–865 (2010). · DOI · Paper page
  6. Grosjean, H. & Benne, R. Modification and Editing of RNA (American Society for Microbiology Press, 1998). · DOI · Paper page
  7. Grosjean, H. Fine-Tuning of RNA Functions by Modification and Editing (Springer-Verlag, 2005). · DOI · Paper page
  8. Machnicka, M. A. et al. MODOMICS: a database of RNA modification pathways — 2013 update. Nucleic Acids Res. 41, D262–D267 (2013). · DOI · Paper page
  9. Motorin, Y. & Helm, M. RNA nucleotide methylation. Wiley Interdiscip. Rev. RNA 2, 611–631 (2011). · DOI · Paper page
  10. Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012). · DOI · Paper page
  11. Wei, C. M., Gershowitz, A. & Moss, B. Methylated nucleotides block 5′ terminus of HeLa-cell messenger-RNA. Cell 4, 379–386 (1975). · DOI · Paper page
  12. Krug, R. M., Morgan, M. A. & Shatkin, A. J. Influenza viral mRNA contains internal N6-methyladenosine and 5′-terminal 7-methylguanosine in cap structures. J. Virol. 20, 45–53 (1976). · DOI · Paper page
  13. Rottman, F. M., Desrosiers, R. C. & Friderici, K. Nucleotide methylation patterns in eukaryotic mRNA. Prog. Nucleic Acid. Res. Mol. Biol. 19, 21–38 (1976). · DOI
  14. Beemon, K. & Keith, J. Localization of N6-methyladenosine in the Rous sarcoma virus genome. J. Mol. Biol. 113, 165–179 (1977). · DOI
  15. Schibler, U., Kelley, D. E. & Perry, R. P. Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells. J. Mol. Biol. 115, 695–714 (1977). · DOI · Paper page
  16. Wei, C. M. & Moss, B. Nucleotide sequences at the N6-methyladenosine sites of HeLa cell messenger ribonucleic acid. Biochemistry 16, 1672–1676 (1977). · DOI · Paper page
  17. Narayan, P. & Rottman, F. M. An in vitro system for accurate methylation of internal adenosine residues in messenger RNA. Science 242, 1159–1162 (1988). · DOI
  18. Csepany, T., Lin, A., Baldick, C. J. Jr & Beemon, K. Sequence specificity of mRNA N6-adenosine methyltransferase. J. Biol. Chem. 265, 20117–20122 (1990). · DOI · Paper page
  19. Narayan, P., Ludwiczak, R. L., Goodwin, E. C. & Rottman, F. M. Context effects on N6-adenosine methylation sites in prolactin mRNA. Nucleic Acids Res. 22, 419–426 (1994). · DOI
  20. Rottman, F., Shatkin, A. J. & Perry, R. P. Sequences containing methylated nucleotides at 5′ termini of messenger-RNAs — possible implications for processing. Cell 3, 197–199 (1974). · DOI · Paper page
  21. Bodi, Z., Button, J. D., Grierson, D. & Fray, R. G. Yeast targets for mRNA methylation. Nucleic Acids Res. 38, 5327–5335 (2010). · DOI
  22. Keith, G. Mobilities of modified ribonucleotides on two-dimensional cellulose thin-layer chromatography. Biochimie 77, 142–144 (1995). · DOI
  23. 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). · DOI · Paper page
  24. Schwartz, S. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409–1421 (2013). This study reveals the dynamics of transcriptome-wide m6A changes during yeast meiosis. · DOI · Paper page
  25. 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). · DOI · Paper page
  26. 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). · DOI
  27. 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). · DOI · Paper page
  28. 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). · DOI
  29. Vilfan, I. D. et al. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J. Nanobiotechnol. 11, 8 (2013). · DOI · Paper page
  30. 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 pivotal study identifies METTL3 as a key SAM-binding subunit of the RNA methyltransferase complex.
  31. Bokar, J. A. in Fine-Tuning of RNA Functions by Modification and Editing 141–177 (Springer-Verlag, 2005). · DOI
  32. Liu, J. et al. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nature Chem. Biol. 10, 93–95 (2014). This paper uncovers the core components of the m6A RNA methyltransferase complex and reveals an overall negative correlation between the levels of m6A mRNA methylation and gene expression. · DOI · Paper page
  33. Bujnicki, J. M., Feder, M., Radlinska, M. & Blumenthal, R. M. Structure prediction and phylogenetic analysis of a functionally diverse family of proteins homologous to the MT-A70 subunit of the human mRNA:m6A methyltransferase. J. Mol. Evol. 55, 431–444 (2002). · DOI · Paper page
  34. Wang, Y. et al. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nature Cell Biol. 16, 191–198 (2014). This study discovered that the m6A modification on mRNA affects embryonic cell differentiation. · DOI · Paper page
  35. Alexandrov, A., Martzen, M. R. & Phizicky, E. M. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8, 1253–1266 (2002). · DOI · Paper page
  36. Chujo, T. & Suzuki, T. Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs. RNA 18, 2269–2276 (2012). · DOI · Paper page
  37. 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). · DOI
  38. Leulliot, N. et al. Structure of the yeast tRNA m7G methylation complex. Structure 16, 52–61 (2008). · DOI
  39. 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). · DOI · Paper page
  40. 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). · DOI · Paper page
  41. Little, N. A., Hastie, N. D. & Davies, R. C. Identification of WTAP, a novel Wilms' tumour 1-associating protein. Hum. Mol. Genet. 9, 2231–2239 (2000). · DOI · Paper page
  42. Ping, X. L. et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24, 177–189 (2014). · DOI · Paper page
  43. Horiuchi, K. et al. Identification of Wilms' Tumor 1-associating protein complex and its role in alternative splicing and the cell cycle. J. Biol. Chem. 288, 33292–33302 (2013). · DOI · Paper page
  44. 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 (2012). · DOI · Paper page
  45. 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). · DOI · Paper page
  46. Peters, T., Ausmeier, K. & Ruther, U. Cloning of Fatso (Fto), a novel gene deleted by the Fused toes (Ft) mouse mutation. Mamm. Genome 10, 983–986 (1999). · doi:10.1007/s003359901121
  47. Dina, C. et al. Variation in FTO contributes to childhood obesity and severe adult obesity. Nature Genet. 39, 724–726 (2007). · DOI · Paper page
  48. Frayling, T. M. et al. A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science 316, 889–894 (2007). · DOI · Paper page
  49. Gerken, T. et al. The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science 318, 1469–1472 (2007). · DOI · Paper page
  50. Fischer, J. et al. Inactivation of the Fto gene protects from obesity. Nature 458, 894–898 (2009). · DOI · Paper page
  51. Church, C. et al. Overexpression of Fto leads to increased food intake and results in obesity. Nature Genet. 42, 1086–1092 (2010). · DOI · Paper page
  52. Boissel, S. et al. Loss-of-function mutation in the dioxygenase-encoding FTO gene causes severe growth retardation and multiple malformations. Am. J. Hum. Genet. 85, 106–111 (2009). · DOI · Paper page
  53. He, Y. F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307 (2011). · DOI · Paper page
  54. Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009). · DOI · Paper page
  55. Jia, G. et al. Oxidative demethylation of 3-methylthymine and 3-methyluracil in single-stranded DNA and RNA by mouse and human FTO. FEBS Lett. 582, 3313–3319 (2008). · DOI · Paper page
  56. Hess, M. E. et al. The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry. Nature Neurosci. 16, 1042–1048 (2013). · DOI · Paper page
  57. Gulati, P. et al. Role for the obesity-related FTO gene in the cellular sensing of amino acids. Proc. Natl Acad. Sci. USA 110, 2557–2562 (2013). · DOI · Paper page
  58. Han, Z. et al. Crystal structure of the FTO protein reveals basis for its substrate specificity. Nature 464, 1205–1209 (2010). · DOI · Paper page
  59. Zheng, G. et al. Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases. RNA Biol. 10, 915–918 (2013). · DOI
  60. Baltz, A. G. et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 46, 674–690 (2012). · DOI · Paper page
  61. Fu, Y. et al. FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA. Nature Commun. 4, 1798 (2013). · DOI · Paper page
  62. Rabani, M. et al. Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nature Biotech. 29, 436–442 (2011). · DOI · Paper page
  63. Robbens, S. et al. The FTO gene, implicated in human obesity, is found only in vertebrates and marine algae. J. Mol. Evol. 66, 80–84 (2008). · DOI
  64. Iyer, L. M., Tahiliani, M., Rao, A. & Aravind, L. Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle 8, 1698–1710 (2009). · DOI · Paper page
  65. Isken, O. & Maquat, L. E. The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nature Rev. Genet. 9, 699–712 (2008). · DOI · Paper page
  66. Sheth, U. & Parker, R. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300, 805–808 (2003). · DOI · Paper page
  67. Han, D. et al. IRE1α kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates. Cell 138, 562–575 (2009). · DOI · Paper page
  68. Marzluff, W. F., Wagner, E. J. & Duronio, R. J. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nature Rev. Genet. 9, 843–854 (2008). · DOI · Paper page
  69. Dasgupta, T. & Ladd, A. N. The importance of CELF control: molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins. Wiley Interdiscip. Rev. RNA 3, 104–121 (2012). · DOI · Paper page
  70. Yang, F. & Schoenberg, D. R. Endonuclease-mediated mRNA decay involves the selective targeting of PMR1 to polyribosome-bound substrate mRNA. Mol. Cell 14, 435–445 (2004). · DOI
  71. Ghosh, S. & Jacobson, A. RNA decay modulates gene expression and controls its fidelity. Wiley Interdiscip. Rev. RNA 1, 351–361 (2010). · DOI
  72. He, L. & Hannon, G. J. MicroRNAs: small RNAs with a big role in gene regulation. Nature Rev. Genet. 5, 522–531 (2004). · DOI · Paper page
  73. Harigaya, Y. et al. Selective elimination of messenger RNA prevents an incidence of untimely meiosis. Nature 442, 45–50 (2006). · DOI · Paper page
  74. Kawai, T. & Akira, S. Toll-like receptor and RIG-I-like receptor signaling. Ann. NY Acad. Sci. 1143, 1–20 (2008). · DOI · Paper page
  75. Newby, M. I. & Greenbaum, N. L. Sculpting of the spliceosomal branch site recognition motif by a conserved pseudouridine. Nature Struct. Biol. 9, 958–965 (2002). · DOI
  76. Mukherjee, N. et al. Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol. Cell 43, 327–339 (2011). · DOI · Paper page
  77. Srikantan, S. & Gorospe, M. UneCLIPsing HuR nuclear function. Mol. Cell 43, 319–321 (2011). · DOI
  78. Dormoy-Raclet, V. et al. HuR and miR-1192 regulate myogenesis by modulating the translation of HMGB1 mRNA. Nature Commun. 4, 2388 (2013). · DOI
  79. Barnhart, M. D., Moon, S. L., Emch, A. W., Wilusz, C. J. & Wilusz, J. Changes in cellular mRNA stability, splicing, and polyadenylation through HuR protein sequestration by a cytoplasmic RNA virus. Cell Rep. 5, 909–917 (2013). · DOI
  80. Abdelmohsen, K. & Gorospe, M. Posttranscriptional regulation of cancer traits by HuR. Wiley Interdiscip. Rev. RNA 1, 214–229 (2010). · DOI · Paper page
  81. Chen, K. & Rajewsky, N. The evolution of gene regulation by transcription factors and microRNAs. Nature Rev. Genet. 8, 93–103 (2007). · DOI · Paper page
  82. Filipowicz, W., Bhattacharyya, S. N. & Sonenberg, N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nature Rev. Genet. 9, 102–114 (2008). · DOI
  83. Parker, R. & Sheth, U. P bodies and the control of mRNA translation and degradation. Mol. Cell 25, 635–646 (2007). · DOI · Paper page
  84. Gallego, M. & Virshup, D. M. Post-translational modifications regulate the ticking of the circadian clock. Nature Rev. Mol. Cell Biol. 8, 139–148 (2007). · DOI · Paper page
  85. Eulalio, A., Behm-Ansmant, I. & Izaurralde, E. P bodies: at the crossroads of post-transcriptional pathways. Nature Rev. Mol. Cell Biol. 8, 9–22 (2007). · DOI · Paper page
  86. Fustin, J. M. et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell 155, 793–806 (2013). This study shows that the m6A modification affects the export of several mRNAs that are related to the circadian cycle. · DOI · Paper page
  87. Saletore, Y. et al. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 13, 175 (2012). · DOI · Paper page
  88. Karijolich, J. & Yu, Y. T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395–398 (2011). · DOI · Paper page
  89. Fernandez, I. S. et al. Unusual base pairing during the decoding of a stop codon by the ribosome. Nature 500, 107–110 (2013). · DOI
  90. Ge, J. & Yu, Y. T. RNA pseudouridylation: new insights into an old modification. Trends Biochem. Sci. 38, 210–218 (2013). · DOI · Paper page
  91. Edelheit, S., Schwartz, S., Mumbach, M. R., Wurtzel, O. & Sorek, R. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet. 9, e1003602 (2013). · DOI · Paper page
  92. Hussain, S., Aleksic, J., Blanco, S., Dietmann, S. & Frye, M. Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol. 14, 215 (2013). · DOI
  93. Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023–5033 (2012). · DOI · Paper page
  94. Bykhovskaya, Y., Casas, K., Mengesha, E., Inbal, A. & Fischel-Ghodsian, N. Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA). Am. J. Hum. Genet. 74, 1303–1308 (2004). · DOI · Paper page
  95. Patton, J. R., Bykhovskaya, Y., Mengesha, E., Bertolotto, C. & Fischel-Ghodsian, N. Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation. J. Biol. Chem. 280, 19823–19828 (2005). · DOI
  96. Sahoo, T. et al. Prader–Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nature Genet. 40, 719–721 (2008). · DOI · Paper page
  97. Sedgwick, B. Repairing DNA-methylation damage. Nature Rev. Mol. Cell Biol. 5, 148–157 (2004). · DOI · Paper page
  98. Mishina, Y., Duguid, E. M. & He, C. Direct reversal of DNA alkylation damage. Chem. Rev. 106, 215–232 (2006). · DOI
  99. Fu, Y. et al. The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. Angew. Chem. Int. Ed Engl. 49, 8885–8888 (2010). · DOI
  100. van den Born, E. et al. ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA. Nature Commun. 2, 172 (2011). · DOI · Paper page
  101. Aik, W. et al. Structure of human RNA N6-methyladenine demethylase ALKBH5 provides insights into its mechanisms of nucleic acid recognition and demethylation. Nucleic Acids Res. http://dx.doi.org/10.1093/nar/gku085 (2014). · DOI · Paper page
  102. Chen, W. et al. Crystal structure of the RNA demethylase ALKBH5 from zebrafish. FEBS Lett. 588, 892–898 (2014). · DOI

Cited by

See all 1,935

Metadata

Authors
Fu, Y., Dominissini, D., Rechavi, G., & He, C.
Venue
Nature Reviews Genetics
Publisher
Springer Science and Business Media LLC
Published
2014-03-25
Volume
15
Issue
5
Pages
293-306
ISSN
  • 1471-0056 (ISSN-L)
  • 1471-0064
DOI
10.1038/nrg3724
OpenAlex
W2091724447
Cited by
1,935
References
20
FWCI
5.01
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Gene expression regulation mediated through reversible m6A RNA methylation. https://app.cochat.ai/papers/10.1038/nrg3724
The paper
Fu, Y., Dominissini, D., Rechavi, G., & He, C. (2014). Gene expression regulation mediated through reversible m6A RNA methylation. Nature Reviews Genetics. https://doi.org/10.1038/nrg3724

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.