Thursday, May 28, 2026
No menu items!
HomeNatureSubstrate selectivity of the human RNA m5C methyltransferase NSUN2

Substrate selectivity of the human RNA m5C methyltransferase NSUN2

  • Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol. 22, 375–392 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Delaunay, S., Helm, M. & Frye, M. RNA modifications in physiology and disease: towards clinical applications. Nat. Rev. Genet. 25, 104–122 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sun, H., Li, K., Liu, C. & Yi, C. Regulation and functions of non-m6A mRNA modifications. Nat. Rev. Mol. Cell Biol. 24, 714–731 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bohnsack, K. E., Höbartner, C. & Bohnsack, M. T. Eukaryotic 5-methylcytosine (m5C) RNA methyltransferases: mechanisms, cellular functions, and links to disease. Genes 10, 102 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, X. et al. 5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 27, 606–625 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, F. et al. RNA m5C methylation mediated by Ybx1 ensures hematopoietic stem and progenitor cell expansion. Cell Rep. 44, 115324 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ma, H. L. et al. SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer. Mol. Cell 83, 4239–4254.e10 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, Y. -S., Yang, W. -L., Zhao, Y. -L. & Yang, Y. -G. Dynamic transcriptomic m5 C and its regulatory role in RNA processing. Wiley Interdiscip. Rev. RNA 12, e1639 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guarnacci, M. et al. Substrate diversity of NSUN enzymes and links of 5-methylcytosine to mRNA translation and turnover. Life Sci. Alliance 7, e202402613 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, T., Chen, W., Liu, J., Gu, N. & Zhang, R. Genome-wide identification of mRNA 5-methylcytosine in mammals. Nat. Struct. Mol. Biol. 26, 380–388 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, S. -Y. et al. RNA bisulfite sequencing reveals NSUN2-mediated suppression of epithelial differentiation in pancreatic cancer. Oncogene 41, 3162–3176 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Lu, L. et al. Base-resolution m5C profiling across the mammalian transcriptome by bisulfite-free enzyme-assisted chemical labeling approach. Mol. Cell 84, 2984–3000 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Abbasi-Moheb, L. et al. Mutations in NSUN2 cause autosomal-recessive intellectual disability. Am. J. Hum. Genet. 90, 847–855 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Khan, M. A. et al. Mutation in NSUN2, which encodes an RNA methyltransferase, causes autosomal-recessive intellectual disability. Am. J. Hum. Genet. 90, 856–863 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martinez, F. J. et al. Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. J. Med. Genet. 49, 380–385 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, Q., Zhang, Q., Qin, Z., Yi, S. & Luo, J. A novel variant in NSUN2 causes intellectual disability in a Chinese family. BMC Med. Genom. 17, 95 (2024).

    Article 
    CAS 

    Google Scholar
     

  • Zhou, J. et al. Unveiling the potential impact of RNA m5C methyltransferases NSUN2 and NSUN6 on cellular aging. Front. Genet. 16, 1477542 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Miao, W. et al. Glucose binds and activates NSUN2 to promote translation and epidermal differentiation. Nucleic Acids Res. 52, 13577–13593 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, Y. et al. 5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer. J. Biol. Chem. 300, 106793 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, X. et al. NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m5C methylation. Breast Cancer Res. 26, 94 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Y. et al. NSUN2 promotes colorectal cancer progression and increases lapatinib sensitivity by enhancing CUL4B/ErbB-STAT3 signalling in a non-m5C manner. Clin. Transl. Med. 15, e70282 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Y. et al. NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation. Cell Death Dis. 12, 842 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, H. et al. YBX1 promotes 5-fluorouracil resistance in gastric cancer via m5C-dependent ATG9A mRNA stabilization through autophagy. Oncogene 44, 2357–2371 (2025).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zou, Z. et al. RNA m5C oxidation by TET2 regulates chromatin state and leukaemogenesis. Nature 634, 986–994 (2024).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Auxilien, S., Guérineau, V., Szweykowska-Kulińska, Z. & Golinelli-Pimpaneau, B. The human tRNA m5C methyltransferase Misu is multisite-specific. RNA Biol. 9, 1331–1338 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Squires, J. E. et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res. 40, 5023–5033 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Z. -L. et al. NSUN2-mediated HCV RNA m5C methylation facilitates viral RNA stability and replication. Genomics Proteom. Bioinform. 23, qzaf008 (2025).

    Article 
    CAS 

    Google Scholar
     

  • Blanco, S. et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J. 33, 2020–2039 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tuorto, F. et al. RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nat. Struct. Mol. Biol. 19, 900–905 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Brzezicha, B. et al. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA \(\left(\begin{array}{c}\mathrm{Leu}\\ \mathrm{CAA}\end{array}\right)\). Nucleic Acids Res. 34, 6034–6043 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Selmi, T. et al. Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6. Nucleic Acids Res. 49, 1006–1022 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • King, M. Y. & Redman, K. L. RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. Biochemistry 41, 11218–11225 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liu, R.-J., Long, T., Li, J., Li, H. & Wang, E.-D. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Nucleic Acids Res. 45, 6684–6697 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sondka, Z. et al. COSMIC: a curated database of somatic variants and clinical data for cancer. Nucleic Acids Res. 52, D1210–D1217 (2024).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Antika, T. R. et al. Sequence-specific targeting of Caenorhabditis elegans C-Ala to the D-loop of tRNAAla. J. Biol. Chem. 299, 105149 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ruiz-Arroyo, V. M. et al. Structures and mechanisms of tRNA methylation by METTL1–WDR4. Nature 613, 383–390 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, J. et al. Structural basis of regulated m7G tRNA modification by METTL1–WDR4. Nature 613, 391–397 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shinoda, S. et al. Mammalian NSUN2 introduces 5-methylcytidines into mitochondrial tRNAs. Nucleic Acids Res. 47, 8734–8745 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van Haute, L. et al. NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res. 47, 8720–8733 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, J. et al. Sequence- and structure-selective mRNA m5C methylation by NSUN6 in animals. Natl Sci. Rev. 8, nwaa273 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gonskikh, Y. et al. Spatial regulation of NSUN2-mediated tRNA m5C installation in cognitive function. Nucleic Acids Res. 53, gkae1169 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, Y. et al. Long noncoding RNA DIAPH2-AS1 promotes neural invasion of gastric cancer via stabilizing NSUN2 to enhance the m5C modification of NTN1. Cell Death Dis. 14, 260 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Studier, F. W. Protein production by auto-induction in high-density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chan, P. P. & Lowe, T. M. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res. 44, D184–D189 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kuhle, B., Hirschi, M., Doerfel, L. K., Lander, G. C. & Schimmel, P. Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA. Nat. Commun. 13, 5100 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70–W74 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Keller, S. et al. High-precision isothermal titration calorimetry with automated peak shape analysis. Anal. Chem. 84, 5066–5073 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao, H., Piszczek, G. & Schuck, P. SEDPHAT – a platform for global ITC analysis and global multi-method analysis of molecular interactions. Methods 76, 137–148 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Brautigam, C. A., Zhao, H., Vargas, C., Keller, S. & Schuck, P. Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions. Nat. Protoc. 11, 882–894 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).

    Article 
    PubMed 

    Google Scholar
     

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr. D Biol. Crystallogr. 65, 1074–1080 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nicholls, R. A. et al. Modelling covalent linkages in CCP4. Acta Crystallogr. D Struct. Biol. 77, 712–726 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Armon, A., Graur, D. & Ben-Tal, N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307, 447–463 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Madeira, F. et al. The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Res. 52, W521–W525 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morin, A. et al. Cutting edge: collaboration gets the most out of software. eLife 2, e01456 (2013).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments