Friday, June 27, 2025
No menu items!
HomeNatureRNA codon expansion via programmable pseudouridine editing and decoding

RNA codon expansion via programmable pseudouridine editing and decoding

  • Liu, C. C. & Schultz, P. G. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413–444 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lemke, E. A. The exploding genetic code. ChemBioChem 15, 1691–1694 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chin, J. W. Expanding and reprogramming the genetic code. Nature 550, 53–60 (2017).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Song, J. et al. CRISPR-free, programmable RNA pseudouridylation to suppress premature termination codons. Mol. Cell 83, 139–155.e139 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Neumann, H., Wang, K., Davis, L., Garcia-Alai, M. & Chin, J. W. Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome. Nature 464, 441–444 (2010).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Orelle, C. et al. Protein synthesis by ribosomes with tethered subunits. Nature 524, 119–124 (2015).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Fried, S. D., Schmied, W. H., Uttamapinant, C. & Chin, J. W. Ribosome subunit stapling for orthogonal translation in E. coli. Angew. Chem. Int. Ed. 54, 12791–12794 (2015).

    Article 
    CAS 

    Google Scholar
     

  • Isaacs, F. J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348–353 (2011).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ostrov, N. et al. Design, synthesis, and testing toward a 57-codon genome. Science 353, 819–822 (2016).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, K. et al. Defining synonymous codon compression schemes by genome recoding. Nature 539, 59–64 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nyerges, A. et al. Synthetic genomes unveil the effects of synonymous recoding. Preprint at bioRxiv https://doi.org/10.1101/2024.06.16.599206 (2024).

  • Grome, M. W. et al. Engineering a genomically recoded organism with one stop codon. Nature 639, 512–521 (2025).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Malyshev, D. A. et al. A semi-synthetic organism with an expanded genetic alphabet. Nature 509, 385–388 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fischer, E. C. et al. New codons for efficient production of unnatural proteins in a semisynthetic organism. Nat. Chem. Biol. 16, 570–576 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thompson, D. B. et al. The future of multiplexed eukaryotic genome engineering. ACS Chem. Biol. 13, 313–325 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Reinkemeier, C. D., Girona, G. E. & Lemke, E. A. Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science 363, eaaw2644 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Reinkemeier, C. D. & Lemke, E. A. Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation. Cell 184, 4886–4903.e4821 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, M. et al. Tracking endogenous proteins based on RNA editing-mediated genetic code expansion. Nat. Chem. Biol. 20, 721–731 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ranjan, N. & Leidel, S. A. The epitranscriptome in translation regulation: mRNA and tRNA modifications as the two sides of the same coin? FEBS Lett. 593, 1483–1493 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Boccaletto, P. et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 50, D231–D235 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shi, H., Chai, P., Jia, R. & Fan, X. Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation. Mol. Cancer 19, 78 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karijolich, J. & Yu, Y.-T. Converting nonsense codons into sense codons by targeted pseudouridylation. Nature 474, 395–398 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, N. et al. Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons. Nat. Biotechnol. 48, 114–123 (2025).

    Article 

    Google Scholar
     

  • Charette, M. & Gray, M. W. Pseudouridine in RNA: what, where, how, and why. IUBMB Life 49, 341–351 (2000).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, M. et al. Quantitative profiling of pseudouridylation landscape in the human transcriptome. Nat. Chem. Biol. 19, 1185–1195 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hofhuis, J. et al. The functional readthrough extension of malate dehydrogenase reveals a modification of the genetic code. Open Biol. 6, 160246 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dunkelmann, D. L., Willis, J. C. W., Beattie, A. T. & Chin, J. W. Engineered triply orthogonal pyrrolysyl–tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids. Nat. Chem. 12, 535–544 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Seelam Prabhakar, P., Takyi, N. A. & Wetmore, S. D. Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations. RNA 27, 202–220 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nozawa, K. et al. Pyrrolysyl-tRNA synthetase–tRNAPyl structure reveals the molecular basis of orthogonality. Nature 457, 1163–1167 (2009).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Suzuki, T. et al. Crystal structures reveal an elusive functional domain of pyrrolysyl-tRNA synthetase. Nat. Chem. Biol. 13, 1261–1266 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Landrum, M. J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wang, J. et al. AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice. Nature 604, 343–348 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hollingsworth, T. J. & Gross, A. K. The severe autosomal dominant retinitis pigmentosa rhodopsin mutant Ter349Glu mislocalizes and induces rapid rod cell death. J. Biol. Chem. 288, 29047–29055 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vidal, R. et al. A stop-codon mutation in the BRI gene associated with familial British dementia. Nature 399, 776–781 (1999).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Shibata, N. et al. Degradation of stop codon read-through mutant proteins via the ubiquitin–proteasome system causes hereditary disorders. J. Biol. Chem. 290, 28428–28437 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Namy, O., Duchateau-Nguyen, G. & Rousset, J.-P. Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae. Mol. Microbiol. 43, 641–652 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Capone, J. P., Sharp, P. A. & RajBhandary, U. L. Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene. EMBO J. 4, 213–221 (1985).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wangen, J. R. & Green, R. Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. eLife 9, e52611 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schueren, F. et al. Peroxisomal lactate dehydrogenase is generated by translational readthrough in mammals. eLife 3, e03640 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shi, N. et al. Restoration of dystrophin expression in mice by suppressing a nonsense mutation through the incorporation of unnatural amino acids. Nat. Biomed. Eng. 6, 195–206 (2022).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yeatman, T. J. A renaissance for SRC. Nat. Rev. Cancer 4, 470–480 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, G. et al. Bioorthogonal chemical activation of kinases in living systems. ACS Cent. Sci. 2, 325–331 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sletten, E. M. & Bertozzi, C. R. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew. Chem. Int. Ed. 48, 6974–6998 (2009).

    Article 
    CAS 

    Google Scholar
     

  • Li, J. & Chen, P. R. Development and application of bond cleavage reactions in bioorthogonal chemistry. Nat. Chem. Biol. 12, 129–137 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, J., Jia, S. & Chen, P. R. Diels–Alder reaction-triggered bioorthogonal protein decaging in living cells. Nat. Chem. Biol. 10, 1003–1005 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bian, Y. et al. Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder. Nat. Chem. Biol. 12, 959–966 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jang, H. S., Jana, S., Blizzard, R. J., Meeuwsen, J. C. & Mehl, R. A. Access to faster eukaryotic cell labeling with encoded tetrazine amino acids. J. Am. Chem. Soc. 142, 7245–7249 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bryson, D. I. et al. Continuous directed evolution of aminoacyl-tRNA synthetases. Nat. Chem. Biol. 13, 1253–1260 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ding, W. et al. Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells. Science 384, 1134–1142 (2024).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Liang, S.-H. & Clarke, M. F. Regulation of p53 localization. Eur. J. Biochem. 268, 2779–2783 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • O’Keefe, K., Li, H. & Zhang, Y. Nucleocytoplasmic shuttling of p53 is essential for MDM2-mediated cytoplasmic degradation but not ubiquitination. Mol. Cell. Biol. 23, 6396–6405 (2003).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gautier, A. et al. Genetically encoded photocontrol of protein localization in mammalian cells. J. Am. Chem. Soc. 132, 4086–4088 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guangcan, S. et al. How to use open-pFind in deep proteomics data analysis?—A protocol for rigorous identification and quantitation of peptides and proteins from mass spectrometry data. Biophys. Rep. 7, 207–226 (2021).

    Article 

    Google Scholar
     

  • Wilson, C., Chen, P. J., Miao, Z. & Liu, D. R. Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat. Biotechnol. 38, 1431–1440 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, X.-M., Zhou, J., Mao, Y., Ji, Q. & Qian, S.-B. Programmable RNA N6-methyladenosine editing by CRISPR–Cas9 conjugates. Nat. Chem. Biol. 15, 865–871 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. Biol. 6, 26 (2011).

    Article 
    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
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).

    Article 

    Google Scholar
     

  • Kim, D., Paggi, J. M., Park, C., Bennett, C. & Salzberg, S. L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907–915 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smith, T., Heger, A. & Sudbery, I. UMI-tools: modeling sequencing errors in unique molecular identifiers to improve quantification accuracy. Genome Res. 27, 491–499 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7, 1534–1550 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lauria, F. et al. riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data. PLoS Comp. Biol. 14, e1006169 (2018).

    Article 

    Google Scholar
     

  • Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation 2, 100141 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dong, M. et al. Sensitive, robust, and cost-effective approach for tyrosine phosphoproteome analysis. Anal. Chem. 89, 9307–9314 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367–1372 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Demichev, V., Messner, C. B., Vernardis, S. I., Lilley, K. S. & Ralser, M. DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat. Methods 17, 41–44 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shaw, J. J. & Green, R. Two distinct components of release factor function uncovered by nucleophile partitioning analysis. Mol. Cell 28, 458–467 (2007).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gagnon, K. T. & Maxwell, E. S. Electrophoretic mobility shift assay for characterizing RNA–protein interaction. Methods Mol. Biol. 703, 275–291 (2011).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Case, D. A. et al. AmberTools. J. Chem. Inf. Model. 63, 6183–6191 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eastman, P. et al. OpenMM 8: molecular dynamics simulation with machine learning potentials. J. Phys. Chem. B 128, 109–116 (2024).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McGibbon, RobertT. et al. MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys. J. 109, 1528–1532 (2015).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins Struct. Funct. Bioinformatics 78, 1950–1958 (2010).

    Article 
    CAS 

    Google Scholar
     

  • Zgarbová, M. et al. Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput. 7, 2886–2902 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).

    Article 
    ADS 
    CAS 

    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
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments