Schimmel, P. The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat. Rev. Mol. Cell Biol. 19, 45–58 (2018).
Novoa, E. M. & Ribas de Pouplana, L. Speeding with control: codon usage, tRNAs, and ribosomes. Trends Genet. 28, 574–581 (2012).
Phizicky, E. M. & Hopper, A. K. tRNA biology charges to the front. Genes Dev. 24, 1832–1860 (2010).
Pan, T. Modifications and functional genomics of human transfer RNA. Cell Res. 28, 395–404 (2018).
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).
Zheng, G. et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol. Cell 49, 18–29 (2013).
Klungland, A. & Dahl, J. A. Dynamic RNA modifications in disease. Curr. Opin. Genet. Dev. 26, 47–52 (2014).
Liu, F. et al. ALKBH1-mediated tRNA demethylation regulates translation. Cell 167, 1897 (2016).
Motorin, Y. & Helm, M. tRNA stabilization by modified nucleotides. Biochemistry 49, 4934–4944 (2010).
Chernyakov, I., Whipple, J. M. & Kotelawala, L. Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′–3′ exonucleases Rat1 and Xrn1. Genes Dev. 22, 1369–1380 (2008).
Alexandrov, A. et al. Rapid tRNA decay can result from lack of nonessential modifications. Mol. Cell 21, 87–96 (2006).
Wang, X. et al. Queuosine modification protects cognate tRNAs against ribonuclease cleavage. RNA 24, 1305–1313 (2018).
Pereira, M. et al. m5U54 tRNA hypomodification by lack of TRMT2A drives the generation of tRNA-derived small RNAs. Int. J. Mol. Sci. 22, 2941 (2021).
Jonkhout, N. et al. The RNA modification landscape in human disease. RNA 23, 1754–1769 (2017).
Torres, A. G., Batlle, E. & Ribas de Pouplana, L. Role of tRNA modifications in human diseases. Trends Mol. Med. 20, 306–314 (2014).
Schaffrath, R. & Leidel, S. A. Wobble uridine modifications—a reason to live, a reason to die?! RNA Biol. 14, 1209–1222 (2017).
de Crécy-Lagard, V. et al. Matching tRNA modifications in humans to their known and predicted enzymes. Nucleic Acids Res. 47, 2143–2159 (2019).
de Crécy-Lagard, V. & Jaroch, M. Functions of bacterial tRNA modifications: from ubiquity to diversity. Trends Microbiol. 29, 41–53 (2021).
Motorin, Y. & Grosjean, H. tRNA Modification. (Wiley, 2001).
Boccaletto, P. et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 46, D303–D307 (2018).
Gustilo, E. M., Vendeix, F. A. & Agris, P. F. tRNA’s modifications bring order to gene expression. Curr. Opin. Microbiol. 11, 134–140 (2008).
Boccaletto, P. & Bagiński, B. MODOMICS: an operational guide to the use of the RNA modification pathways database. Methods Mol. Biol. 2284, 481–505 (2021).
Sajek, M. P., Woźniak, T., Sprinzl, M., Jaruzelska, J. & Barciszewski, J. T-psi-C: user friendly database of tRNA sequences and structures. Nucleic Acids Res. 48, D256–D260 (2020).
Salowe, S. P., Wiltsie, J., Hawkins, J. C. & Sonatore, L. M. The catalytic flexibility of tRNAIle-lysidine synthetase can generate alternative tRNA substrates for isoleucyl-tRNA synthetase. J. Biol. Chem. 284, 9656–9662 (2009).
Ranjan, N. & Rodnina, M. V. tRNA wobble modifications and protein homeostasis. Translation (Austin) 4, e1143076 (2016).
Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014).
Behm-Ansmant, I., Branlant, C. & Motorin, Y. The Saccharomyces cerevisiae Pus2 protein encoded by YGL063w ORF is a mitochondrial tRNA:Ψ27/28-synthase. RNA 13, 1641–1647 (2007).
Giegé, R., Sissler, M. & Florentz, C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26, 5017–5035 (1998).
Sylvers, L. A., Rogers, K. C., Shimizu, M., Ohtsuka, E. & Söll, D. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 32, 3836–3841 (1993).
Suzuki T. The ‘polysemous’ codon—a codon with multiple amino acid assignment caused by dual specificity of tRNA identity. EMBO J. 16, 1122–1134 (1997).
Niimi, T. et al. Recognition of the anticodon loop of tRNAIle1 by isoleucyl-tRNA synthetase from Escherichia coli. Nucleosides and Nucleotides 13, 1231–1237 (1994).
Agris, P. F. et al. Celebrating wobble decoding: half a century and still much is new. RNA Biol. 15, 537–553 (2018).
Machnicka, M. A., Olchowik, A., Grosjean, H. & Bujnicki, J. M. Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol. 11, 1619–1629 (2014).
El Yacoubi, B., Bailly, M. & de Crécy-Lagard, V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu. Rev. Genet. 46, 69–95 (2012).
Rafels-Ybern, À. et al. The expansion of inosine at the wobble position of tRNAs, and its role in the evolution of proteomes. Mol. Biol. Evol. 36, 650–662 (2019).
Novoa, E. M., Pavon-Eternod, M., Pan, T., Ribas & de Pouplana, L. A role for tRNA modifications in genome structure and codon usage. Cell 149, 202–213 (2012).
Takai, K. & Yokoyama, S. Roles of 5‐substituents of tRNA wobble uridines in the recognition of purine‐ending codons. Nucleic Acids Res. 31, 6383–6391 (2003).
Jackman, J. E. & Alfonzo, J. D. Transfer RNA modifications: nature’s combinatorial chemistry playground. Wiley Interdiscip. Rev. RNA 4, 35–48 (2013).
Soma, A. et al. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12, 689–698 (2003).
Krüger, M. K., Pedersen, S., Hagervall, T. G. & Sørensen, M. A. The modification of the wobble base of tRNAGlu modulates the translation rate of glutamic acid codons in vivo. J. Mol. Biol. 284, 621–631 (1998).
Näsvall, S. J., Chen, P. & Björk, G. R. The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. RNA 13, 2151–2164 (2007).
Näsvall, S. J., Chen, P. & Björk, G. R. The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAProcmo5UGG promotes reading of all four proline codons in vivo. RNA 10, 1662–1673 (2004).
Weixlbaumer, A. et al. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat. Struct. Mol. Biol. 14, 498–502 (2007).
Nilsson, E. M. & Alexander, R. W. Bacterial wobble modifications of NNA-decoding tRNAs. IUBMB Life 71, 1158–1166 (2019).
Wei, J. et al. Differential m6A, m6Am, and m1A demethylation mediated by FTO in the cell nucleus and cytoplasm. Mol. Cell 71, 973–985 (2018).
Ueda, Y. et al. AlkB homolog 3-mediated tRNA demethylation promotes protein synthesis in cancer cells. Sci Rep. 7, 42271 (2017).
Chen, Z. et al. Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs. Nucleic Acids Res. 47, 2533–2545 (2019).
Chan, C. T. Y. et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet. 6, e1001247 (2010).
Chan, C. T. Y. et al. Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat. Commun. 3, 937 (2012).
Deng, W. et al. Trm9-catalyzed tRNA modifications regulate global protein expression by codon-biased translation. PLoS Genet. 11, e1005706 (2015).
Patil, A. et al. Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle 11, 3656–3665 (2012).
Goodarzi, H. et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416–1427 (2016).
Murphy, T. L., Cooper, I. A., Wray, G. W., Ironside, P. N. & Matthews, J. Transfer RNA and transfer RNA methylase activity in spleens of patients with Hodgkin’s disease and histiocytic lymphoma. J. Natl Cancer Inst. 56, 215–219 (1976).
Bullinger, D. et al. Metabolic signature of breast cancer cell line MCF-7: profiling of modified nucleosides via LC-IT MS coupling. BMC Biochem. 8, 25 (2007).
Frickenschmidt, A. et al. Metabonomics in cancer diagnosis: mass spectrometry-based profiling of urinary nucleosides from breast cancer patients. Biomarkers 13, 435–449 (2008).
Rapino, F. et al. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605–609 (2018).
Torrent, M., Chalancon, G., de Groot, N. S., Wuster, A. & Madan Babu, M. Cells alter their tRNA abundance to selectively regulate protein synthesis during stress conditions. Sci Signal. 11, eaat6409 (2018).
Pang, Y. L. J., Abo, R., Levine, S. S. & Dedon, P. C. Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number. Nucleic Acids Res. 42, e170 (2014).
Pavon-Eternod, M. et al. tRNA over-expression in breast cancer and functional consequences. Nucleic Acids Res. 37, 7268–7280 (2009).
Gingold, H. et al. A dual program for translation regulation in cellular proliferation and differentiation. Cell 158, 1281–1292 (2014).
Abbott, J. A., Francklyn, C. S. & Robey-Bond, S. M. Transfer RNA and human disease. Front. Genet. 5, 158 (2014).
Grewal, S. S. Why should cancer biologists care about tRNAs? tRNA synthesis, mRNA translation and the control of growth. Biochim. Biophys. Acta 1849, 898–907 (2015).
Hernandez-Alias, X., Benisty, H., Schaefer, M. H. & Serrano, L. Translational efficiency across healthy and tumor tissues is proliferation-related. Mol. Syst. Biol. 16, e9275 (2020).
Thüring, K., Schmid, K., Keller, P. & Helm, M. Analysis of RNA modifications by liquid chromatography–tandem mass spectrometry. Methods. 107, 48–56 (2016).
Nakayama, H. et al. Method for direct mass-spectrometry-based identification of monomethylated RNA nucleoside positional isomers and its application to the analysis of leishmania rRNA. Anal. Chem. 91, 15634–15643 (2019).
Sarin, L. P. et al. Nano LC–MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels. RNA 24, 1403–1417 (2018).
Su, D. et al. Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nat. Protoc. 9, 828–841 (2014).
Kellner, S. et al. Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Nucleic Acids Res. 42, e142 (2014).
Espadas, G. et al. High-performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry. J. Chromatogr. A 1665, 462803 (2022).
Nikcevic, I., Wyrzykiewicz, T. K. & Limbach, P. A. Detecting low-level synthesis impurities in modified phosphorothioate oligonucleotides using liquid chromatography–high resolution mass spectrometry. Int. J. Mass Spectrom. 304, 98–104 (2011).
Heiss, M., Borland, K., Yoluç, Y. & Kellner, S. Quantification of modified nucleosides in the context of NAIL-MS. Methods Mol. Biol. 2298, 279–306 (2021).
Helm, M., Schmidt-Dengler, M. C., Weber, M. & Motorin, Y. General principles for the detection of modified nucleotides in RNA by specific reagents. Adv. Biol. (Weinh). 5, e2100866 (2021).
Dittmar, K. A., Goodenbour, J. M. & Pan, T. Tissue-specific differences in human transfer RNA expression. PLoS Genet. 2, e221 (2006).
Cozen, A. E. et al. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat. Methods 12, 879–884 (2015).
Zheng, G. et al. Efficient and quantitative high-throughput tRNA sequencing. Nat. Methods 12, 835–837 (2015).
Shigematsu, M. et al. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res. 45, e70 (2017).
Behrens, A., Rodschinka, G. & Nedialkova, D. D. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol. Cell 81, 1802–1815 (2021).
Pinkard, O., McFarland, S., Sweet, T. & Coller, J. Quantitative tRNA-sequencing uncovers metazoan tissue-specific tRNA regulation. Nat. Commun. 11, 4104 (2020).
Hu, J. F. et al. Quantitative mapping of the cellular small RNA landscape with AQRNA-seq. Nat. Biotechnol. 39, 978–988 (2021).
Gogakos, T. et al. Characterizing expression and processing of precursor and mature human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Rep. 20, 1463–1475 (2017).
Erber, L. et al. LOTTE-seq (long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3′-CCA end for high-throughput sequencing. RNA Biol. 17, 23–32 (2020).
Arimbasseri, A. G. et al. RNA polymerase III output is functionally linked to tRNA dimethyl-G26 modification. PLoS Genet. 11, e1005671 (2015).
Alexander Ebhardt, H. et al. Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications. Nucleic Acids Res. 37, 2461–2470 (2009).
Werner, S. et al. Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes. Nucleic Acids Res. 48, 3734–3746 (2020).
Ryvkin, P. et al. HAMR: high-throughput annotation of modified ribonucleotides. RNA 19, 1684–1692 (2013).
Motorin, Y., Muller, S., Behm‐Ansmant, I. & Branlant, C. Identification of modified residues in RNAs by reverse transcription‐based methods. Methods Enzymol. 425, 21–453 (2007).
Wang, Y. et al. A high-throughput screening method for evolving a demethylase enzyme with improved and new functionalities. Nucleic Acids Res. 49, e30 (2021).
Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
Henley, R. Y. et al. Electrophoretic deformation of individual transfer RNA molecules reveals their identity. Nano Lett. 16, 138–144 (2016).
Wang, Y. et al. Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A. Nat. Commun. 12, 3368 (2021).
Smith, A. M., Abu-Shumays, R., Akeson, M. & Bernick, D. L. Capture, unfolding, and detection of individual tRNA molecules using a nanopore device. Front. Bioeng. Biotechnol. 3, 91 (2015).
Thomas, N. K. et al. Direct nanopore sequencing of individual full length tRNA strands. ACS Nano. 15, 16642–16653 (2021).
Workman, R. E., Tang, A. D., Tang, P. S., Jain, M. & Tyson, J. R. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat. Methods 16, 1297–1305 (2019).
Liu, H. et al. Accurate detection of m6A RNA modifications in native RNA sequences. Nat. Commun. 10, 4079 (2019).
Gleeson, J. et al. Accurate expression quantification from nanopore direct RNA sequencing with NanoCount. Nucleic Acids Res. 50, e19 (2022).
Saville, L. et al. NERD-seq: a novel approach of nanopore direct RNA sequencing that expands representation of non-coding RNAs. Preprint at bioRxiv (2021).
Li, R. et al. Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development. Genome Res. 30, 287–298 (2020).
Begik, O. et al. Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nat. Biotechnol. 39, 1278–1291 (2021).
Mulroney, L. et al. Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing. RNA 28, 162–176 (2021).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Bullard, D. R. & Bowater, R. P. Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4. Biochem. J. 398, 135–144 (2006).
Jenjaroenpun, P. et al. Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Res. 49, e7 (2021).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Abuín, J. M., Pichel, J. C., Pena, T. F. & Amigo, J. BigBWA: approaching the Burrows–Wheeler aligner to Big Data technologies. Bioinformatics 31, 4003–4005 (2015).
Stephenson, W. et al. Direct detection of RNA modifications and structure using single molecule nanopore sequencing. Cell Genomics 2, 100097 (2022).
Leger, A. et al. RNA modifications detection by comparative nanopore direct RNA sequencing. Nat. Commun. 12, 7198 (2021).
Parker, M. T. et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife 9, e49658 (2020).
Price, A. M. et al. Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing. Nat. Commun. 11, 6016 (2020).
Pratanwanich, P. N. et al. Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nat. Biotechnol. 39, 1394–1402 (2021).
Becker, H. F., Motorin, Y., Planta, R. J. & Grosjean, H. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of Ψ55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25, 4493–4499 (1997).
Huang, S. et al. Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling. Genome Biol. 22, 330 (2021).
Tavakoli, S. et al. Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing. Nat. Commun. 14, 334 (2023).
Motorin, Y. et al. The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. RNA 4, 856–869 (1998).
Massenet, S. et al. Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase Pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA. Mol. Cell. Biol. 19, 2142–2154 (1999).
Behm-Ansmant, I. et al. A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs. RNA 12, 1583–1593 (2006).
Behm-Ansmant, I. et al. The Saccharomyces cerevisiae U2 snRNA:pseudouridine-synthase Pus7p is a novel multisite–multisubstrate RNA:Ψ-synthase also acting on tRNAs. RNA 9, 1371–1382 (2003).
Kimura, S., Dedon, P. C. & Waldor, M. K. Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications. Nat. Chem. Biol. 16, 964–972 (2020).
Huang, Z.-X. et al. Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2. Nucleic Acids Res. 49, 13045–13061 (2021).
Müller, M. et al. Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Nucleic Acids Res. 43, 10952–10962 (2015).
Barraud, P. et al. Time-resolved NMR monitoring of tRNA maturation. Nat. Commun. 10, 3373 (2019).
Marchand, V. et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res. 48, e110 (2020).
Alings, F., Sarin, L. P., Fufezan, C., Drexler, H. C. A. & Leidel, S. A. An evolutionary approach uncovers a diverse response of tRNA 2-thiolation to elevated temperatures in yeast. RNA 21, 202–212 (2015).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Thorvaldsdóttir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14, 178–192 (2013).
Robinson, J. T., Thorvaldsdóttir, H., Wenger, A. M., Zehir, A. & Mesirov, J. P. Variant review with the Integrative Genomics Viewer. Cancer Res. 77, e31–e34 (2017).
Czech, A., Wende, S., Mörl, M., Pan, T. & Ignatova, Z. Reversible and rapid transfer-RNA deactivation as a mechanism of translational repression in stress. PLoS Genet. 9, e1003767 (2013).
Mahlab, S., Tuller, T. & Linial, M. Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA 18, 640–652 (2012).
Tuller, T. et al. An evolutionarily conserved mechanism for controlling the efficiency of protein translation. Cell 141, 344–354 (2010).
Shah, P. & Gilchrist, M. A. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc. Natl Acad. Sci. USA 108, 10231–10236 (2011).
Moriyama, E. N. & Powell, J. R. Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45, 514–523 (1997).
Randerath, K., Agrawal, H. P. & Randerath, E. tRNA alterations in cancer. Recent Results Cancer Res. 84, 103–120 (1983).
Krishnan, P. et al. Genome-wide profiling of transfer RNAs and their role as novel prognostic markers for breast cancer. Sci Rep. 6, 32843 (2016).
Gustafsson, H. T. et al. Deep sequencing of yeast and mouse tRNAs and tRNA fragments using OTTR. Preprint at bioRxiv (2022).
Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol. 22, 375–392 (2021).
Agris, P. F., Narendran, A., Sarachan, K., Väre, V. Y. P. & Eruysal, E. The importance of being modified: the role of RNA modifications in translational fidelity. Enzymes 41, 1–50 (2017).
Han, L., Marcus, E., D’Silva, S. & Phizicky, E. M. S. cerevisiae Trm140 has two recognition modes for 3-methylcytidine modification of the anticodon loop of tRNA substrates. RNA 23, 406–419 (2017).
Guy, M. P. & Phizicky, E. M. Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification. RNA Biol. 11, 1608–1618 (2014).
Grosjean, H., Droogmans, L., Roovers, M. & Keith, G. Detection of enzymatic activity of transfer RNA modification enzymes using radiolabeled tRNA substrates. Methods Enzymol. 425, 55–101 (2007).
Carey, M. F., Peterson, C. L. & Smale, S. T. The primer extension assay. Cold Spring Harb. Protoc. 2013, 164–173(2013).
Suzuki, T., Ikeuchi, Y., Noma, A., Suzuki, T. & Sakaguchi, Y. Mass spectrometric identification and characterization of RNA-modifying enzymes. Methods Enzymol. 425, 211–229 (2007).
Heiss, M., Hagelskamp, F., Marchand, V., Motorin, Y. & Kellner, S. Cell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo. Nat. Commun. 12, 389 (2021).
Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).
Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).
Lyons, S. M., Fay, M. M. & Ivanov, P. The role of RNA modifications in the regulation of tRNA cleavage. FEBS Lett. 592, 2828–2844 (2018).
Santos, M., Fidalgo, A., Varanda, A. S., Oliveira, C. & Santos, M. A. S. tRNA deregulation and its consequences in cancer. Trends Mol. Med. 25, 853–865 (2019).
Hoffmann, A. et al. Accurate mapping of tRNA reads. Bioinformatics 34, 2339 (2018).
Saint-Léger, A. et al. Saturation of recognition elements blocks evolution of new tRNA identities. Sci. Adv. 2, e1501860 (2016).
Sampson, J. R. & Uhlenbeck, O. C. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl Acad. Sci. USA 85, 1033–1037 (1988).
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).
Hermand, D. Anticodon wobble uridine modification by elongator at the crossroad of cell signaling, differentiation, and diseases. Epigenomes 4, 7 (2020).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Blighe, K., Rana, S. & Lewis, M. EnhancedVolcano: publication-ready volcano plots with enhanced colouring and labeling. (2022).
Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. European Nucleotide Archive. https://www.ebi.ac.uk/ena/browser/view/PRJEB55684
Lucas, M. C. et al. Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing. GitHub.