ArticleNucleic acids research2023
tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- qMAP decodes RNA fragmentation dynamics in development and disease.Molecular systems biology · 2026Article
- RNAViruses · 2026Review
- Remodeling of tRNA modification in Trypanosoma cruzi life forms.PLoS pathogens · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- GlycoRNAdb: a database of glycoRNA sequences, structures, abundance, and glycan information across tissues and cell lines.Nucleic acids research · 2026Article
- ENSURE: the encyclopedia of suppressor tRNA with an AI assistant.Nucleic acids research · 2026Article
- Transfer RNA expression, modification, and derived small RNAs in cancer biology and clinical potential.Frontiers in immunology · 2026Review
- Targeting tRNA methyltransferases: from molecular mechanisms to drug discovery.Science China. Life sciences · 2025Review
- Emerging roles of transfer RNA fragments in the CNS.Brain : a journal of neurology · 2025Review
- Altered tRNA expression profile associated with codon-specific proteomic changes in the suicide brain.Molecular psychiatry · 2025Article
- MapID-based quantitative mapping of chemical modifications and expression of human transfer RNA.Cell chemical biology · 2025Article
- High-Sensitivity Fluorescence-Based Detection of Reverse Transcriptase Read-Through of GC-Rich Short Tandem Repeat RNA.Analytical chemistry · 2025Article
- NAIL-MS reveals tRNA and rRNA hypomodification as a consequence of 5-fluorouracil treatment.Nucleic acids research · 2025Article
- tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators.Biomolecules · 2024Review
- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
- [Advances in mapping analysis of ribonucleic acid modifications through sequencing].Se pu = Chinese journal of chromatography · 2024Review
- Advances in methods for tRNA sequencing and quantification.Trends in genetics : TIG · 2024Review
- Roles of Noncoding RNAs in Regulation of Mitochondrial Electron Transport Chain and Oxidative Phosphorylation.International journal of molecular sciences · 2023Review
- Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods.Briefings in bioinformatics · 2023Article
- The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.Nucleic acids research · 2023Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
tRNA molecules contain dense, abundant modifications that affect tRNA structure, stability, mRNA decoding and tsRNA formation. tRNA modifications and related enzymes are responsive to environmental cues and are associated with a range of physiological and pathological processes. However, there is a lack of resources that can be used to mine and analyse these dynamically changing tRNA modifications. In this study, we established tModBase (https://www.tmodbase.com/) for deciphering the landscape of tRNA modification profiles from epitranscriptome data. We analysed 103 datasets generated with second- and third-generation sequencing technologies and illustrated the misincorporation and termination signals of tRNA modification sites in ten species. We thus systematically demonstrate the modification profiles across different tissues/cell lines and summarize the characteristics of tRNA-associated human diseases. By integrating transcriptome data from 32 cancers, we developed novel tools for analysing the relationships between tRNA modifications and RNA modification enzymes, the expression of 1442 tRNA-derived small RNAs (tsRNAs), and 654 DNA variations. Our database will provide new insights into the features of tRNA modifications and the biological pathways in which they participate.
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