ArticleGenome research2020
Predicting transfer RNA gene activity from sequence and genome context.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Multilevel genomic constraints shape nuclear tRNA gene organization in plants.The Plant journal : for cell and molecular biology · 2026Article
- The regulation, function and disease relevance of cytoplasmic tRNAs.Nature reviews. Molecular cell biology · 2026Review
- Comparative analysis of tRNAs across mouse strains reveals gene-specific conservation, divergence, and copy number variation.BMC genomics · 2026Article
- Regulation of tRNA expression during the social cycle of the amoeba Dictyostelium discoideum.BMC molecular and cell biology · 2026Article
- Allelic Variation at tRNA Genes in Three Nematode Species Indicates Mutation Load Despite Strong Purifying Selection.Genome biology and evolution · 2026Article
- How Does Transcription-Associated Mutagenesis Shape tRNA Microevolution?Genome biology and evolution · 2026Article
- Mistranslation from an endogenous tRNA variant in human pan-genome cell lines.Nucleic acids research · 2026Article
- An Improved Description of the Small RNA Landscape of the Human Fungal Pathogen Aspergillus fumigatus.Molecular microbiology · 2026Article
- An engineered UGA suppressor tRNA gene for disease-agnostic AAV delivery.Nature biotechnology · 2026Article
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- A tRNA gene potential to activate interferon signaling involves selective termination and is suppressible by La protein/SSB.Nucleic acids research · 2025Article
- Natural human tRNARNA (New York, N.Y.) · 2025Article
- Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer.Non-coding RNA · 2025Article
- Glutamine missense suppressor transfer RNAs inhibit polyglutamine aggregation.Molecular therapy. Nucleic acids · 2025Article
- Genome Sequencing, Assembly, and Characterization ofJournal of fungi (Basel, Switzerland) · 2025Article
- Mechanisms and Delivery of tRNA Therapeutics.Chemical reviews · 2024Review
- Genome-Wide Computational Prediction and Analysis of Noncoding RNAs inMicroorganisms · 2024Article
- Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in Pseudomonas fluorescens SBW25.Nucleic acids research · 2024Article
- AbioRxiv : the preprint server for biology · 2024Article
- tRNA therapeutics for genetic diseases.Nature reviews. Drug discovery · 2024Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined with difficulty in measuring transcript abundance and high sequence identity across transcripts, has severely limited our collective understanding of tRNA gene expression regulation and evolution. We establish sequence-based correlates to tRNA gene expression and develop a tRNA gene classification method that does not require, but benefits from, comparative genomic information and achieves accuracy comparable to molecular assays. We observe that guanine + cytosine (G + C) content and CpG density surrounding tRNA loci is exceptionally well correlated with tRNA gene activity, supporting a prominent regulatory role of the local genomic context in combination with internal sequence features. We use our tRNA gene activity predictions in conjunction with a comprehensive tRNA gene ortholog set spanning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other clades, as well as exploration of functional diversification of members of large gene families.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.