ArticleNucleic acids research2023
Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing.
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 14 papers.
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Who cites it
14 citing papers in PubMed, 22 citations in OpenAlex.
- QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.NAR genomics and bioinformatics · 2026Article
- Toward a comprehensive modification landscape of yeast mitochondrial tRNAs using Nanopore direct RNA sequencing and dihydrouridine sequencing.Nucleic acids research · 2026Article
- Evaluation of Dorado v5.2.0 de novo basecalling models for the detection of tRNA modifications using RNA004 chemistry.BMC genomics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing.Nucleic acids research · 2026Article
- tRNA modifications: greasing the wheels of translation and beyond.RNA biology · 2025Review
- WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.Nucleic acids research · 2025Article
- MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers.Nucleic acids research · 2025Article
- Quantitative and Multiplexing Analysis of MicroRNAs by Direct Full-Length Sequencing in Nanopores.Journal of the American Chemical Society · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors.Nucleic acids research · 2024Article
- Comparative analysis of 43 distinct RNA modifications by nanopore tRNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Queuosine (Q) is a complex tRNA modification found in bacteria and eukaryotes at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that 7-deazaguanine-derivatives such as queuosine are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.
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