ArticleNucleic acids research2022
Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 40 citations in OpenAlex.
- Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.Genome biology · 2026Article
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Ribosome-associated quality control of aberrant protein production during amino acid limitation.bioRxiv : the preprint server for biology · 2026Article
- tRNA modifications: greasing the wheels of translation and beyond.RNA biology · 2025Review
- Gold-Mediated Base Pairs in Nucleic Acids: Selective Coordination to Natural and Thiocarbonyl-Modified Cytosines Dependent upon the Oxidation State of Gold.Chembiochem : a European journal of chemical biology · 2025Article
- High-fat diet driven post-operative colon cancer recurrence is dependent upon genetic susceptibility to deoxycholic acid.Cancer letters · 2025Article
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
- Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control.Nature cell biology · 2025Article
- Mammalian Queuosine tRNA Modification Impacts Translation to Enhance Cell Proliferation and MHC-II Expression.Journal of molecular biology · 2025Article
- Queuosine tRNA Modification: Connecting the Microbiome to the Translatome.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Aminoglycoside tolerance ineLife · 2025Article
- The landscape of Arabidopsis tRNA aminoacylation.The Plant journal : for cell and molecular biology · 2024Article
- Article
- Analysis of RNA and Its Modifications.Annual review of analytical chemistry (Palo Alto, Calif.) · 2024Review
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- A robust method for measuring aminoacylation through tRNA-Seq.bioRxiv : the preprint server for biology · 2024Article
- General Principles and Limitations for Detection of RNA Modifications by Sequencing.Accounts of chemical research · 2024Article
- Research progress of N1-methyladenosine RNA modification in cancer.Cell communication and signaling : CCS · 2024Review
- Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing.Nucleic acids research · 2023Article
- A dual-purpose polymerase engineered for direct sequencing of pseudouridine and queuosine.Nucleic acids research · 2023Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
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