Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing Article Swipe
Christopher D. Katanski
,
Christopher Watkins
,
Wen Zhang
,
Matthew Reyer
,
Samuel Miller
,
Tao Pan
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac517
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkac517
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.
Related Topics
Concepts
Transfer RNA
Biology
Wobble base pair
Biochemistry
RNA
Stable isotope labeling by amino acids in cell culture
Genetics
Proteomics
Computational biology
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkac517
- https://academic.oup.com/nar/article-pdf/50/17/e99/45989992/gkac517.pdf
- OA Status
- gold
- Cited By
- 35
- References
- 47
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4283065699
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4283065699Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gkac517Digital Object Identifier
- Title
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Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencingWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2022Year of publication
- Publication date
-
2022-06-17Full publication date if available
- Authors
-
Christopher D. Katanski, Christopher Watkins, Wen Zhang, Matthew Reyer, Samuel Miller, Tao PanList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkac517Publisher landing page
- PDF URL
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https://academic.oup.com/nar/article-pdf/50/17/e99/45989992/gkac517.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://academic.oup.com/nar/article-pdf/50/17/e99/45989992/gkac517.pdfDirect OA link when available
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Transfer RNA, Biology, Wobble base pair, Biochemistry, RNA, Stable isotope labeling by amino acids in cell culture, Genetics, Proteomics, Computational biology, GeneTop concepts (fields/topics) attached by OpenAlex
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35Total citation count in OpenAlex
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2025: 11, 2024: 15, 2023: 8, 2022: 1Per-year citation counts (last 5 years)
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47Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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