Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling
Open accessPublished version of a preprint
Abstract
Abstract Tandem mass spectrometry (MS/MS) is an accurate tool to assess modified ribonucleosides and their dynamics in mammalian cells. Yet, MS/MS quantification of lowly abundant modifications in non-ribosomal RNAs is unreliable, and the dynamic features of various modifications poorly understood. We developed a 13 C labeling approach, 13 C-dynamods, to quantify the turnover of base modifications in newly transcribed RNA. This turnover-based approach helped to resolve mRNA from ncRNA modifications in purified RNA or free ribonucleosides, and showed the distinct kinetics of N 6-methyladenosine (m 6 2 A) versus 7-methylguanosine (m 7 G) in polyA+-purified RNA. We uncovered that N 6, N 6-dimethyladenosine (m 6 2 A) exhibits a distinct turnover in small RNAs and free ribonucleosides when compared to the known m 6 A-modified large rRNAs. Finally, combined measurements of turnover and abundance informed on the transcriptional versus posttranscriptional sensitivity of modified ncRNAs and mRNAs, respectively, to stress conditions. Thus, 13 C-dynamods enables studies of origin of modified RNAs at steady-state and their dynamics under non-stationary conditions.
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References 85 · Cited by 10
- Authors
- Gameiro, P. A., Encheva, V., Dos Santos, M. S., MacRae, J. I., & Ule, J.
- Affiliations
- The Francis Crick Institute (GB)
- Corresponding author
- Gameiro, Paulo A.
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 2021-11
- Volume
- 297
- Issue
- 5
- Pages
- 101294
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC8567201
- OpenAlex
- W3203998404
- Cited by
- 10
- References
- 85
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 1 · 2023: 1 · 2022: 2
- FWCI
- 0.31
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- The Francis Crick Institute (cc-by)
- Funders
- H2020 Marie Skłodowska-Curie Actions (701730)
- University College London Institute of Neurology (103760/Z/14/Z)
- Seventh Framework Programme (617837)
- Medical Research Council
- Cancer Research UK (FC001002)
- European Research Council
- Wellcome Trust
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- 13C labeling, N6-methyladenosine, 7-methylguanosine, mRNA modification, small RNA, post-transcriptional modification, transcriptional regulation, stress response
- MeSH terms
- Adenosine, Carbon Isotopes, Guanosine, Isotope Labeling, RNA, RNA Processing, Post-Transcriptional, Tandem Mass Spectrometry
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