ArticleMethods in enzymology2015
A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.
Article in Methods in enzymology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 93 citations in OpenAlex.
- Harmonized nucleoside mass spectrometry enables reproducible cross-platform RNA modification quantification.bioRxiv : the preprint server for biology · 2026Article
- Long-term stability of RNA nucleoside standards for accurate LC-MS quantification.Nucleic acids research · 2026Article
- EnterohemorrhagicmSystems · 2026Article
- tRNA modifications: greasing the wheels of translation and beyond.RNA biology · 2025Review
- Toward standardized epitranscriptome analytics: an inter-laboratory comparison of mass spectrometric detection and quantification of modified ribonucleosides in human RNA.Nucleic acids research · 2025Article
- tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa.Nucleic acids research · 2025Article
- tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities.bioRxiv : the preprint server for biology · 2024Article
- Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease.eLife · 2024Article
- Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease.bioRxiv : the preprint server for biology · 2024Article
- tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory.bioRxiv : the preprint server for biology · 2023Article
- Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans.Nucleic acids research · 2023Article
- Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function.EMBO reports · 2023Article
- Small RNA modifications: regulatory molecules and potential applications.Journal of hematology & oncology · 2023Review
- Dysfunctional tRNA reprogramming and codon-biased translation in cancer.Trends in molecular medicine · 2022Review
- RNA modifications: an overview of select web-based tools.RNA (New York, N.Y.) · 2022Review
- The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12.Metallomics : integrated biometal science · 2022Article
- Data-Independent Acquisition for the Detection of Mononucleoside RNA Modifications by Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2022Article
- Review
- Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen.Genes · 2022Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response. The methods described here should find wide use in virtually any analysis involving RNA modifications.
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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.