ArticleJournal of the American Chemical Society2014
Quantitative analysis of rRNA modifications using stable isotope labeling and mass spectrometry.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers, 1 of them a synthesis that pooled it.
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Who cites it
69 citing papers in PubMed, 1 synthesis or guideline pooled it, 119 citations in OpenAlex.
- Systematic Review of Plant Ribosome Heterogeneity and Specialization.Frontiers in plant science · 2020Pooled it
- 16S ribosomal RNA modification drives transcript-specific translation efficiency.Cell reports · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming during 50S Biogenesis.Biochemistry · 2026Article
- Functional characterization of dynamic nascent RNA folding ensembles in real time.Science advances · 2026Article
- Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.RNA (New York, N.Y.) · 2026Review
- Capturing ribosomal structures in cellular extracts with cryoPRISM: A purification-free cryoEM approach reveals novel structural states.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming During 50S Biogenesis.bioRxiv : the preprint server for biology · 2026Article
- Nanopore sequencing reveals operon-specific ribosome remodeling accompanying naphthyridone resistance inbioRxiv : the preprint server for biology · 2025Article
- Functions and therapeutic applications of pseudouridylation.Nature reviews. Molecular cell biology · 2025Review
- Quantifying the mRNA epitranscriptome reveals epitranscriptome signatures and roles in cancer.Cellular and molecular life sciences : CMLS · 2025Article
- Post-Transcriptional Modifications of the Large Ribosome Subunit Assembly Intermediates inBiochemistry · 2025Article
- The detection, function, and therapeutic potential of RNA 2'-O-methylation.The innovation life · 2025Article
- Quantitative detection of pseudouridine in RNA by mass spectrometry.Scientific reports · 2024Article
- Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly.Nucleic acids research · 2024Article
- Complete list of canonical post-transcriptional modifications in thebioRxiv : the preprint server for biology · 2024Article
- Advantages and challenges associated with bisulfite-assisted nanopore direct RNA sequencing for modifications.RSC chemical biology · 2023Article
- Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in theACS chemical biology · 2023Article
- Bisulfite and Nanopore Sequencing for Pseudouridine in RNA.Accounts of chemical research · 2023Article
- KsgA facilitates ribosomal small subunit maturation by proofreading a key structural lesion.Nature structural & molecular biology · 2023Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Post-transcriptional RNA modifications that are introduced during the multistep ribosome biogenesis process are essential for protein synthesis. The current lack of a comprehensive method for a fast quantitative analysis of rRNA modifications significantly limits our understanding of how individual modification steps are coordinated during biogenesis inside the cell. Here, an LC-MS approach has been developed and successfully applied for quantitative monitoring of 29 out of 36 modified residues in the 16S and 23S rRNA from Escherichia coli . An isotope labeling strategy is described for efficient identification of ribose and base methylations, and a novel metabolic labeling approach is presented to allow identification of MS-silent pseudouridine modifications. The method was used to measure relative abundances of modified residues in incomplete ribosomal subunits compared to a mature (15)N-labeled rRNA standard, and a number of modifications in both 16S and 23S rRNA were present in substoichiometric amounts in the preribosomal particles. The RNA modification levels correlate well with previously obtained profiles for the ribosomal proteins, suggesting that RNA is modified in a schedule comparable to the association of the ribosomal proteins. Importantly, this study establishes an efficient workflow for a global monitoring of ribosomal modifications that will contribute to a better understanding of mechanisms of RNA modifications and their impact on intracellular processes in the future.
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Registered trials
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.