ArticleNature communications2024
Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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The trial behind it
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Who cites it
29 citing papers in PubMed.
- Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.MicrobiologyOpen · 2026Article
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Article
- The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation.Nature communications · 2026Article
- Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.Nature communications · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming during 50S Biogenesis.Biochemistry · 2026Article
- Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.Nature communications · 2026Article
- Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.RNA (New York, N.Y.) · 2026Review
- Review
- Direct RNA Sequencing Reveals Stress-Dependent and Pathway-Specific rRNA Modification Reprogramming During 50S Biogenesis.bioRxiv : the preprint server for biology · 2026Article
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Nanopore sequencing reveals operon-specific ribosome remodeling accompanying naphthyridone resistance inbioRxiv : the preprint server for biology · 2025Article
- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- Article
- Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne ParasitebioRxiv : the preprint server for biology · 2025Article
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
- MoDorado: enhanced detection of tRNA modifications in nanopore sequencing by off-label use of modification callers.Nucleic acids research · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The biological relevance and dynamics of mRNA modifications have been extensively studied; however, whether rRNA modifications are dynamically regulated, and under which conditions, remains unclear. Here, we systematically characterize bacterial rRNA modifications upon exposure to diverse antibiotics using native RNA nanopore sequencing. To identify significant rRNA modification changes, we develop NanoConsensus, a novel pipeline that is robust across RNA modification types, stoichiometries and coverage, with very low false positive rates, outperforming all individual algorithms tested. We then apply NanoConsensus to characterize the rRNA modification landscape upon antibiotic exposure, finding that rRNA modification profiles are altered in the vicinity of A and P-sites of the ribosome, in an antibiotic-specific manner, possibly contributing to antibiotic resistance. Our work demonstrates that rRNA modification profiles can be rapidly altered in response to environmental exposures, and provides a robust workflow to study rRNA modification dynamics in any species, in a scalable and reproducible manner.
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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.