ArticleCell reports methods2025
Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing.
Article in Cell reports methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 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
- QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.NAR genomics and bioinformatics · 2026Article
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 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
- Epitranscriptomic control of stress adaptations in Escherichia coli.Nucleic acids research · 2026Article
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Improved long-transcript representation in Oxford Nanopore direct RNA sequencing with UltraMarathonRT.bioRxiv : the preprint server for biology · 2025Article
- SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
7 authors.
Funding
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Abstract
RNA modifications play crucial roles in prokaryotic cellular processes. In this study, we found that the recent advances in direct RNA sequencing have improved yield, accuracy, and signal-to-noise ratio in bacterial samples. By evaluating four current RNA modification calling models in Escherichia coli transcriptome using native and in vitro transcribed (IVT) RNA, we found the models identified most known rRNA modifications but produced false positives. To address this, we developed nanoSundial, a comparative method leveraging raw current signals from native and IVT samples to de novo identify multiple RNA modifications. We optimized nanoSundial on well-studied E. coli rRNA modification sites and validated its effectiveness with tRNAs. It identified 190 stably modified mRNA regions, which enriched near the ends of highly expressed operons. This study highlighted the strengths and limitations of current nanopore-based modification detection methods on bacterial RNA, introduced a robust comparative tool, and elucidated previously uncharacterized mRNA modification landscapes.
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Registered trials
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