ArticleNucleic acids research2024
Analysis of bacterial transcriptome and epitranscriptome using nanopore direct RNA sequencing.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 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
- High-resolution profiling of bacterial transcriptomes by SEnd-seq.The Biochemical journal · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Probiotics in colorectal cancer: mechanisms, biomarkers, and adjunct strategies.Cancer biology & medicine · 2026Review
- Nanopore direct RNA sequencing reveals transmissible gastroenteritis virus epitranscriptomic and transcriptomic landscapes modulated by gene 7.Microbial genomics · 2026Article
- Illuminating the mechanism: gene expression responses to antimicrobial photodynamic therapy.BMC genomics · 2026Review
- Epitranscriptomics as a Candidate Universal Modulator of Dormancy Transitions.Ecology and evolution · 2026Review
- Epitranscriptomic control of stress adaptations in Escherichia coli.Nucleic acids research · 2026Article
- Review
- Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.Advanced genetics (Hoboken, N.J.) · 2025Review
- Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing.Cell reports methods · 2025Article
- ExcludonFinder: mapping transcriptional overlaps between neighboring genes.Nucleic acids research · 2025Article
- Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.Communications biology · 2025Article
- Quantitative and Multiplexing Analysis of MicroRNAs by Direct Full-Length Sequencing in Nanopores.Journal of the American Chemical Society · 2025Article
- Nanopore Environmental Analysis.JACS Au · 2025Review
- Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Bacterial gene expression is a complex process involving extensive regulatory mechanisms. Along with growing interests in this field, Nanopore Direct RNA Sequencing (DRS) provides a promising platform for rapid and comprehensive characterization of bacterial RNA biology. However, the DRS of bacterial RNA is currently deficient in the yield of mRNA-mapping reads and has yet to be exploited for transcriptome-wide RNA modification mapping. Here, we showed that pre-processing of bacterial total RNA (size selection followed by ribosomal RNA depletion and polyadenylation) guaranteed high throughputs of sequencing data and considerably increased the amount of mRNA reads. This way, complex transcriptome architectures were reconstructed for Escherichia coli and Staphylococcus aureus and extended the boundaries of 225 known E. coli operons and 89 defined S. aureus operons. Utilizing unmodified in vitro-transcribed (IVT) RNA libraries as a negative control, several Nanopore-based computational tools globally detected putative modification sites in the E. coli and S. aureus transcriptomes. Combined with Next-Generation Sequencing-based N6-methyladenosine (m6A) detection methods, 75 high-confidence m6A candidates were identified in the E. coli protein-coding transcripts, while none were detected in S. aureus. Altogether, we demonstrated the potential of Nanopore DRS in systematic and convenient transcriptome and epitranscriptome analysis.
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Registered trials
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