ArticleNucleic acids research2025
Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Short-chain fatty acids activate the glutamate-dependent acid resistance system via the tRNA-modifying Mnm pathway inJournal of bacteriology · 2026Article
- Toward a comprehensive modification landscape of yeast mitochondrial tRNAs using Nanopore direct RNA sequencing and dihydrouridine sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing.RNA (New York, N.Y.) · 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
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
- The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae.PLoS genetics · 2025Article
- 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
- RNA modification is the mark and strategy for host-microbe interactions.Cellular and molecular life sciences : CMLS · 2025Review
- ExcludonFinder: mapping transcriptional overlaps between neighboring genes.Nucleic acids research · 2025Article
- Prior exposure strongly influences mechanisms underpinning survival of heat shock inFrontiers in microbiology · 2025Article
- Depletion of mMicrobiology spectrum · 2024Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Modifications of RNA, known as the epitranscriptome, affect gene expression, translation, and splicing in eukaryotes, with implications for developmental processes, cancer, and viral infections. In prokaryotes, regulation at the level of the epitranscriptome is still poorly understood. Here, we used nanopore direct RNA sequencing of Escherichia coli to study RNA modifications and their changes under heat stress. With a single sequencing reaction, we detected most known modification types in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). RNA sequencing was complemented by a multifaceted approach that included mass spectrometry, deletion mutants, single-nucleotide polymerase chain reaction, and in vitro methylation. Known 5-methylcytidine (m5C) and N6-methyladenosine (m6A) sites in the rRNA were confirmed, but these types of modifications could not be localized in the mRNA. In response to heat stress, levels of m5C, m6A, and N6,N6-dimethyladenosine increased in the 16S rRNA. Sequencing and mass spectrometry data demonstrated a decrease in tRNA modification abundance in the anticodon loop at 45°C. In general, mRNA modifications at 37°C were enriched in the coding regions of genes associated with general metabolism and RNA processing, which shifted to genes involved in cell wall synthesis and membrane transport under heat stress. This study provides new insights into the complexity of post-transcriptional regulation in bacteria.
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