ArticleNucleic acids research2019
Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome.
Article in Nucleic acids research, 2019. 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 41 papers.
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Who cites it
41 citing papers in PubMed.
- Bacterial type II topoisomerases cleave DNA in a species-specific manner.Nucleic acids research · 2026Article
- DNA deformability in sequence-dependent capture of E. coli gyrase.Nature communications · 2026Article
- Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.Nucleic acids research · 2025Article
- Regulation of DNA Topology in Archaea: State of the Art and Perspectives.Molecular microbiology · 2025Review
- Menadione as Antibiotic Adjuvant AgainstAntibiotics (Basel, Switzerland) · 2025Article
- Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.Nucleic acids research · 2025Article
- Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.bioRxiv : the preprint server for biology · 2024Article
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Structural basis of chiral wrap and T-segment capture byProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Temporospatial control of topoisomerases by essential cellular processes.Current opinion in microbiology · 2024Review
- Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq.Nucleic acids research · 2024Article
- Highly sensitive mapping ofbioRxiv : the preprint server for biology · 2024Article
- Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin.Nature communications · 2024Article
- Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma.Journal of bacteriology · 2024Review
- Assessing in vivo the impact of gene context on transcription through DNA supercoiling.Nucleic acids research · 2023Article
- Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli.Microbiology spectrum · 2023Article
- Basis for the discrimination of supercoil handedness during DNA cleavage by human and bacterial type II topoisomerases.Nucleic acids research · 2023Article
- Characterization of a pathway of genomic instability induced by R-loops and its regulation by topoisomerases in E. coli.PLoS genetics · 2023Article
- Genome-wide mapping of fluoroquinolone-stabilized DNA gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence.Nucleic acids research · 2023Article
- Single-nucleotide resolution detection of Topo IV cleavage activity in theFrontiers in microbiology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.
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