ArticleNucleic acids research2024
Differential roles of positive and negative supercoiling in organizing the E. coli genome.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- A chromatin-structure-guided framework for predictive and interpretable regulatory genomics.Briefings in bioinformatics · 2026Article
- Apical localization of RNA polymerases modulates transcription dynamics and supercoiling domains revealed by cryo-ET.Molecular cell · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Apical Localization of RNA Polymerases Modulate Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET.bioRxiv : the preprint server for biology · 2026Article
- Characterizing the Impact of Nucleoid-Associated Proteins on HU-DNA Interactions by Live-Cell Single-Molecule Tracking.bioRxiv : the preprint server for biology · 2026Article
- The biophysical properties of the bacterial nucleoid are dynamic, heterogeneous, and responsive to perturbations of cellular processes.bioRxiv : the preprint server for biology · 2026Article
- The Roles of Topoisomerases in Transcriptional Regulation.International journal of molecular sciences · 2026Review
- Population structure, antimicrobial resistance, and virulence factors of diabetic foot-associatedMicrobiology spectrum · 2026Article
- A Chromatin-Structure-Guided Framework for Predictive and Interpretable Regulatory Genomics.bioRxiv : the preprint server for biology · 2025Article
- Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution.Nucleic acids research · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- Genome-wide mapping of spontaneous DNA replication error-hotspots using mismatch repair proteins in rapidly proliferating Escherichia coli.Nucleic acids research · 2025Article
- Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures.NAR genomics and bioinformatics · 2024Article
- DNA topology: A central dynamic coordinator in chromatin regulation.Current opinion in structural biology · 2024Review
- Accelerating Diverse Cell-Based Therapies Through Scalable Design.Annual review of chemical and biomolecular engineering · 2024Review
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Spatial Chromosome Organization and Adaptation ofMicroorganisms · 2024Article
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Authors and funding
4 authors.
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Abstract
This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). We find that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled. Surprisingly, positive supercoiling corresponds to higher spatial contact than negative supercoiling. Additionally, positive, but not negative, supercoiling could be identified from Hi-C data with high accuracy. We further find that the majority of positive and negative supercoils coincide with highly active transcription units, with a minor group likely associated with replication and other genomic processes. Our results show that both positive and negative supercoiling enhance spatial contact, with positive supercoiling playing a larger role in bringing genomic loci closer in space. Based on our results, we propose new physical models of how the E. coli chromosome is organized by positive and negative supercoils.
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