ArticleNucleic acids research2022
Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Chromosome topology gates productive RecA homology search.bioRxiv : the preprint server for biology · 2026Article
- The bacterial RNA polymerase-associated CarD protein couples promoter activity to DNA supercoiling.Nature communications · 2026Article
- Torsion is a dynamic regulator of DNA replication stalling and reactivation.Nature communications · 2025Article
- Article
- Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization.PLoS computational biology · 2025Article
- Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.The journal of physical chemistry. B · 2025Article
- 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
- Future Directions of the Prokaryotic Chromosome Field.Molecular microbiology · 2025Article
- Clues to transcription/replication collision-induced DNA damage: it was RNAP, in the chromosome, with the fork.FEBS letters · 2025Review
- Prokaryotic homeostasis - a solution to thrive and survive.Frontiers in molecular biosciences · 2025Review
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- DNA supercoiling enhances DNA condensation by ParB proteins.Nucleic acids research · 2024Article
- Article
- Architectural engineering of Cyborg Bacteria with intracellular hydrogel.Materials today. Bio · 2024Article
- Nucleosomes play a dual role in regulating transcription dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.Nucleic acids research · 2024Article
- Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: ThebioRxiv : the preprint server for biology · 2024Article
- Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.Nature structural & molecular biology · 2024Article
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Authors and funding
6 authors.
Funding
Abstract
DNA supercoiling is a key regulator of all DNA metabolic processes including replication, transcription, and recombination, yet a reliable genomic assay for supercoiling is lacking. Here, we present a robust and flexible method (Psora-seq) to measure whole-genome supercoiling at high resolution. Using this tool in Escherichia coli, we observe a supercoiling landscape that is well correlated to transcription. Supercoiling twin-domains generated by RNA polymerase complexes span 25 kb in each direction - an order of magnitude farther than previous measurements in any organism. Thus, ribosomal and many other highly expressed genes strongly affect the topology of about 40 neighboring genes each, creating highly integrated gene circuits. Genomic patterns of supercoiling revealed by Psora-seq could be aptly predicted from modeling based on gene expression levels alone, indicating that transcription is the major determinant of chromosome supercoiling. Large-scale supercoiling patterns were highly symmetrical between left and right chromosome arms (replichores), indicating that DNA replication also strongly influences supercoiling. Skew in the axis of symmetry from the natural ori-ter axis supports previous indications that the rightward replication fork is delayed several minutes after initiation. Implications of supercoiling on DNA replication and chromosome domain structure are discussed.
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