Topological domain structure of the Escherichia coli chromosome.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Genes & Development

• Publication date

  2004-07-15

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1101/GAD.1207504PMID 15256503PMCID PMC478196
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• The Bacterial Condensin MukBEF Compacts DNA into a Repetitive, Stable Structure

  2004cited by this paper
• Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome.

  2004cited by this paper
• A topological view of the replicon

  2004cited by this paper
• Temporal regulation of topoisomerase IV activity in E. coli.

  2003cited by this paper
• Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management.

  2003cited by this paper
• Bacterial Chromosome Dynamics

  2003cited by this paper
• FtsK Is a DNA motor protein that activates chromosome dimer resolution by switching the catalytic state of the XerC and XerD recombinases.

  2002cited by this paper
• Structural Maintenance of Chromosomes Protein of Bacillussubtilis Affects Supercoiling In Vivo

  2002cited by this paper
• Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

  2002cited by this paper
• Transcription induces a supercoil domain barrier in bacteriophage Mu.

  2001cited by this paper
• DNA topoisomerases: structure, function, and mechanism.

  2001cited by this paper
• Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome.

  2000cited by this paper
• An efficient recombination system for chromosome engineering in Escherichia coli.

  2000cited by this paper
• Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling.

  2000cited by this paper
• Suppression of chromosome segregation defects of Escherichia coli muk mutants by mutations in topoisomerase I.

  2000cited by this paper
• Phage Mu transposition immunity reflects supercoil domain structure of the chromosome

  1999cited by this paper
• The complete genome sequence of Escherichia coli K-12.

  1997influential reference
• Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli.

  1997cited by this paper
• Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium

  1996influential reference
• Unlinking of DNA by Topoisomerases During DNA Replication

  1995cited by this paper
• Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I

  1993cited by this paper
• Monte Carlo analysis of the conformation of DNA catenanes.

  1993cited by this paper
• The new gene mukB codes for a 177 kd protein with coiled‐coil domains involved in chromosome partitioning of E. coli.

  1991cited by this paper
• Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers.

  1990cited by this paper
• DNA supercoiling and prokaryotic transcription.

  1989cited by this paper
• Chromosome partitioning in Escherichia coli: novel mutants producing anucleate cells

  1989cited by this paper
• Repair of the Escherichia coli chromosome after in vivo scission by the EcoRI endonuclease.

  1989cited by this paper
• Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology

  1987cited by this paper
• Use of site-specific recombination as a probe of DNA structure and metabolism in vivo.

  1987cited by this paper
• Supercoiling of the DNA template during transcription.

  1987cited by this paper
• Complete enzymatic replication of plasmids containing the origin of the Escherichia coli chromosome.

  1986cited by this paper
• Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling.

  1981cited by this paper
• Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells.

  1980cited by this paper
• Nalidixic acid resistance: a second genetic character involved in DNA gyrase activity.

  1977cited by this paper
• Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase.

  1976cited by this paper
• Electron microscopy of membrane-associated folded chromosomes of Escherichia coli

  1976cited by this paper
• Electron microscopy of membrane-free folded chromosomes from Escherichia coli

  1976influential reference
• Electron microscopic studies on the folded chromosome of Escherichia coli.

  1974cited by this paper
• On the structure of the folded chromosome of Escherichia coli.

  1972cited by this paper
• The structure of chromatin.

  1971cited by this paper
• Structure of chromatin.

  1971cited by this paper

• De novo design of synthetic microbial genomes

  2026cites this paper
• New Insights into the Geometry and Topology of DNA Replication Intermediates

  2025cites this paper
• Towards a Better Control of Engineered Circuit Transcription in Bacterial Genomes

  2025cites this paper
• Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

  2025cites this paper
• Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks

  2025influential citation
• TOP2B modulates DNA supercoiling and chromatin contacts during transcriptional induction

  2025cites this paper
• Repair of Single-Stranded Breaks in Hyperthermophilic DNA.

  2025cites this paper
• Dynamics of bacterial operons during genome-wide stresses is influenced by premature terminations and internal promoters

  2025cites this paper
• Gene loci fluctuations reveal bacterial chromosome dynamical organization

  2025cites this paper
• TORCphysics: A physical model of DNA-topology-controlled gene expression

  2025cites this paper
• The role of macromolecular crowders in the formation and compaction of the Escherichia coli nucleoid

  2025cites this paper
• Differential effect of supercoiling on bacterial transcription in topological domains

  2025cites this paper
• Learning the dynamic organization of a replicating bacterial chromosome from time-course Hi-C data

  2025cites this paper
• Effects of cooling on E. coli’s DNA organization, structure, and gene expression

  2025cites this paper
• The Structure of the Biocrystalline Nucleoid and Its Role in the Regulation of Dissociative Phenotypic Heterogeneity of Microbial Populations

  2024cites this paper
• Reentrant DNA shells tune polyphosphate condensate size

  2024cites this paper
• Transcribing RNA polymerases : Dynamics of Twin Supercoiled Domains.

  2024cites this paper
• Nucleosomes play a dual role in regulating transcription dynamics

  2024cites this paper
• Transcription Attenuation in Synthetic Promoters in Nonoverlapping Tandem Formation

  2024cites this paper
• Spatio-temporal organization of the E. coli chromosome from base to cellular length scales

  2024cites this paper
• Memory effects of transcription regulator−DNA interactions in bacteria

  2024influential citation
• Spatial Chromosome Organization and Adaptation of Escherichia coli under Heat Stress

  2024cites this paper
• A mean-field theory for predicting single polymer collapse induced by neutral crowders

  2024cites this paper
• Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements

  2024cites this paper
• Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma

  2024cites this paper
• DNA packaging by molecular motors: from bacteriophage to human chromosomes

  2024cites this paper
• Topological regulation of the estrogen transcriptional response by ZATT-mediated inhibition of TOP2B activity

  2024cites this paper
• Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome.

  2024cites this paper
• Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization

  2024cites this paper
• Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes

  2024cites this paper
• DNA supercoiling enhances DNA condensation by ParB proteins

  2024cites this paper
• Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.

  2024cites this paper
• Topology in soft and biological matter

  2024cites this paper
• The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein

  2023cites this paper
• DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

  2023cites this paper
• Reentrant DNA shells tune polyphosphate condensate size

  2023cites this paper
• Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments

  2023cites this paper
• spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes

  2023cites this paper
• Development of a Data-driven Integrative Model of Bacterial Chromosome

  2023cites this paper
• DNA Segregation in Enterobacteria

  2023cites this paper
• Dissection of 3D chromosome organization in Streptomyces coelicolor A3(2) leads to biosynthetic gene cluster overexpression

  2023cites this paper
• DNA supercoiling in bacteria : state of play and challenges from a modeling viewpoint

  2023cites this paper
• Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: The E. coli RRS Elements

  2023influential citation
• Topology-dependent DNA binding

  2023cites this paper
• Transcription attenuation in synthetic promoters in tandem formation

  2023cites this paper
• Emergence of Supercoiling-Mediated Regulatory Networks through Bacterial Chromosome Organization

  2023influential citation
• Regulation of chromatin transcription dynamics by DNA supercoiling

  2023cites this paper
• Quantitative spatial analysis of bacterial transcriptome and chromosome structural data with GRATIOSA: application to twin-supercoiled domain distribution

  2023cites this paper
• Coarse-Grained Modeling Reveals the Impact of Supercoiling and Loop Length in DNA Looping Kinetics.

  2022cites this paper
• Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF

  2022cites this paper
• Psoralen mapping reveals a bacterial genome supercoiling landscape dominated by transcription

  2022cites this paper
• Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma?

  2022cites this paper
• Machine learning classification of trajectories from molecular dynamics simulations of chromosome segregation

  2022cites this paper
• Extended sister-chromosome catenation leads to massive reorganization of the E. coli genome

  2022cites this paper
• Mechanisms of sex determination and X-chromosome dosage compensation

  2022cites this paper
• Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering.

  2022cites this paper
• Partition complex structure can arise from sliding and bridging of ParB dimers

  2022cites this paper
• Catastrophic chromosome fragmentation probes the nucleoid structure and dynamics in Escherichia coli

  2022cites this paper
• Enhanced binding of an HU homologue under increased DNA supercoiling preserves chromosome organisation and sustains Streptomyces hyphal growth

  2022cites this paper
• Models of topological barriers and molecular motors of bacterial DNA

  2022cites this paper
• Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring

  2022cites this paper
• Transcriptional units form the elementary constraining building blocks of the bacterial chromosome

  2022influential citation
• Emergence of Supercoiling-Mediated Regulatory Networks through Bacterial Chromosome Rearrangements

  2022cites this paper
• Equilibrium fluctuations of DNA plectonemes.

  2022cites this paper
• Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?

  2022cites this paper
• Torsional behaviour of supercoiled DNA regulates recognition of architectural protein Fis on minicircle DNA

  2022cites this paper
• The X chromosome in C. elegans sex determination and dosage compensation.

  2022cites this paper
• ATAC-seq reveals megabase-scale domains of a bacterial nucleoid

  2021cites this paper
• Understanding transcription across scales: From base pairs to chromosomes.

  2021cites this paper
• A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation

  2021cites this paper
• Special Issue: Role of Bacterial Chromatin in Environmental Sensing, Adaptation and Evolution

  2021cites this paper
• DNA fluctuations reveal the size and dynamics of topological domains

  2021cites this paper
• Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria

  2021cites this paper
• What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii

  2021cites this paper
• 1 0 O ct 2 02 1 DNA-polymer architecture orchestrates the segregation and spatio-temporal organization of E . coli chromosomes during replication in slow growth conditions

  2021cites this paper
• The interplay of supercoiling and thymine dimers in DNA

  2021cites this paper
• DNA-polymer architecture orchestrates the segregation and spatio-temporal organization of E. coli chromosomes during replication in slow growth

  2021cites this paper
• Bacterial transcription during growth arrest

  2021cites this paper
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom

  2021cites this paper
• Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli.

  2021cites this paper
• Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans

  2021cites this paper
• Mechanisms for Chromosome Segregation in Bacteria

  2021cites this paper
• Transcription-mediated supercoiling regulates genome folding and loop formation.

  2021cites this paper
• Two-phase dynamics of DNA supercoiling based on DNA polymer physics

  2021cites this paper
• Genomic contacts reveal the control of sister chromosome decatenation in E. coli

  2021cites this paper
• DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

  2021cites this paper
• The regulation of DNA supercoiling across evolution

  2021cites this paper
• Diversity and Functions of Type II Topoisomerases

  2021cites this paper
• Local Rigidification and Possible Coacervation of the E. coli DNA by Cationic Nylon-3 Polymers.

  2021cites this paper
• A Well-Mixed E. coli Genome: Widespread Contacts Revealed by Tracking Mu Transposition.

  2020cites this paper
• Emerging roles for R-loop structures in the management of topological stress

  2020cites this paper
• Dissecting the in vivo dynamics of transcription locking due to positive supercoiling buildup.

  2020influential citation
• Dynamique des génomes du genre Streptomyces

  2020cites this paper
• References

  2020cites this paper
• Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes – Observing Strong Local Effects of Nucleoid Structure on Gene Regulation

  2020cites this paper
• The highly conserved chromosomal periodicity of transcriptomes and the correlation of its amplitude with the growth rate in Escherichia coli

  2020cites this paper
• Complex Diffusion in Bacteria.

  2020cites this paper
• Correlated chromosomal periodicities according to the growth rate and gene expression

  2020cites this paper
• Requirements for DNA-Bridging Proteins to Act as Topological Barriers of the Bacterial Genome

  2020cites this paper
• Computational Elucidation of self-organization of E. coli chromosome underlying HI-C data

  2020cites this paper