ArticleNucleic acids research2013
Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 124 citations in OpenAlex.
- Transcription and Three-Dimensional Genome Organization: Cause, Consequence, or Coordination?BioEssays : news and reviews in molecular, cellular and developmental biology · 2026Review
- Bacterial 3D genome architecture: organization, regulation, and synthetic biology applications.Genome biology · 2026Review
- PolyP inhibits CobB deacetylase triggering a regulatory coupling to prevent DNA replication initiation.Nucleic acids research · 2026Article
- Article
- Spatio-temporal organization of theEcoSal Plus · 2024Review
- Controlling genome topology with sequences that trigger post-replication gap formation during replisome passage: the E. coli RRS elements.Nucleic acids research · 2024Article
- Spatial Chromosome Organization and Adaptation ofMicroorganisms · 2024Article
- Article
- Controlling Genome Topology with Sequences that Trigger Post-replication Gap Formation During Replisome Passage: ThebioRxiv : the preprint server for biology · 2024Article
- Direct observation of a crescent-shape chromosome in expanded Bacillus subtilis cells.Nature communications · 2024Article
- Combined Study of Gene Expression and Chromosome Three-Dimensional Structure in Escherichia coli During Growth Process.Current microbiology · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.Methods in molecular biology (Clifton, N.J.) · 2024Review
- High-Throughput Mapping of Chromosomal Conformations in E. coli Under Physiological Conditions Using Massively Multiplexed Mu Transposition.Methods in molecular biology (Clifton, N.J.) · 2024Article
- IHF and Fis asInternational journal of molecular sciences · 2023Review
- Generation and Repair of Postreplication Gaps in Escherichia coli.Microbiology and molecular biology reviews : MMBR · 2023Review
- TheHeliyon · 2023Article
- Variable DNA topology is an epigenetic generator of physiological heterogeneity in bacterial populations.Molecular microbiology · 2023Review
- The Spatial Organization of Bacterial Transcriptional Regulatory Networks.Microorganisms · 2022Article
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
19 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, 'histone-like' protein (i.e. Fis, IHF and H-NS) -binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.