ArticleNucleic acids research2021
A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 34 citations in OpenAlex.
- Exploring the energy landscape of bacterial chromosome segregation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- Protein translation can fluidize bacterial cytoplasm.PNAS nexus · 2024Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics.Nucleic acids research · 2024Article
- MksB is a novel mycobacterial condensin that orchestrates spatiotemporal positioning of replication machinery.Scientific reports · 2024Article
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- Chromosome structure modeling tools and their evaluation in bacteria.Briefings in bioinformatics · 2024Review
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Interpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model.Biophysical journal · 2023Article
- Mycobacterial IHF is a highly dynamic nucleoid-associated protein that assists HupB in organizing chromatin.Frontiers in microbiology · 2023Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- Relationship between the Chromosome Structural Dynamics and Gene Expression-A Chicken and Egg Dilemma?Microorganisms · 2022Review
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3 authors at 1 institution in 1 country.
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Abstract
The chromosome of Escherichia coli is riddled with multi-faceted complexity. The emergence of chromosome conformation capture techniques are providing newer ways to explore chromosome organization. Here we combine a beads-on-a-spring polymer-based framework with recently reported Hi-C data for E. coli chromosome, in rich growth condition, to develop a comprehensive model of its chromosome at 5 kb resolution. The investigation focuses on a range of diverse chromosome architectures of E. coli at various replication states corresponding to a collection of cells, individually present in different stages of cell cycle. The Hi-C data-integrated model captures the self-organization of E. coli chromosome into multiple macrodomains within a ring-like architecture. The model demonstrates that the position of oriC is dependent on architecture and replication state of chromosomes. The distance profiles extracted from the model reconcile fluorescence microscopy and DNA-recombination assay experiments. Investigations into writhe of the chromosome model reveal that it adopts helix-like conformation with no net chirality, earlier hypothesized in experiments. A genome-wide radius of gyration map captures multiple chromosomal interaction domains and identifies the precise locations of rrn operons in the chromosome. We show that a model devoid of Hi-C encoded information would fail to recapitulate most genomic features unique to E. coli.
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