ArticleNucleic acids research2018
High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- The chromatin landscape of the histone-possessingGenome research · 2025Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Article
- 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
- Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.Current research in structural biology · 2024Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- The landscape of the histone-organized chromatin of Bdellovibrionota bacteria.bioRxiv : the preprint server for biology · 2023Article
- Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.Nature structural & molecular biology · 2023Article
- Interpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model.Biophysical journal · 2023Article
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.Cold Spring Harbor perspectives in biology · 2022Review
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.Nucleic acids research · 2021Article
- Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales.Nature communications · 2021Article
- Connection Between Chromosomal Location and Function of CtrA Phosphorelay Genes in Alphaproteobacteria.Frontiers in microbiology · 2021Article
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-resolution three-dimensional models of Caulobacter crescentus nucleoid structures were generated via a multi-scale modeling protocol. Models were built as a plectonemically supercoiled circular DNA and by incorporating chromosome conformation capture based data to generate an ensemble of base pair resolution models consistent with the experimental data. Significant structural variability was found with different degrees of bending and twisting but with overall similar topologies and shapes that are consistent with C. crescentus cell dimensions. The models allowed a direct mapping of the genomic sequence onto the three-dimensional nucleoid structures. Distinct spatial distributions were found for several genomic elements such as AT-rich sequence elements where nucleoid associated proteins (NAPs) are likely to bind, promoter sites, and some genes with common cellular functions. These findings shed light on the correlation between the spatial organization of the genome and biological functions.
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