ArticleNature communications2021
Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Exploring the energy landscape of bacterial chromosome segregation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- SMC ensures efficient chromosome replication and oriC positioning during Streptomyces spore germination.Scientific reports · 2026Article
- Closing the loops: chromatin loop dynamics after DNA damage.Nucleus (Austin, Tex.) · 2025Review
- Minimax entropy: The statistical physics of optimal models.Physical review. E · 2025Article
- Statistical physics of large-scale neural activity with loops.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- 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
- Motorized chain models of the ideal chromosome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation.Nature communications · 2024Article
- [Advances in methods and applications of single-cell Hi-C data analysis].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2023Article
- Polymer folding through active processes recreates features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.Nature communications · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- DeepBacs for multi-task bacterial image analysis using open-source deep learning approaches.Communications biology · 2022Article
- Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales.Nature communications · 2021Article
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 2021Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, we develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus. The predictive power of our model is validated by independent experiments. We find that on large genomic scales, organizational features are predominantly present along the long cell axis: chromosomal loci exhibit striking long-ranged two-point axial correlations, indicating emergent order. This organization is associated with large genomic clusters we term Super Domains (SuDs), whose existence we support with super-resolution microscopy. On smaller genomic scales, our model reveals chromosome extensions that correlate with transcriptional and loop extrusion activity. Finally, we quantify the information contained in chromosome organization that may guide cellular processes. Our approach can be extended to other species, providing a general strategy to resolve variability in single-cell chromosomal organization.
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