ArticleNucleic acids research2014
Spatial confinement is a major determinant of the folding landscape of human chromosomes.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Effects of chromatin-lamina attachment on extra-long-range chromatin interactions.Biophysical journal · 2026Article
- Extrinsic heterogeneity: Collectivity in isotropic conformational fluctuations of chromosomes.Biophysical journal · 2025Article
- pC-SAC: A method for high-resolution 3D genome reconstruction from low-resolution Hi-C data.Nucleic acids research · 2025Article
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.Bioinformatics (Oxford, England) · 2025Article
- Article
- Modeling properties of chromosome territories using polymer filaments in diverse confinement geometries.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Article
- The scales, mechanisms, and dynamics of the genome architecture.Science advances · 2024Review
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
- Uncovering the Quantitative Relationships Among Chromosome Fluctuations, Epigenetics, and Gene Expressions of Transdifferentiation on Waddington Landscape.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Modeling and simulation of cell nuclear architecture reorganization process.Journal of computational physics · 2022Article
- Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C.Frontiers in molecular biosciences · 2022Review
- Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.Current opinion in structural biology · 2021Review
- Extracting multi-way chromatin contacts from Hi-C data.PLoS computational biology · 2021Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- High-resolution single-cell 3D-models of chromatin ensembles during Drosophila embryogenesis.Nature communications · 2021Article
- Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.Biophysical journal · 2020Article
- A Lamin-Associated Chromatin Model for Chromosome Organization.Biophysical journal · 2020Article
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4 authors.
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Abstract
The global architecture of the cell nucleus and the spatial organization of chromatin play important roles in gene expression and nuclear function. Single-cell imaging and chromosome conformation capture-based techniques provide a wealth of information on the spatial organization of chromosomes. However, a mechanistic model that can account for all observed scaling behaviors governing long-range chromatin interactions is missing. Here we describe a model called constrained self-avoiding chromatin (C-SAC) for studying spatial structures of chromosomes, as the available space is a key determinant of chromosome folding. We studied large ensembles of model chromatin chains with appropriate fiber diameter, persistence length and excluded volume under spatial confinement. We show that the equilibrium ensemble of randomly folded chromosomes in the confined nuclear volume gives rise to the experimentally observed higher-order architecture of human chromosomes, including average scaling properties of mean-square spatial distance, end-to-end distance, contact probability and their chromosome-to-chromosome variabilities. Our results indicate that the overall structure of a human chromosome is dictated by the spatial confinement of the nuclear space, which may undergo significant tissue- and developmental stage-specific size changes.
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