ArticleNucleic acids research2020
Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Different relative scalings between transient forces and thermal fluctuations tune regimes of dynamic clustering.Physical review. E · 2025Article
- TopoLoop: A new tool for chromatin loop detection in live cells via single-particle tracking.The Journal of chemical physics · 2024Article
- Transient crosslinking controls the condensate formation pathway within chromatin networks.Physical review. E · 2024Article
- Article
- Polymer models reveal how chromatin modification can modulate force at the kinetochore.Molecular biology of the cell · 2022Article
- DNA sliding and loop formation byBiochemistry and biophysics reports · 2022Article
- DNA damage reduces heterogeneity and coherence of chromatin motions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations.Nucleic acids research · 2022Article
- Diffusion and distal linkages govern interchromosomal dynamics during meiotic prophase.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Review
- Shaping centromeres to resist mitotic spindle forces.Journal of cell science · 2022Article
- It's all in the numbers: Cohesin stoichiometry.Frontiers in molecular biosciences · 2022Review
- DNA-loop-extruding SMC complexes can traverse one another in vivo.Nature structural & molecular biology · 2021Article
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Authors and funding
8 authors.
Funding
Abstract
The revolution in understanding higher order chromosome dynamics and organization derives from treating the chromosome as a chain polymer and adapting appropriate polymer-based physical principles. Using basic principles, such as entropic fluctuations and timescales of relaxation of Rouse polymer chains, one can recapitulate the dominant features of chromatin motion observed in vivo. An emerging challenge is to relate the mechanical properties of chromatin to more nuanced organizational principles such as ubiquitous DNA loops. Toward this goal, we introduce a real-time numerical simulation model of a long chain polymer in the presence of histones and condensin, encoding physical principles of chromosome dynamics with coupled histone and condensin sources of transient loop generation. An exact experimental correlate of the model was obtained through analysis of a model-matching fluorescently labeled circular chromosome in live yeast cells. We show that experimentally observed chromosome compaction and variance in compaction are reproduced only with tandem interactions between histone and condensin, not from either individually. The hierarchical loop structures that emerge upon incorporation of histone and condensin activities significantly impact the dynamic and structural properties of chromatin. Moreover, simulations reveal that tandem condensin-histone activity is responsible for higher order chromosomal structures, including recently observed Z-loops.
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