ArticlePLoS computational biology2016
Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Integrative modeling of the genome structure and dynamics in fission yeast.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.Nature genetics · 2026Article
- Cohesin prevents local mixing of condensed euchromatic domains in living human cells.bioRxiv : the preprint server for biology · 2026Article
- Electrostatic properties of disordered regions control transcription factor search and pioneer activity.Nature communications · 2026Article
- The Influence of Cohesin on the Short-Scale Dynamics of Intact and Damaged Chromatin in Different Phases of the Cell Cycle.International journal of molecular sciences · 2025Article
- Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction.bioRxiv : the preprint server for biology · 2025Article
- Article
- The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.Science advances · 2025Article
- Probing chromatin condensation dynamics in live cells using interferometric scattering correlation spectroscopy.Communications biology · 2024Article
- Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway.Entropy (Basel, Switzerland) · 2024Article
- Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.Nature communications · 2024Article
- Individual transcription factors modulate both the micromovement of chromatin and its long-range structure.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Nucleosome spacing controls chromatin spatial structure and accessibility.Biophysical journal · 2024Article
- Article
- Chromatin Organization after High-LET Irradiation Revealed by Super-Resolution STED Microscopy.International journal of molecular sciences · 2024Article
- Diffusion controls local versus dispersed inheritance of histones during replication and shapes epigenomic architecture.PLoS computational biology · 2023Article
- Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome.Science (New York, N.Y.) · 2023Article
- DNA double-strand break end synapsis by DNA loop extrusion.Nature communications · 2023Article
- Condensed but liquid-like domain organization of active chromatin regions in living human cells.Science advances · 2023Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100-500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells.
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