ArticleProceedings of the National Academy of Sciences of the United States of America2018
Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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73 citing papers in PubMed, 176 citations in OpenAlex.
- Active processes shape and move the genome and nucleoplasm.Current opinion in genetics & development · 2026Review
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- Centromeres and telomeres as rheological probes of the human cell nucleus.Biophysical journal · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- Transcriptional condensates encode a "golden mean" to optimize enhancer-promoter communication across genomic distances.Proceedings of the National Academy of Sciences of the United States of America · 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
- Decoding biomolecular condensate dynamics: an energy landscape approach.PLoS computational biology · 2025Article
- Transcription-dependent mobility of single genes and genome-wide motions in live human cells.Nature communications · 2024Article
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- Motorized chain models of the ideal chromosome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Modelling Heterogeneous Anomalous Dynamics of Radiation-Induced Double-Strand Breaks in DNA during Non-Homologous End-Joining Pathway.Entropy (Basel, Switzerland) · 2024Article
- The scales, mechanisms, and dynamics of the genome architecture.Science advances · 2024Review
- Nucleosome spacing controls chromatin spatial structure and accessibility.Biophysical journal · 2024Article
- OpenNucleome for high resolution nuclear structural and dynamical modeling.bioRxiv : the preprint server for biology · 2024Article
- Non-Markovian Diffusion and Adsorption-Desorption Dynamics: Analytical and Numerical Results.Entropy (Basel, Switzerland) · 2024Article
- Transcription-induced active forces suppress chromatin motion.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- Leveraging polymer modeling to reconstruct chromatin connectivity from live images.Biophysical journal · 2023Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell's life cycle. Tracking the motion of chromosomal loci provides information about the organization of the genome and the physical processes shaping that organization. Optical experiments report that loci move with subdiffusive dynamics and that there is spatially coherent motion of the chromatin. We recently showed that it is possible to predict the 3D architecture of genomes through a physical model for chromosomes that accounts for the biochemical interactions mediated by proteins and regulated by epigenetic markers through a transferable energy landscape. Here, we study the temporal dynamics generated by this quasi-equilibrium energy landscape assuming Langevin dynamics at an effective temperature. Using molecular dynamics simulations of two interacting human chromosomes, we show that the very same interactions that account for genome architecture naturally reproduce the spatial coherence, viscoelasticity, and the subdiffusive behavior of the motion in interphase chromosomes as observed in numerous experiments. The agreement between theory and experiments suggests that even if active processes are involved, an effective quasi-equilibrium landscape model can largely mimic their dynamical effects.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.