ArticlePLoS computational biology2018
How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 93 citations in OpenAlex.
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.Nucleic acids research · 2026Article
- Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids.Nucleic acids research · 2026Article
- Self-assembly Monte Carlo reveals localized entanglement in giant polymer melts.Nature communications · 2026Article
- A universal polymer signature in Hi-C resolves cohesin loop density and supports monomeric extrusion.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Chromatin unfolding via loops can drive clustered transposon insertion.Biophysical journal · 2025Article
- Monte Carlo study of gold nanoparticle-mediated radiosensitization effects using nanoscale cell model combined with fractal-based DNA model.Medical physics · 2025Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Polymer Physics Models Reveal Structural Folding Features of Single-Molecule Gene Chromatin Conformations.International journal of molecular sciences · 2024Article
- Motorized chain models of the ideal chromosome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Predicting scale-dependent chromatin polymer properties from systematic coarse-graining.Nature communications · 2023Article
- Epigenetic switching with asymmetric bridging interactions.Biophysical journal · 2023Article
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility.Life science alliance · 2023Article
- Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.PLoS computational biology · 2023Article
- Simulation of DNA damage using Geant4-DNA: an overview of the "molecularDNA" example application.Precision radiation oncology · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The 3D organization of chromosomes is crucial for regulating gene expression and cell function. Many experimental and polymer modeling efforts are dedicated to deciphering the mechanistic principles behind chromosome folding. Chromosomes are long and densely packed-topologically constrained-polymers. The main challenges are therefore to develop adequate models and simulation methods to investigate properly the multi spatio-temporal scales of such macromolecules. Here, we proposed a generic strategy to develop efficient coarse-grained models for self-avoiding polymers on a lattice. Accounting accurately for the polymer entanglement length and the volumic density, we show that our simulation scheme not only captures the steady-state structural and dynamical properties of the system but also tracks the same dynamics at different coarse-graining. This strategy allows a strong power-law gain in numerical efficiency and offers a systematic way to define reliable coarse-grained null models for chromosomes and to go beyond the current limitations by studying long chromosomes during an extended time period with good statistics. We use our formalism to investigate in details the time evolution of the 3D organization of chromosome 3R (20 Mbp) in drosophila during one cell cycle (20 hours). We show that a combination of our coarse-graining strategy with a one-parameter block copolymer model integrating epigenomic-driven interactions quantitatively reproduce experimental data at the chromosome-scale and predict that chromatin motion is very dynamic during the cell cycle.
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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.