ArticlePLoS computational biology2017
Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Compaction of chromatin domains regulates target search times of proteins.PLoS computational biology · 2026Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Predicting gene expression changes from chromatin structure modification.NPJ systems biology and applications · 2025Article
- Insulation between adjacent TADs is controlled by the width of their boundaries through distinct mechanisms.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The scales, mechanisms, and dynamics of the genome architecture.Science advances · 2024Review
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- 4D nucleome equation predicts gene expression controlled by long-range enhancer-promoter interaction.PLoS computational biology · 2023Article
- Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries.Nature communications · 2023Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- A guide for single-particle chromatin tracking in live cell nuclei.Cell biology international · 2022Review
- Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin.Genome research · 2022Article
- Hi-D: nanoscale mapping of nuclear dynamics in single living cells.Genome biology · 2020Article
- Conformational heterogeneity in human interphase chromosome organization reconciles the FISH and Hi-C paradox.Nature communications · 2019Article
- Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers.Nature communications · 2019Article
- Interphase human chromosome exhibits out of equilibrium glassy dynamics.Nature communications · 2018Article
- Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration.Scientific reports · 2017Article
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2 authors.
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Abstract
Chromatin organization can be probed by Chromosomal Capture (5C) data, from which the encounter probability (EP) between genomic sites is presented in a large matrix. This matrix is averaged over a large cell population, revealing diagonal blocks called Topological Associating Domains (TADs) that represent a sub-chromatin organization. To study the relation between chromatin organization and gene regulation, we introduce a computational procedure to construct a bead-spring polymer model based on the EP matrix. The model permits exploring transient properties constrained by the statistics of the 5C data. To construct the polymer model, we proceed in two steps: first, we introduce a minimal number of random connectors inside restricted regions to account for diagonal blocks. Second, we account for long-range frequent specific genomic interactions. Using the constructed polymer, we compute the first encounter time distribution and the conditional probability of three key genomic sites. By simulating single particle trajectories of loci located on the constructed polymers from 5C data, we found a large variability of the anomalous exponent, used to interpret live cell imaging trajectories. The present polymer construction provides a generic tool to study steady-state and transient properties of chromatin constrained by some physical properties embedded in 5C data.
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