ArticleGenome biology2017
Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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48 citing papers in PubMed, 72 citations in OpenAlex.
- Article
- Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids.Nucleic acids research · 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
- Condensin accelerates long-range intra-chromosomal interactions.Nature communications · 2026Article
- The physical chemistry of interphase loop extrusion.Cell genomics · 2026Article
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Uniform dynamics of cohesin-mediated loop extrusion in living human cells.Nature genetics · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Condensin Accelerates Long-Range Intra-Chromosomal Interactions.bioRxiv : the preprint server for biology · 2025Article
- Review
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization.Nature communications · 2024Article
- Genome wide nucleosome landscape shapes 3D chromatin organization.Science advances · 2024Article
- Mitotic chromosomes are self-entangled and disentangle through a topoisomerase-II-dependent two-stage exit from mitosis.Molecular cell · 2024Article
- Article
- In vivo tracking of functionally tagged Rad51 unveils a robust strategy of homology search.Nature structural & molecular biology · 2023Article
- 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
- Loops and the activity of loop extrusion factors constrain chromatin dynamics.Molecular biology of the cell · 2023Article
Corrections and comments
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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
backgroundThe structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constraints and a small number of structural parameters can explain diverse experimental data on nuclear architecture. However, how assumed chromatin properties affect model predictions was not previously systematically investigated.
resultsWe used hundreds of dynamic chromosome simulations and Bayesian inference to determine chromatin properties consistent with an extensive dataset that includes hundreds of measurements from imaging in fixed and live cells and two Hi-C studies. We place new constraints on average chromatin fiber properties, narrowing down the chromatin compaction to ~53-65 bp/nm and persistence length to ~52-85 nm. These constraints argue against a 20-30 nm fiber as the exclusive chromatin structure in the genome. Our best model provides a much better match to experimental measurements of nuclear architecture and also recapitulates chromatin dynamics measured on multiple loci over long timescales.
conclusionThis work substantially improves our understanding of yeast chromatin mechanics and chromosome architecture and provides a new analytic framework to infer chromosome properties in other organisms.
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