ArticleProceedings of the National Academy of Sciences of the United States of America2019
Nucleosome positions alone can be used to predict domains in yeast chromosomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 60 citations in OpenAlex.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Single-molecule imaging reveals DNA shape read-out by the INO80 chromatin remodeler.Nature communications · 2026Article
- Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.Nature communications · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- The Fluid Mosaic Model of chromatin organization: integrating dynamics, conformational heterogeneity and multiscale organization.Communications biology · 2026Review
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- An experimentally-informed polymer model reveals high resolution organization of genomic loci.Nature communications · 2026Article
- FACT depletion demonstrates a role for nucleosome organization in TAD formation.Molecular systems biology · 2026Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Nucleosome placement and polymer mechanics explain genomic contacts on 100 kb scales.Nucleic acids research · 2025Article
- Coarse-grained chromatin dynamics by tracking multiple similarly labeled gene loci.Biophysical journal · 2025Article
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Linking DNA-packing density distribution and TAD boundary locations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion.Genome biology · 2024Article
- Article
- Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Genome wide nucleosome landscape shapes 3D chromatin organization.Science advances · 2024Article
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
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3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp-sized domains observed in higher eukaryotes). We show that the sole input of nucleosome positioning data is already sufficient to determine the patterns of chromatin interactions and domain boundaries seen experimentally to a high degree of accuracy. Since the nucleosome spacing so strongly affects the larger-scale domain structure, we next examine the genome-wide linker-length distribution in more detail, finding that it is highly irregular and varies in different genomic regions such as gene bodies, promoters, and active and inactive genes. Finally we use our simple simulation model to characterize in more detail how irregular nucleosome spacing may affect local chromatin structure.
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