ArticleProceedings of the National Academy of Sciences of the United States of America2013
Toward a unified physical model of nucleosome patterns flanking transcription start sites.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Motorized chromosome models of mitotic chromosome folding.Nature communications · 2025Article
- A single fiber view of the nucleosome organization in eukaryotic chromatin.Nucleic acids research · 2024Article
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
- Chromatin Regulators Ahc1p and Eaf3p Positively Influence Nitrogen Metabolism inFrontiers in microbiology · 2022Article
- On the role of transcription in positioning nucleosomes.PLoS computational biology · 2021Article
- CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length.Nucleic acids research · 2019Article
- Theory of Active Chromatin Remodeling.Physical review letters · 2019Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- Major Determinants of Nucleosome Positioning.Biophysical journal · 2018Review
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- Genome-wide mapping of nucleosome positions in Saccharomyces cerevisiae in response to different nitrogen conditions.Scientific reports · 2016Article
- Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing.Nucleic acids research · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo.G3 (Bethesda, Md.) · 2015Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density.Molecular and cellular biology · 2015Article
- Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.Nucleic acids research · 2014Article
- Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.PLoS computational biology · 2014Article
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Authors and funding
5 authors at 5 institutions in 2 countries.
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Abstract
Recent genome-wide maps of nucleosome positions in different eukaryotes revealed patterns around transcription start sites featuring a nucleosome-free region flanked by a periodic modulation of the nucleosome density. For Saccharomyces cerevisiae, the average in vivo pattern was previously shown to be quantitatively described by a "nucleosome gas" model based on the statistical positioning mechanism. However, this simple physical description is challenged by the fact that the pattern differs quantitatively between species and by recent experiments that appear incompatible with statistical positioning, indicating important roles for chromatin remodelers. We undertake a data-driven search for a unified physical model to describe the nucleosome patterns of 12 yeast species and also consider an extension of the model to capture remodeling effects. We are led to a nucleosome gas that takes into account nucleosome breathing, i.e., transient unwrapping of nucleosomal DNA segments. This known biophysical property of nucleosomes rationalizes a "pressure"-induced dependence of the effective nucleosome size that is suggested by the data. By fitting this model to the data, we find an average energy cost for DNA unwrapping consistent with previous biophysical experiments. Although the available data are not sufficient to reconstruct chromatin remodeling mechanisms, a minimal model extension by one mechanism yields an "active nucleosome gas" that can rationalize the behavior of systems with reduced histone-DNA ratio and remodeler knockouts. We therefore establish a basis for a physical description of nucleosome patterns that can serve as a null model for sequence-specific effects at individual genes and in models of transcription regulation.
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