ArticleProceedings of the National Academy of Sciences of the United States of America2014
Ubiquitous nucleosome crowding in the yeast genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 37 citations in OpenAlex.
- Review
- Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast.Biology · 2020Review
- Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation.Genome research · 2019Article
- Quantitative MNase-seq accurately maps nucleosome occupancy levels.Genome biology · 2019Article
- Nucleosome positions alone can be used to predict domains in yeast chromosomes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Intracellular nucleosomes constrain a DNA linking number difference of -1.26 that reconciles the Lk paradox.Nature communications · 2018Article
- 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
- Precise genome-wide mapping of single nucleosomes and linkers in vivo.Genome biology · 2018Article
- Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.Epigenetics & chromatin · 2017Article
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo.Nucleic acids research · 2016Article
- Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster.Nucleic acids research · 2016Article
- Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.Genome research · 2015Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- Post-translational modifications of histones that influence nucleosome dynamics.Chemical reviews · 2015Review
- Functional roles of nucleosome stability and dynamics.Briefings in functional genomics · 2015Review
- Replication-guided nucleosome packing and nucleosome breathing expedite the formation of dense arrays.Nucleic acids research · 2014Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Nucleosomes may undergo a conformational change in which a stretch of DNA peels off the histone octamer surface as a result of thermal fluctuations or interactions with chromatin remodelers. Thus, neighboring nucleosomes may invade each other's territories by DNA unwrapping and translocation, or through initial assembly in partially wrapped states. A recent high-resolution map of distances between dyads of neighboring nucleosomes in Saccharomyces cerevisiae reveals that nucleosomes frequently overlap DNA territories of their neighbors. This conclusion is supported by lower-resolution maps of S. cerevisiae nucleosome lengths based on micrococcal nuclease digestion and paired-end sequencing. The average length of wrapped DNA follows a stereotypical pattern in genes and promoters, correlated with the well-known distribution of nucleosome occupancy: nucleosomal DNA tends to be shorter in promoters and longer in coding regions. To explain these observations, we have developed a biophysical model that uses a 10-11-bp periodic histone-DNA binding energy profile. The profile is based on the pattern of histone-DNA contacts in nucleosome crystal structures, as well as the idea of linker length discretization caused by higher-order chromatin structure. Our model is in agreement with the observed genome-wide distributions of interdyad distances, wrapped DNA lengths, and nucleosome occupancies. Furthermore, our approach explains in vitro measurements of the accessibility of nucleosome-covered target sites and nucleosome-induced cooperativity between DNA-binding factors. We rule out several alternative scenarios of histone-DNA interactions as inconsistent with the genomic data.
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