ArticleBiophysical journal2010
A lattice model for transcription factor access to nucleosomal DNA.
Article in Biophysical journal, 2010. 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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Who cites it
16 citing papers in PubMed, 39 citations in OpenAlex.
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- DNA sequence-dependent formation of heterochromatin nanodomains.Nature communications · 2022Article
- Kinetic origin of nucleosome invasion by pioneer transcription factors.Biophysical journal · 2021Article
- Effects of size, cooperativity, and competitive binding on protein positioning on DNA.Biophysical journal · 2021Article
- Quantitative Modeling of Nucleosome Unwrapping from Both Ends.Biophysical journal · 2019Article
- Coupling of replisome movement with nucleosome dynamics can contribute to the parent-daughter information transfer.Nucleic acids research · 2018Article
- The role of DNA sequence in nucleosome breathing.The European physical journal. E, Soft matter · 2017Article
- A New Mechanism for Mendelian Dominance in Regulatory Genetic Pathways: Competitive Binding by Transcription Factors.Genetics · 2017Article
- Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics.Nucleic acids research · 2016Article
- Functional roles of nucleosome stability and dynamics.Briefings in functional genomics · 2015Review
- Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions.PLoS computational biology · 2014Article
- Ubiquitous nucleosome crowding in the yeast genome.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Dynamic regulation of transcriptional states by chromatin and transcription factors.Nature reviews. Genetics · 2014Review
- Toward a unified physical model of nucleosome patterns flanking transcription start sites.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping.Biophysical journal · 2011Article
- Structural constraints in collaborative competition of transcription factors against the nucleosome.Journal of molecular biology · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleosomes, the basic repeating unit of chromatin, consist of 147 basepairs of DNA that are wrapped in almost two turns around a histone protein octamer core. Because ∼3/4 of the human genomic DNA is found within nucleosomes, their position and DNA interaction is an essential determinant for the DNA access of gene-specific transcription factors and other proteins. Here, a DNA lattice model was developed for describing ligand binding in the presence of a nucleosome. The model takes into account intermediate states, in which DNA is partially unwrapped from the histone octamer. This facilitates access of transcription factors to up to 60 DNA basepairs located in the outer turn of nucleosomal DNA, while the inner DNA turn was found to be more resistant to competitive ligand binding. As deduced from quantitative comparisons with recently published experimental data, our model provides a better description than the previously used all-or-none lattice-binding model. Importantly, nucleosome-occupancy maps predicted by the nucleosome-unwrapping model also differed significantly when partial unwrapping of nucleosomal DNA was considered. In addition, large effects on the cooperative binding of transcription factors to multiple binding sites occluded by the nucleosome were apparent. These findings indicate that partial unwrapping of DNA from the histone octamer needs to be taken into account in quantitative models of gene regulation in chromatin.
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