ArticleBiophysical journal2020
Ensembles of Breathing Nucleosomes: A Computational Study.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Disentangling Timescales of Molecular Kinetics with spFRET using ALEX-FCS.Journal of fluorescence · 2025Article
- Chromatin remodelers: a concise introduction for biophysicists.Biophysical reviews · 2024Review
- Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation.The Journal of chemical physics · 2023Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging.Biophysical journal · 2022Article
- Kinetic origin of nucleosome invasion by pioneer transcription factors.Biophysical journal · 2021Article
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Multiscale Genome Organization: Dazzling Subject and Inventive Methods.Biophysical journal · 2020Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
About three-fourths of the human DNA molecules are wrapped into nucleosomes, protein spools with DNA. Nucleosomes are highly dynamic, transiently exposing their DNA through spontaneous unspooling. Recent experiments allowed to observe the DNA of an ensemble of such breathing nucleosomes through x-ray diffraction with contrast matching between the solvent and the protein core. In this study, we calculate such an ensemble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent DNA mechanics. Our analysis gives detailed insights into the sequence dependence of nucleosome breathing observed in the experiment and allows us to determine the adsorption energy of the DNA bound to the protein core as a function of the ionic strength. Moreover, we predict the breathing behavior of other potentially interesting sequences and compare the findings to earlier related experiments.
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