ArticleThe European physical journal. E, Soft matter2017
The role of DNA sequence in nucleosome breathing.
Article in The European physical journal. E, Soft matter, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- FACT weakens the nucleosomal barrier to transcription and preserves its integrity by forming a hexasome-like intermediate.Molecular cell · 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
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.Frontiers in molecular biosciences · 2023Article
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- OCT4 interprets and enhances nucleosome flexibility.Nucleic acids research · 2022Article
- Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts.PLoS computational biology · 2022Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Article
- Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.Biophysical journal · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Molecular Mechanism of Spontaneous Nucleosome Unraveling.Journal of molecular biology · 2019Article
- Telling Left from Right in Breathing Nucleosomes.Biophysical journal · 2018Article
- Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles.Biophysical journal · 2018Article
- The Latest Twists in Chromatin Remodeling.Biophysical journal · 2018Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Roughly 3/4 of human genomes are sequestered by nucleosomes, DNA spools with a protein core, dictating a broad range of biological processes, ranging from gene regulation, recombination, and replication, to chromosome condensation. Nucleosomes are dynamical structures and temporarily expose wrapped DNA through spontaneous unspooling from either end, a process called site exposure or nucleosome breathing. Here we ask how this process is influenced by the mechanical properties of the wrapped DNA, which is known to depend on the underlying base pair sequence. Using a coarse-grained nucleosome model we calculate the accessibility profiles for site exposure. We find that the process is very sensitive to sequence effects, so that evolution could potentially tune the accessibility of nucleosomal DNA and would only need a small number of mutations to do so.
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Registered trials
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