ArticleBiophysical journal2008
The effect of internucleosomal interaction on folding of the chromatin fiber.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 81 citations in OpenAlex.
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
- The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle.bioRxiv : the preprint server for biology · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Nucleosome spacing controls chromatin spatial structure and accessibility.Biophysical journal · 2024Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Cohesin and CTCF complexes mediate contacts in chromatin loops depending on nucleosome positions.Biophysical journal · 2022Article
- The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions.Biochemistry · 2022Article
- A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions.Journal of chemical theory and computation · 2022Article
- Differences in nanoscale organization of regulatory active and inactive human chromatin.Biophysical journal · 2022Article
- How Genomes Emerge, Function, and Evolve: Living Systems Emergence-Genotype-Phenotype-Multilism-Genome/Systems Ecology.Results and problems in cell differentiation · 2022Article
- Simulation of Different Three-Dimensional Models of Whole Interphase Nuclei Compared to Experiments - A Consistent Scale-Bridging Simulation Framework for Genome Organization.Results and problems in cell differentiation · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- A glitch in the snitch: the role of linker histone H1 in shaping the epigenome in normal and diseased cells.Open biology · 2021Review
- Tetranucleosome Interactions Drive Chromatin Folding.ACS central science · 2021Article
- Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.Nucleic acids research · 2020Article
- Irregular Chromatin: Packing Density, Fiber Width, and Occurrence of Heterogeneous Clusters.Biophysical journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.Biophysical journal · 2018Review
- Uncovering the forces between nucleosomes using DNA origami.Science advances · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.