ArticlePhysical chemistry chemical physics : PCCP2009
Mesoscale simulations of two nucleosome-repeat length oligonucleosomes.
Article in Physical chemistry chemical physics : PCCP, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 48 citations in OpenAlex.
- Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome.Computational and structural biotechnology journal · 2024Article
- Structure of native chromatin fibres revealed by Cryo-ET in situ.Nature communications · 2023Article
- Brownian dynamics simulations of mesoscale chromatin fibers.Biophysical journal · 2023Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- 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
- Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin.Scientific reports · 2018Article
- Dependence of the Linker Histone and Chromatin Condensation on the Nucleosome Environment.The journal of physical chemistry. B · 2017Article
- Linking Chromatin Fibers to Gene Folding by Hierarchical Looping.Biophysical journal · 2017Review
- Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements.The journal of physical chemistry. B · 2016Article
- Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.Biophysical journal · 2016Article
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement.Nucleic acids research · 2015Article
- Article
- Forced unraveling of chromatin fibers with nonuniform linker DNA lengths.Journal of physics. Condensed matter : an Institute of Physics journal · 2015Article
- Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding.Nucleic acids research · 2014Article
- Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.Nucleic acids research · 2014Article
- Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.Journal of biological physics · 2013Article
- Effect of capsid confinement on the chromatin organization of the SV40 minichromosome.Nucleic acids research · 2013Article
- Unwinding and rewinding the nucleosome inner turn: force dependence of the kinetic rate constants.Physical review. E, Statistical, nonlinear, and soft matter physics · 2013Article
- Crucial role of dynamic linker histone binding and divalent ions for DNA accessibility and gene regulation revealed by mesoscale modeling of oligonucleosomes.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
The compaction of chromatin, accessed through coarse-grained modeling and simulation, reveals different folding patterns as a function of the nucleosome repeat length (NRL), the presence of the linker histone, and the ionic strength. Our results indicate that the linker histone has negligible influence on short NRL fibers, whereas for longer NRL fibers it works like, and in tandem with, concentrated positive counterions to condense the chromatin fiber. Longer NRL fibers also exhibit structural heterogeneity, with solenoid-like conformations viable in addition to irregular zigzags. These features of chromatin and associated internucleosomal patterns presented here help interpret structural dependencies of the chromatin fiber on internal and external factors. In particular, we suggest that longer-NRL are more advantageous for packing and achieving various levels of fiber compaction throughout the cell cycle.
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