ArticleBiophysical journal2018
Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 24 citations in OpenAlex.
- Mixing chromatin fibers with different nucleosome repeat lengths changes dynamics of chromatin phase separation.The Journal of biological chemistry · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.BMB reports · 2025Review
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- Chromatin fiber breaks into clutches under tension and crowding.Nucleic acids research · 2022Article
- Effects of forces on chromatin.APL bioengineering · 2021Review
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
- Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies.Scientific reports · 2020Article
- Chromatin fibers stabilize nucleosomes under torsional stress.Nature communications · 2020Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The organization of chromatin in 30 nm fibers remains a topic of debate. Here, we quantify the mechanical properties of the linker DNA and evaluate the impact of these properties on chromatin fiber folding. We extended a rigid basepair DNA model to include (un)wrapping of nucleosomal DNA and (un)stacking of nucleosomes in one-start and two-start chromatin fibers. Monte Carlo simulations that mimic single-molecule force spectroscopy experiments of folded nucleosomal arrays reveal different stages of unfolding as a function of force and are largely consistent with a two-start folding for 167 and one-start folding for 197 nucleosome repeat length fibers. The major insight is that nucleosome unstacking and subsequent unwrapping is not necessary to obtain quantitative agreement with experimental force extension curves up to the overstretching plateau of folded chromatin fibers at 3-5 pN. Nucleosome stacking appears better accommodated in one-start than in two-start conformations, and we suggest that this difference can compensate the increased energy for bending the linker DNA. Overall, these simulations capture the dynamic structure of chromatin fibers while maintaining realistic physical properties of the linker DNA.
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