ArticleAIMS biophysics2015
Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription.
Article in AIMS biophysics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- Epigenetic liquid biopsies for minimal residual disease, what's around the corner?Frontiers in oncology · 2023Review
- Histone H3 core domain in chromatin with different DNA linker lengths studied byFrontiers in molecular biosciences · 2022Article
- Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies.Biophysical reports · 2021Review
- Conformational Dynamics of Histone H3 Tails in Chromatin.The journal of physical chemistry letters · 2021Article
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
- Topological polymorphism of nucleosome fibers and folding of chromatin.Biophysical journal · 2021Review
- 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
- Braiding topology and the energy landscape of chromosome organization proteins.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Modelling and DNA topology of compact 2-start and 1-start chromatin fibres.Nucleic acids research · 2019Article
- Sensitive effect of linker histone binding mode and subtype on chromatin condensation.Nucleic acids research · 2019Article
- Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy.Biophysical journal · 2018Article
- Precise genome-wide mapping of single nucleosomes and linkers in vivo.Genome biology · 2018Article
- Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding.The Journal of biological chemistry · 2017Article
- DNA topology in chromatin is defined by nucleosome spacing.Science advances · 2017Article
- Kilobase Pair Chromatin Fiber Contacts Promoted by Living-System-Like DNA Linker Length Distributions and Nucleosome Depletion.The journal of physical chemistry. B · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers-one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers-that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10
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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.