ArticleNucleic acids research2017
Regulation of chromatin folding by conformational variations of nucleosome linker DNA.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 25 citations in OpenAlex.
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- Atomistic Molecular Dynamics Simulations of DNA in Complex 3D Arrangements for Comparison with Lower Resolution Structural Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Structural features of nucleosomes in interphase and metaphase chromosomes.Molecular cell · 2021Article
- DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study.Biophysical journal · 2021Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin.Journal of molecular biology · 2021Review
- A critical role for linker DNA in higher-order folding of chromatin fibers.Nucleic acids research · 2021Article
- [Identification of nucleosome positioning using support vector machine method based on comprehensive DNA sequence feature].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- Article
- New Aspects of Magnesium Function: A Key Regulator in Nucleosome Self-Assembly, Chromatin Folding and Phase Separation.International journal of molecular sciences · 2019Review
- Molecular recognition of nucleosomes by binding partners.Current opinion in structural biology · 2019Review
- Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays.The Journal of biological chemistry · 2019Article
- Dynamics of Chromatin Fibers: Comparison of Monte Carlo Simulations with Force Spectroscopy.Biophysical journal · 2018Article
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.Biophysical journal · 2018Review
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Linker DNA conformational variability has been proposed to direct nucleosome array folding into more or less compact chromatin fibers but direct experimental evidence for such models are lacking. Here, we tested this hypothesis by designing nucleosome arrays with A-tracts at specific locations in the nucleosome linkers to induce inward (AT-IN) and outward (AT-OUT) bending of the linker DNA. Using electron microscopy and analytical centrifugation techniques, we observed spontaneous folding of AT-IN nucleosome arrays into highly compact structures, comparable to those induced by linker histone H1. In contrast, AT-OUT nucleosome arrays formed less compact structures with decreased nucleosome interactions similar to wild-type nucleosome arrays. Adding linker histone H1 further increased compaction of the A-tract arrays while maintaining structural differences between them. Furthermore, restriction nuclease digestion revealed a strongly reduced accessibility of nucleosome linkers in the compact AT-IN arrays. Electron microscopy analysis and 3D computational Monte Carlo simulations are consistent with a profound zigzag linker DNA configuration and closer nucleosome proximity in the AT-IN arrays due to inward linker DNA bending. We propose that the evolutionary preferred positioning of A-tracts in DNA linkers may control chromatin higher-order folding and thus influence cellular processes such as gene expression, transcription and DNA repair.
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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.