ArticleBiophysical journal2020
Structural Studies of Overlapping Dinucleosomes in Solution.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 21 citations in OpenAlex.
- Molecular dynamics guided all-atom reconstruction of cryo-ET maps reveals mechanisms of histone tail mediated chromatin compaction.Nature communications · 2026Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- Size-exclusion chromatography-small-angle neutron scattering system optimized for an instrument with medium neutron flux.Journal of applied crystallography · 2025Article
- In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli.Communications biology · 2024Article
- Asymmetric fluctuation of overlapping dinucleosome studied by cryoelectron microscopy and small-angle X-ray scattering.PNAS nexus · 2024Article
- Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.Communications biology · 2024Article
- Structural and Dynamic Changes of Nucleosome upon GATA3 Binding.Journal of molecular biology · 2023Article
- Derivation of the small-angle scattering profile of a target biomacromolecule from a profile deteriorated by aggregates. AUC-SAS.Journal of applied crystallography · 2023Article
- The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells.BMC genomics · 2023Article
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.Scientific reports · 2022Article
- Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs.Current opinion in structural biology · 2022Review
- Molecular dynamics analysis of biomolecular systems including nucleic acids.Biophysics and physicobiology · 2022Article
- Structural studies of functional nucleosome complexes with transacting factors.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2022Review
- Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility.Nucleic acids research · 2021Article
- Deuteration Aiming for Neutron Scattering.Biophysics and physicobiology · 2021Article
- Multiscale Genome Organization: Dazzling Subject and Inventive Methods.Biophysical journal · 2020Article
- Overview of the big data bioinformatics symposium (2SCA) at BSJ2019.Biophysical reviews · 2020Article
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Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
Abstract
An overlapping dinucleosome (OLDN) is a structure composed of one hexasome and one octasome and appears to be formed through nucleosome collision promoted by nucleosome remodeling factor(s). In this study, the solution structure of the OLDN was investigated through the integration of small-angle x-ray and neutron scattering (SAXS and SANS, respectively), computer modeling, and molecular dynamics simulations. Starting from the crystal structure, we generated a conformational ensemble based on normal mode analysis and searched for the conformations that reproduced the SAXS and SANS scattering curves well. We found that inclusion of histone tails, which are not observed in the crystal structure, greatly improved model quality. The obtained structural models suggest that OLDNs adopt a variety of conformations stabilized by histone tails situated at the interface between the hexasome and octasome, simultaneously binding to both the hexasomal and octasomal DNA. In addition, our models define a possible direction for the conformational changes or dynamics, which may provide important information that furthers our understanding of the role of chromatin dynamics in gene regulation.
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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.