ArticleNucleic acids research2014
Revealing transient structures of nucleosomes as DNA unwinds.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 81 citations in OpenAlex.
- Evaluating high-fidelity CRISPR-Cas nucleases in nucleosomal contexts using a quantitative framework.Frontiers in genome editing · 2026Article
- Control of Gene Expression by Proteins That Bind Many Alternative Nucleic Acid Structures Through the Same Domain.International journal of molecular sciences · 2025Article
- Solution conformational differences between conventional and CENP-A nucleosomes are accentuated by reversible deformation under high pressure.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Advances in microfluidic mixers for time-resolved structural biology with X-rays.Biophysical reviews · 2025Review
- Article
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
- The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology.Biomolecules · 2023Article
- Histone divergence in trypanosomes results in unique alterations to nucleosome structure.Nucleic acids research · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Biologically relevant small variations of intra-cellular pH can have significant effect on stability of protein-DNA complexes, including the nucleosome.Frontiers in molecular biosciences · 2023Article
- Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Nucleosome assembly and disassembly pathways in vitro.PloS one · 2022Article
- Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis.Methods in enzymology · 2022Article
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.Nucleic acids research · 2021Article
- Solution structure(s) of trinucleosomes from contrast variation SAXS.Nucleic acids research · 2021Article
- Nucleosome composition regulates the histone H3 tail conformational ensemble and accessibility.Nucleic acids research · 2021Article
- Effects of H2A.B incorporation on nucleosome structures and dynamics.Biophysical journal · 2021Article
- Histone H4 Tails in Nucleosomes: a Fuzzy Interaction with DNA.Angewandte Chemie (International ed. in English) · 2021Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
The modulation of DNA accessibility by nucleosomes is a fundamental mechanism of gene regulation in eukaryotes. The nucleosome core particle (NCP) consists of 147 bp of DNA wrapped around a symmetric octamer of histone proteins. The dynamics of DNA packaging and unpackaging from the NCP affect all DNA-based chemistries, but depend on many factors, including DNA positioning sequence, histone variants and modifications. Although the structure of the intact NCP has been studied by crystallography at atomic resolution, little is known about the structures of the partially unwrapped, transient intermediates relevant to nucleosome dynamics in processes such as transcription, DNA replication and repair. We apply a new experimental approach combining contrast variation with time-resolved small angle X-ray scattering (TR-SAXS) to determine transient structures of protein and DNA constituents of NCPs during salt-induced disassembly. We measure the structures of unwrapping DNA and monitor protein dissociation from Xenopus laevis histones reconstituted with two model NCP positioning constructs: the Widom 601 sequence and the sea urchin 5S ribosomal gene. Both constructs reveal asymmetric release of DNA from disrupted histone cores, but display different patterns of protein dissociation. These kinetic intermediates may be biologically important substrates for gene regulation.
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Registered trials
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.