ArticleBiophysical journal2018
Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles.
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 22 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
22 citing papers in PubMed, 43 citations in OpenAlex.
- 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
- Structural insights into how Cas9 targets nucleosomes.Nature communications · 2024Article
- Nucleosomal asymmetry: a novel mechanism to regulate nucleosome function.Biochemical Society transactions · 2024Review
- Chromatin remodelers: a concise introduction for biophysicists.Biophysical reviews · 2024Review
- Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions.JACS Au · 2024Review
- Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization.Current opinion in structural biology · 2024Review
- The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics.Nucleic acids research · 2023Article
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- Stochastic models of nucleosome dynamics reveal regulatory rules of stimulus-induced epigenome remodeling.Cell reports · 2022Article
- 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
- Surprising Twists in Nucleosomal DNA with Implication for Higher-order Folding.Journal of molecular biology · 2021Article
- Solution structure(s) of trinucleosomes from contrast variation SAXS.Nucleic acids research · 2021Article
- Phase separation of DNA: From past to present.Biophysical journal · 2021Review
- Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes.eLife · 2020Article
- The human telomeric nucleosome displays distinct structural and dynamic properties.Nucleic acids research · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
- The role of histone tails in nucleosome stability: An electrostatic perspective.Computational and structural biotechnology journal · 2020Article
- Salt Dependence of A-Form RNA Duplexes: Structures and Implications.The journal of physical chemistry. B · 2019Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
DNA is tightly wrapped around histone proteins in nucleosome core particles (NCPs) yet must become accessible for processing in the cell. This accessibility, a key component of transcription regulation, is influenced by the properties of both the histone proteins and the DNA itself. Small angle x-ray scattering with contrast variation is used to examine how sequence variations affect DNA unwrapping from NCPs at different salt concentrations. Salt destabilizes NCPs, populating multiple unwrapped states as many possible unwrapping pathways are explored by the complexes. We apply coarse-grained Monte Carlo methods to generate realistic sequence-dependent unwrapped structures for the nucleosomal DNA with thermal variations. An ensemble optimization method is employed to determine the composition of the overall ensemble as electrostatic interactions are weakened. Interesting DNA-sequence-dependent differences are revealed in the unwrapping paths and equilibrium constants. These differences are correlated with specific features within the nucleic acid sequences.
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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.