ArticleNucleic acids research2017
Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.
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 15 papers.
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Who cites it
15 citing papers in PubMed.
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Initiation of base excision repair is modulated by nucleosome occupancy modifying sequences.DNA repair · 2025Article
- Histone tetrasome dynamics affects chromatin transcription.Nucleic acids research · 2025Article
- Molecular Dynamics Simulations of Nucleosomes Containing Histone Variant H2A.J.International journal of molecular sciences · 2024Article
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- Interactions of Nucleosomes with Acidic Patch-Binding Peptides: A Combined Structural Bioinformatics, Molecular Modeling, Fluorescence Polarization, and Single-Molecule FRET Study.International journal of molecular sciences · 2023Article
- Article
- Recent Advances in Investigating Functional Dynamics of Chromatin.Frontiers in genetics · 2022Review
- Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails.Nature communications · 2021Article
- Histone dynamics mediate DNA unwrapping and sliding in nucleosomes.Nature communications · 2021Article
- Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.Nature communications · 2021Article
- Molecular recognition of nucleosomes by binding partners.Current opinion in structural biology · 2019Review
- Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.Nature protocols · 2018Article
- Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres.Genes & development · 2017Article
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6 authors.
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Abstract
Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical footprinting (HRF) of protein-DNA complexes is a chemical technique that probes nucleosome organization in solution with a high precision unattainable by other methods. In this work we propose an integrative modeling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments. Our method precisely identifies DNA positioning on nucleosome by combining HRF data for both DNA strands with the pseudo-symmetry constraints. We performed high-resolution HRF for Saccharomyces cerevisiae centromeric nucleosome of unknown structure and characterized it using our integrative modeling approach. Our model provides the basis for further understanding the cooperative engagement and interplay between Cse4p protein and the A-tracts important for centromere function.
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