ArticleNucleic acids research2009
Using DNA mechanics to predict in vitro nucleosome positions and formation energies.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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Who cites it
94 citing papers in PubMed, 182 citations in OpenAlex.
- Interfacial water confers transcription factors with dinucleotide specificity.Nature structural & molecular biology · 2025Article
- The importance of DNA sequence for nucleosome positioning in transcriptional regulation.Life science alliance · 2024Article
- The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology.Biomolecules · 2023Article
- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- DNA Sequence-Dependent Properties of Nucleosome Positioning in Regions of Distinct Chromatin States in Mouse Embryonic Stem Cells.International journal of molecular sciences · 2022Article
- DeepNup: Prediction of Nucleosome Positioning from DNA Sequences Using Deep Neural Network.Genes · 2022Article
- DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.Nucleic acids research · 2021Article
- Energetics of twisted DNA topologies.Biophysical journal · 2021Review
- A deformation energy model reveals sequence-dependent property of nucleosome positioning.Chromosoma · 2021Article
- Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.PLoS computational biology · 2021Article
- Nucleosome Positioning around Transcription Start Site Correlates with Gene Expression Only for Active Chromatin State in Drosophila Interphase Chromosomes.International journal of molecular sciences · 2020Article
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Molecular Mechanisms of PARP-1 Inhibitor 7-Methylguanine.International journal of molecular sciences · 2020Article
- Deform-nu: A DNA Deformation Energy-Based Predictor for Nucleosome Positioning.Frontiers in cell and developmental biology · 2020Article
- Theory of Active Chromatin Remodeling.Physical review letters · 2019Article
- Static Kinks or Flexible Hinges: Multiple Conformations of Bent DNA Bound to Integration Host Factor Revealed by Fluorescence Lifetime Measurements.The journal of physical chemistry. B · 2018Article
- Article
- Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.PLoS computational biology · 2018Article
- Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.Nature protocols · 2018Article
- Bend-Induced Twist Waves and the Structure of Nucleosomal DNA.Physical review letters · 2018Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While competition with other DNA-binding factors and action of chromatin remodeling enzymes significantly affect nucleosome formation in vivo, nucleosome positions in vitro are determined by steric exclusion and sequence alone. We have developed a biophysical model, DNABEND, for the sequence dependence of DNA bending energies, and validated it against a collection of in vitro free energies of nucleosome formation and a set of in vitro nucleosome positions mapped at high resolution. We have also made a first ab initio prediction of nucleosomal DNA geometries, and checked its accuracy against the nucleosome crystal structure. We have used DNABEND to design both strong and weak histone- binding sequences, and measured the corresponding free energies of nucleosome formation. We find that DNABEND can successfully predict in vitro nucleosome positions and free energies, providing a physical explanation for the intrinsic sequence dependence of histone-DNA interactions.
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