ArticlePLoS computational biology2018
Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.eLife · 2026Article
- Nucleosome positioning shapes cryptic antisense transcription.PLoS genetics · 2026Article
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- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Article
- Chromatin remodelers: a concise introduction for biophysicists.Biophysical reviews · 2024Review
- Article
- Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning.Nucleic acids research · 2023Article
- Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin.Research square · 2023Article
- Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.Polymers · 2023Review
- Multiplexing mechanical and translational cues on genes.Biophysical journal · 2022Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.PLoS computational biology · 2021Article
- Histone tails cooperate to control the breathing of genomic nucleosomes.PLoS computational biology · 2021Article
- Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer.International journal of molecular sciences · 2021Review
- Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability.International journal of molecular sciences · 2020Review
- Article
- Bottom-Up Meets Top-Down: The Crossroads of Multiscale Chromatin Modeling.Biophysical journal · 2020Review
- Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding.Biophysical journal · 2020Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
ATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning, ejecting, or editing nucleosomes, activities that confer them essential regulatory roles on gene expression and DNA replication. Here, we investigate the molecular mechanism of active nucleosome sliding by means of molecular dynamics simulations of the Snf2 remodeler translocase in complex with a nucleosome. During its inchworm motion driven by ATP consumption, the translocase overwrites the original nucleosome energy landscape via steric and electrostatic interactions to induce sliding of nucleosomal DNA unidirectionally. The sliding is initiated at the remodeler binding location via the generation of a pair of twist defects, which then spontaneously propagate to complete sliding throughout the entire nucleosome. We also reveal how remodeler mutations and DNA sequence control active nucleosome repositioning, explaining several past experimental observations. These results offer a detailed mechanistic picture of remodeling important for the complete understanding of these key biological processes.
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