ArticleNucleic acids research2023
Bi-directional nucleosome sliding by the Chd1 chromatin remodeler integrates intrinsic sequence-dependent and ATP-dependent nucleosome positioning.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.Bioinformatics (Oxford, England) · 2026Article
- The Future of Epigenetics: Emerging Technologies and Clinical Applications.ACS pharmacology & translational science · 2026Review
- Multiplexed single-molecule characterization at the library scale.Nature protocols · 2026Review
- HDGS-Net: nucleosome occupancy prediction based on a hybrid dilated gated separable convolutional neural network.BMC genomics · 2026Article
- Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.Nucleic acids research · 2025Article
- Gene promoters are genomically encoded to facilitate histone exchange/incorporation.PLoS biology · 2025Article
- H2A.Z deposition by the SWR complex is stimulated by polyadenine DNA sequences in nucleosomes.PLoS biology · 2025Article
- H3K56 acetylation regulates chromatin maturation following DNA replication.Nature communications · 2025Article
- Interpretable deep residual network uncovers nucleosome positioning and associated features.Nucleic acids research · 2024Article
- Article
- Genome organization across scales: mechanistic insights from in vitro reconstitution studies.Biochemical Society transactions · 2024Review
- Energy-driven genome regulation by ATP-dependent chromatin remodellers.Nature reviews. Molecular cell biology · 2024Review
- Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking.Nature communications · 2024Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Chromatin remodelers use a helicase-type ATPase motor to shift DNA around the histone core. Although not directly reading out the DNA sequence, some chromatin remodelers exhibit a sequence-dependent bias in nucleosome positioning, which presumably reflects properties of the DNA duplex. Here, we show how nucleosome positioning by the Chd1 remodeler is influenced by local DNA perturbations throughout the nucleosome footprint. Using site-specific DNA cleavage coupled with next-generation sequencing, we show that nucleosomes shifted by Chd1 can preferentially localize DNA perturbations - poly(dA:dT) tracts, DNA mismatches, and single-nucleotide insertions - about a helical turn outside the Chd1 motor domain binding site, super helix location 2 (SHL2). This phenomenon occurs with both the Widom 601 positioning sequence and the natural +1 nucleosome sequence from the Saccharomyces cerevisiae SWH1 gene. Our modeling indicates that localization of DNA perturbations about a helical turn outward from SHL2 results from back-and-forth sliding due to remodeler action on both sides of the nucleosome. Our results also show that barrier effects from DNA perturbations can be extended by the strong phasing of nucleosome positioning sequences.
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