ArticleJournal of molecular biology2008
Spontaneous access to DNA target sites in folded chromatin fibers.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- Structural basis of PARP2 recognition of nucleosomal DNA breaks and inhibitor trapping.Nucleic acids research · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Pioneer-factor activity requires stable chromatin occupancy mediated by both sequence-specific binding and disordered protein domains.Science advances · 2026Article
- Article
- 5-Formylcytosine functions as a chemical regulator of nucleosome positioning.Nature communications · 2026Article
- DNA bendability regulates transcription factor binding to nucleosomes.Nature structural & molecular biology · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- Nucleosome wrapping states encode principles of 3D genome organization.Nature communications · 2025Article
- ISWI catalyzes nucleosome sliding in condensed nucleosome arrays.Nature structural & molecular biology · 2024Article
- scATAcat: cell-type annotation for scATAC-seq data.NAR genomics and bioinformatics · 2024Article
- Exploring the reciprocity between pioneer factors and development.Development (Cambridge, England) · 2024Review
- From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.Annual review of biophysics · 2024Review
- ISWI catalyzes nucleosome sliding in condensed nucleosome arrays.bioRxiv : the preprint server for biology · 2023Article
- Cryoelectron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination.Molecular cell · 2023Article
- The nucleosome unwrapping free energy landscape defines distinct regions of transcription factor accessibility and kinetics.Nucleic acids research · 2023Article
- Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility.Nature communications · 2023Article
- Characterization of chromatin accessibility patterns in different mouse cell types using machine learning methods at single-cell resolution.Frontiers in genetics · 2023Article
- Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula.BMC biology · 2022Article
- DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules.Biophysics reports · 2022Article
- Molecular dynamics simulations reveal how H3K56 acetylation impacts nucleosome structure to promote DNA exposure for lesion sensing.DNA repair · 2021Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
DNA wrapped in nucleosomes is sterically occluded from many protein complexes that must act on it; how such complexes gain access to nucleosomal DNA is not known. In vitro studies on isolated nucleosomes show that they undergo spontaneous partial unwrapping conformational transitions, which make the wrapped nucleosomal DNA transiently accessible. Thus, site exposure might provide a general mechanism allowing access of protein complexes to nucleosomal DNA. However, existing quantitative analyses of site exposure focused on single nucleosomes, while the presence of neighbor nucleosomes and concomitant chromatin folding might significantly influence site exposure. In this work, we carried out quantitative studies on the accessibility of nucleosomal DNA in homogeneous nucleosome arrays. Two striking findings emerged. Organization into chromatin fibers changes the accessibility of nucleosomal DNA only modestly, from approximately 3-fold decreases to approximately 8-fold increases in accessibility. This means that nucleosome arrays are intrinsically dynamic and accessible even when they are visibly condensed. In contrast, chromatin folding decreases the accessibility of linker DNA by as much as approximately 50-fold. Thus, nucleosome positioning dramatically influences the accessibility of target sites located inside nucleosomes, while chromatin folding dramatically regulates access to target sites in linker DNA.
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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.