ArticleNucleic acids research2019
Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Molecular dynamics guided all-atom reconstruction of cryo-ET maps reveals mechanisms of histone tail mediated chromatin compaction.Nature communications · 2026Article
- Genome-wide rotational and translational phasing of nucleosomes with human transcription factors.Molecular cell · 2026Article
- Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline.PLoS computational biology · 2026Article
- Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq) of Cancer Cells in Culture.Methods in molecular biology (Clifton, N.J.) · 2026Article
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- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- Adenovirus maturation establishes the transcription competent packaging of its genome.EMBO reports · 2025Article
- Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor.Nucleic acids research · 2025Article
- Epigenetic Modifications in the Retinal Pigment Epithelium of the Eye During RPE-Related Regeneration or Retinal Diseases in Vertebrates.Biomedicines · 2025Review
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- The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2025Review
- Article
- Rethinking chromatin accessibility: from compaction to dynamic interactions.Current opinion in genetics & development · 2025Review
- H3K56 acetylation regulates chromatin maturation following DNA replication.Nature communications · 2025Article
- In vivo assembly of complete eukaryotic nucleosomes and (H3-H4)-only non-canonical nucleosomal particles in the model bacterium Escherichia coli.Communications biology · 2024Article
- Dinochromosome Heterotermini with Telosomal Anchorages.International journal of molecular sciences · 2024Article
- Evolution of Einkorn wheat centromeres is driven by the mutualistic interplay of two LTR retrotransposons.Mobile DNA · 2024Article
- nucMACC: An MNase-seq pipeline to identify structurally altered nucleosomes in the genome.Science advances · 2024Article
- Chromatin structure and dynamics: one nucleosome at a time.Histochemistry and cell biology · 2024Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Packaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. We assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions, performed statistical analyses and computer modelling. We found no difference in MNase accessibility, suggesting no difference in fiber folding between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially organized domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.
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