ArticleNucleic acids research2019
Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo.
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 92 papers.
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92 citing papers in PubMed.
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- Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.Nature genetics · 2026Article
- Article
- Geometrically Encoded Positioning of Introns, Intergenic Segments, and Exons in the Human Genome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Revealing the biophysics of lamina-associated domain formation by integrating theoretical modeling and high-resolution imaging.Nature communications · 2025Article
- Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Chromatin heterogeneity modulates nuclear condensate dynamics and phase behavior.Nature communications · 2025Article
- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
32 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Chromatin organization is crucial for regulating gene expression. Previously, we showed that nucleosomes form groups, termed clutches. Clutch size correlated with the pluripotency grade of mouse embryonic stem cells and human induced pluripotent stem cells. Recently, it was also shown that regions of the chromatin containing activating epigenetic marks were composed of small and dispersed chromatin nanodomains with lower DNA density compared to the larger silenced domains. Overall, these results suggest that clutch size may regulate DNA packing density and gene activity. To directly test this model, we carried out 3D, two-color super-resolution microscopy of histones and DNA with and without increased histone tail acetylation. Our results showed that lower percentage of DNA was associated with nucleosome clutches in hyperacetylated cells. We further showed that the radius and compaction level of clutch-associated DNA decreased in hyperacetylated cells, especially in regions containing several neighboring clutches. Importantly, this change was independent of clutch size but dependent on the acetylation state of the clutch. Our results directly link the epigenetic state of nucleosome clutches to their DNA packing density. Our results further provide in vivo support to previous in vitro models that showed a disruption of nucleosome-DNA interactions upon hyperacetylation.
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