ArticleJournal of molecular biology2021
Nucleosome Clutches are Regulated by Chromatin Internal Parameters.
Article in Journal of molecular biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- 3D Genome Engineering Using CRISPR/dCas Systems.International journal of molecular sciences · 2026Review
- Topology Resetting During Transcription-Coupled Nucleotide Excision Repair.International journal of molecular sciences · 2026Review
- Condensin IDC has a functional ATPase that is required for X-Chromosome dosage compensation in C. elegans.Genetics · 2026Article
- Material-Induced Nuclear Deformation Controls Chromatin Architecture in Adipose Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- Nucleosome spacing across cell types, diseases, and ages.Nucleic acids research · 2026Review
- Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states.bioRxiv : the preprint server for biology · 2025Article
- Mechanistic basis for the opposing effects of H2A and H2B ubiquitination on nucleosome stability and dynamics.Epigenetics & chromatin · 2025Article
- A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements.bioRxiv : the preprint server for biology · 2025Article
- Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation.DNA and cell biology · 2025Review
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- Regulation of Genome Architecture in Huntington's Disease.Biochemistry · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- SIRT1 retention in elongating spermatids interferes with histone displacement by counteracting MOF-dependent H4K16 acetylation.Frontiers in cell and developmental biology · 2025Article
- Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model.bioRxiv : the preprint server for biology · 2024Article
- Advanced environmental scanning electron microscopy reveals natural surface nano-morphology of condensed mitotic chromosomes in their native state.Scientific reports · 2024Article
- Nucleosome spacing controls chromatin spatial structure and accessibility.Biophysical journal · 2024Article
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Authors and funding
6 authors.
Funding
Abstract
Nucleosomes cluster together when chromatin folds in the cell to form heterogeneous groups termed "clutches". These structural units add another level of chromatin regulation, for example during cell differentiation. Yet, the mechanisms that regulate their size and compaction remain obscure. Here, using our chromatin mesoscale model, we dissect clutch patterns in fibers with different combinations of nucleosome positions, linker histone density, and acetylation levels to investigate their role in clutch regulation. First, we isolate the effect of each chromatin parameter by studying systems with regular nucleosome spacing; second, we design systems with naturally-occurring linker lengths that fold onto specific clutch patterns; third, we model gene-encoding fibers to understand how these combined factors contribute to gene structure. Our results show how these chromatin parameters act together to produce different-sized nucleosome clutches. The length of nucleosome free regions (NFRs) profoundly affects clutch size, while the length of linker DNA has a moderate effect. In general, higher linker histone densities produce larger clutches by a chromatin compaction mechanism, while higher acetylation levels produce smaller clutches by a chromatin unfolding mechanism. We also show that it is possible to design fibers with naturally-occurring DNA linkers and NFRs that fold onto specific clutch patterns. Finally, in gene-encoding systems, a complex combination of variables dictates a gene-specific clutch pattern. Together, these results shed light into the mechanisms that regulate nucleosome clutches and suggest a new epigenetic mechanism by which chromatin parameters regulate transcriptional activity via the three-dimensional folded state of the genome at a nucleosome level.
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