ArticleNucleic acids research2021
A critical role for linker DNA in higher-order folding of chromatin fibers.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 41 citations in OpenAlex.
- Multiscale physical effects of CpG methylation on DNA mechanics, nucleosome wrapping, and chromatin condensates.EMBO reports · 2026Article
- Mixing chromatin fibers with different nucleosome repeat lengths changes dynamics of chromatin phase separation.The Journal of biological chemistry · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Quantifying the effect of magnesium ions on nucleosome stability in chromatin fibers.Biophysical journal · 2026Article
- Insights from single-molecule force spectroscopy into chromatin topology.Biophysical reviews · 2026Review
- Direct visualization and tracing of chromatin folding in the Drosophila embryo.The EMBO journal · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Multiscale structure of chromatin condensates explains phase separation and material properties.Science (New York, N.Y.) · 2025Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- Heterogeneity as a feature: unraveling chromatin's role in nuclear mechanics.Nucleus (Austin, Tex.) · 2025Review
- Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture.Science advances · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
- Beyond the mono-nucleosome.Biochemical Society transactions · 2025Review
- Dynamics of nucleosomes and chromatin fibers revealed by single-molecule measurements.BMB reports · 2025Review
- dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility.Briefings in bioinformatics · 2024Article
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin.The EMBO journal · 2024Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleosome-nucleosome interactions drive the folding of nucleosomal arrays into dense chromatin fibers. A better physical account of the folding of chromatin fibers is necessary to understand the role of chromatin in regulating DNA transactions. Here, we studied the unfolding pathway of regular chromatin fibers as a function of single base pair increments in linker length, using both rigid base-pair Monte Carlo simulations and single-molecule force spectroscopy. Both computational and experimental results reveal a periodic variation of the folding energies due to the limited flexibility of the linker DNA. We show that twist is more restrictive for nucleosome stacking than bend, and find the most stable stacking interactions for linker lengths of multiples of 10 bp. We analyzed nucleosomes stacking in both 1- and 2-start topologies and show that stacking preferences are determined by the length of the linker DNA. Moreover, we present evidence that the sequence of the linker DNA also modulates nucleosome stacking and that the effect of the deletion of the H4 tail depends on the linker length. Importantly, these results imply that nucleosome positioning in vivo not only affects the phasing of nucleosomes relative to DNA but also directs the higher-order structure of chromatin.
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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.