ArticleProceedings of the National Academy of Sciences of the United States of America2020
Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 47 citations in OpenAlex.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells.Science advances · 2026Article
- Linker histone H1 represses H3 tail acetylation induced by H4 tail acetylation and alters its dynamics.Communications biology · 2026Article
- Recent advances in machine learning and coarse-grained potentials for biomolecular simulations.Biophysical journal · 2026Review
- Dynamic networks of intrinsically disordered regions in nuclear proteins.Biophysics and physicobiology · 2026Article
- Article
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.bioRxiv : the preprint server for biology · 2025Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Interplay of chromatin organization and mechanics of the cell nucleus.Biophysical journal · 2024Article
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy.Nucleic acids research · 2024Article
- Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes.PLoS computational biology · 2023Article
- Review
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
- Chromatin transitions triggered by LH density as epigenetic regulators of the genome.Nucleic acids research · 2022Article
- On the stability and layered organization of protein-DNA condensates.Biophysical journal · 2022Article
- Stripenn detects architectural stripes from chromatin conformation data using computer vision.Nature communications · 2022Article
- Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein.Nature chemistry · 2022Article
- RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins.PLoS computational biology · 2022Article
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Authors and funding
6 authors at 3 institutions in 4 countries.
Funding
Abstract
Protein flexibility and disorder is emerging as a crucial modulator of chromatin structure. Histone tail disorder enables transient binding of different molecules to the nucleosomes, thereby promoting heterogeneous and dynamic internucleosome interactions and making possible recruitment of a wide-range of regulatory and remodeling proteins. On the basis of extensive multiscale modeling we reveal the importance of linker histone H1 protein disorder for chromatin hierarchical looping. Our multiscale approach bridges microsecond-long bias-exchange metadynamics molecular dynamics simulations of atomistic 211-bp nucleosomes with coarse-grained Monte Carlo simulations of 100-nucleosome systems. We show that the long C-terminal domain (CTD) of H1-a ubiquitous nucleosome-binding protein-remains disordered when bound to the nucleosome. Notably, such CTD disorder leads to an asymmetric and dynamical nucleosome conformation that promotes chromatin structural flexibility and establishes long-range hierarchical loops. Furthermore, the degree of condensation and flexibility of H1 can be fine-tuned, explaining chromosomal differences of interphase versus metaphase states that correspond to partial and hyperphosphorylated H1, respectively. This important role of H1 protein disorder in large-scale chromatin organization has a wide range of biological implications.
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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.