ArticleCell reports2021
Mesoscale Modeling and Single-Nucleosome Tracking Reveal Remodeling of Clutch Folding and Dynamics in Stem Cell Differentiation.
Article in Cell reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 79 citations in OpenAlex.
- BLeaching In-cell Single-molecule burstS (BLISS) reveals a small dynamic fraction of HP1α clusters in undifferentiated embryonic stem cells.bioRxiv : the preprint server for biology · 2026Article
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- The influence of 10n and 10n+5 linker lengths on chromatin fiber topologies explored by mesoscale modeling.Biophysical journal · 2026Article
- Chromatin higher-order folding as influenced by preferred values of linker DNA.Current opinion in structural biology · 2025Review
- 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
- Deep learning in chromatin organization: from super-resolution microscopy to clinical applications.Cellular and molecular life sciences : CMLS · 2025Review
- 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
- Single nucleosome imaging reveals principles of transient multiscale chromatin reorganization triggered by histone ADP-ribosylation at DNA lesions.Nature communications · 2025Article
- 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
- Transcription dynamics and genome organization in the mammalian nucleus: Recent advances.Molecular cell · 2025Review
- Article
- Understanding and Simulating the Dynamics of a Polymer-Like Chromatin.Methods in molecular biology (Clifton, N.J.) · 2025Review
- The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition.Nucleic acids research · 2024Article
- YAP condensates are highly organized hubs.iScience · 2024Article
- Microscopy methods to visualize nuclear organization in biomechanical studies.Current opinion in biomedical engineering · 2024Article
- Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization.Nature communications · 2024Article
- Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment.Nature communications · 2024Article
- A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features.Nature machine intelligence · 2024Article
- Interplay between stochastic enzyme activity and microtubule stability drives detyrosination enrichment on microtubule subsets.Current biology : CB · 2023Article
Corrections and comments
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Authors and funding
11 authors at 6 institutions in 4 countries.
Funding
Abstract
Nucleosomes form heterogeneous groups in vivo, named clutches. Clutches are smaller and less dense in mouse embryonic stem cells (ESCs) compared to neural progenitor cells (NPCs). Using coarse-grained modeling of the pluripotency Pou5f1 gene, we show that the genome-wide clutch differences between ESCs and NPCs can be reproduced at a single gene locus. Larger clutch formation in NPCs is associated with changes in the compaction and internucleosome contact probability of the Pou5f1 fiber. Using single-molecule tracking (SMT), we further show that the core histone protein H2B is dynamic, and its local mobility relates to the structural features of the chromatin fiber. H2B is less stable and explores larger areas in ESCs compared to NPCs. The amount of linker histone H1 critically affects local H2B dynamics. Our results have important implications for how nucleosome organization and H2B dynamics contribute to regulate gene activity and cell identity.
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