Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefits the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors. They act as multi-subunit complexes one of which tri-methylates histone H3 at Lysine 27 (H3K27). Here we describe a novel Monte Carlo-Molecular Dynamics simulation framework, which we employed to discover that stochastic interaction of Polycomb Repressive Complex 1 (PRC1) with tri-methylated H3K27 is sufficient to fold the methylated chromatin. Unexpectedly, such chromatin folding leads to spatial clustering of the DNA elements bound by PRC1. Our results provide further insight into mechanisms of epigenetic repression and the process of chromatin folding in response to histone methylation.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10470199 | PMC |
| http://dx.doi.org/10.1016/j.jbc.2023.105080 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Thermodynamics of nucleosome breathing and positioning.
J Chem Phys
January 2025
Department of Physics and Astronomy and Center for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
Nucleosomes are fundamental units of chromatin in which a length of genomic DNA is wrapped around a histone octamer spool in a left-handed superhelix. Large-scale nucleosome maps show a wide distribution of DNA wrapping lengths, which in some cases are tens of base pairs (bp) shorter than the 147 bp canonical wrapping length observed in nucleosome crystal structures. Here, we develop a thermodynamic model that assumes a constant free energy cost of unwrapping a nucleosomal bp.
View Article and Find Full Text PDFCG modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability.
J Chem Phys
January 2025
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
Eukaryotic DNA is packaged in the cell nucleus into chromatin, composed of arrays of DNA-histone protein octamer complexes, the nucleosomes. Over the past decade, it has become clear that chromatin structure in vivo is not a hierarchy of well-organized folded nucleosome fibers but displays considerable conformational variability and heterogeneity. In vitro and in vivo studies, as well as computational modeling, have revealed that attractive nucleosome-nucleosome interaction with an essential role of nucleosome stacking defines chromatin compaction.
View Article and Find Full Text PDFBisphenol A exposure during gestation and lactation in mice: sex-specific consequences on oligodendrocytes and myelination.
Toxicology
December 2024
Université Paris Cité, Inserm, HERA Team, CRESS UMR 1153, F-75006 Paris, France. Electronic address:
Bisphenol A (BPA), a ubiquitous environmental endocrine disruptor, is suspected of disturbing brain development through largely unknown cellular and molecular mechanisms. In the central nervous system, oligodendrocytes are responsible for forming myelin sheaths, which enhance the propagation of action potentials along axons. Disruption of axon myelination can have lifelong consequences, making oligodendrocyte differentiation and myelination critical stages of brain development.
View Article and Find Full Text PDFA constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa.
BMC Genomics
December 2024
Department of Chemistry & Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
Background: Organization of the eukaryotic genome is essential for proper function, including gene expression. In metazoans, chromatin loops and Topologically Associated Domains (TADs) organize genes into transcription factories, while chromosomes occupy nuclear territories in which silent heterochromatin is compartmentalized at the nuclear periphery and active euchromatin localizes to the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation typified by heterochromatic centromeres and telomeres independently clustering at the nuclear membrane, while interspersed heterochromatic loci aggregate across Megabases of linear genomic distance to loop chromatin in TAD-like structures.
View Article and Find Full Text PDFChromatin folding through nonuniform motorization by responsive motor proteins.
J Chem Phys
December 2024
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA.
Chromatin is partially structured through the effects of biological motors. "Swimming motors" such as RNA polymerases and chromatin remodelers are thought to act differentially on the active parts of the genome and the stored inactive part. By systematically expanding the many-body master equation for chromosomes driven by swimming motors, we show that this nonuniform aspect of motorization leads to heterogeneously folded conformations, thereby contributing to chromosome compartmentalization.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!