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CG modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability
Stockholm University, Faculty of Science, Department of Physics. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0002-9390-5719
Number of Authors: 42025 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 162, no 2, article id 024101Article in journal (Refereed) Published
Abstract [en]

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. The internal structure of compacted nucleosome arrays is regulated by the flexible and dynamic histone N-terminal tails. Since DNA is a highly negatively charged polyelectrolyte, electrostatic forces make a decisive contribution to chromatin formation and require the histones, particularly histone tails, to carry a significant positive charge. This also results in an essential role of mobile cations of the cytoplasm (K+, Na+, Mg2+) in regulating electrostatic interactions. Building on a previously successfully established bottom-up coarse-grained (CG) nucleosome model, we have developed a CG nucleosome array (chromatin fiber) model with the explicit presence of mobile ions and studied its conformational variability as a function of Na+ and Mg2+ ion concentration. With progressively elevated ion concentrations, we identified four main conformational states of nucleosome arrays characterized as extended, flexible, nucleosome-clutched, and globular fibers.

Place, publisher, year, edition, pages
2025. Vol. 162, no 2, article id 024101
National Category
Cell and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-240037DOI: 10.1063/5.0242509ISI: 001394006000013PubMedID: 39774881Scopus ID: 2-s2.0-85214863461OAI: oai:DiVA.org:su-240037DiVA, id: diva2:1941917
Available from: 2025-03-03 Created: 2025-03-03 Last updated: 2025-03-03Bibliographically approved

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Lyubartsev, Alexander P.

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