51. How enzymatic activity is involved in chromatin organization
- Author
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Rakesh Das, Takahiro Sakaue, GV Shivashankar, Jacques Prost, and Tetsuya Hiraiwa
- Subjects
Quantitative Biology - Subcellular Processes ,General Immunology and Microbiology ,Biological Physics (physics.bio-ph) ,General Neuroscience ,FOS: Biological sciences ,Soft Condensed Matter (cond-mat.soft) ,FOS: Physical sciences ,Physics - Biological Physics ,General Medicine ,Condensed Matter - Soft Condensed Matter ,Subcellular Processes (q-bio.SC) ,General Biochemistry, Genetics and Molecular Biology - Abstract
Spatial organization of chromatin plays a critical role in genome regulation. Previously, various types of affinity mediators and enzymes have been attributed to regulate spatial organization of chromatin from a thermodynamics perspective. However, at the mechanistic level, enzymes act in their unique ways and perturb the chromatin. Here, we construct a polymer physics model following the mechanistic scheme of Topoisomerase-II, an enzyme resolving topological constraints of chromatin, and investigate how it affects interphase chromatin organization. Our computer simulations demonstrate Topoisomerase-II's ability to phase separate chromatin into eu- and heterochromatic regions with a characteristic wall-like organization of the euchromatic regions. We realized that the ability of the euchromatic regions to cross each other due to enzymatic activity of Topoisomerase-II induces this phase separation. This realization is based on the physical fact that partial absence of self-avoiding interaction can induce phase separation of a system into its self-avoiding and non-self-avoiding parts, which we reveal using a mean-field argument. Furthermore, motivated from recent experimental observations, we extend our model to a bidisperse setting and show that the characteristic features of the enzymatic activity-driven phase separation survive there. The existence of these robust characteristic features, even under the non-localized action of the enzyme, highlights the critical role of enzymatic activity in chromatin organization., eLife, 11, ISSN:2050-084X
- Published
- 2021
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