1. Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei
- Author
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Bela M. Mulder, J. Wellink, S. de Nooijer, and T. Bisseling
- Subjects
Models, Molecular ,architecture ,Nucleolus ,Heterochromatin ,Arabidopsis ,arabidopsis-thaliana ,Biology ,Chromosomes, Plant ,Genetics ,medicine ,Laboratorium voor Moleculaire Biologie ,Computer Simulation ,genome organization ,Interphase ,Cell Nucleus ,EPS-2 ,Computational Biology ,Laboratorium voor Celbiologie ,chromosome territories ,biology.organism_classification ,compartmentalization ,matrix ,Chromatin ,Cell biology ,Cell nucleus ,Laboratory of Cell Biology ,medicine.anatomical_structure ,Chromosome Territory ,cells ,chromatin ,Laboratory of Molecular Biology ,confined polymers ,transcription ,Nucleus ,Cell Nucleolus - Abstract
The organization of the eukaryote nucleus into functional compartments arises by self-organization both through specific protein–protein and protein–DNA interactions and non-specific interactions that lead to entropic effects, such as e.g. depletion attraction. While many specific interactions have so far been demonstrated, the contributions of non-specific interactions are still unclear. We used coarse-grained molecular dynamics simulations of previously published models for Arabidopsis thaliana chromatin organization to show that non-specific interactions can explain the in vivo localization of nucleoli and chromocenters. Also, we quantitatively demonstrate that chromatin looping contributes to the formation of chromosome territories. Our results are consistent with the previously published Rosette model for Arabidopsis chromatin organization and suggest that chromocenter-associated loops play a role in suppressing chromocenter clustering.
- Published
- 2009