Nucleic Acids Research Advance Access originally published online on September 2, 2009
Nucleic Acids Research 2009 37(19):6316-6322; doi:10.1093/nar/gkp702
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Nucleic Acids Research, 2009, Vol. 37, No. 19 6316-6322
© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Topological origins of chromosomal territories
Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Switzerland
*To whom correspondence should be addressed. Tel: +41 21 692 4282; Fax: +41 21 692 4105; Email: andrzej.stasiak{at}unil.ch
Received July 1, 2009. Revised August 5, 2009. Accepted August 9, 2009.
Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.