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Nucleic Acids Research Advance Access originally published online on April 9, 2009
Nucleic Acids Research 2009 37(11):3558-3568; doi:10.1093/nar/gkp219
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Nucleic Acids Research, 2009, Vol. 37, No. 11 3558-3568
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei

S. de Nooijer1,2, J. Wellink1,*, B. Mulder3,4 and T. Bisseling1,2

1Laboratory for Molecular Biology, Wageningen University, Drovendaalsesteeg 1, 6708PB Wageningen, 2Netherlands Consortium for Systems Biology, P.O. Box 93035, 2509 AA The Hague, 3Laboratory of Plant Cell Biology, Wageningen University, Arboretumlaan 4, 6703BD Wageningen and 4FOM Institute for Atomic and Molecular Physics, Kruislaan 407, Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 (0)317 483266; Fax: +31 (0)317 418094; Email: joan.wellink{at}wur.nl

Received March 1, 2009. Revised March 10, 2009. Accepted March 20, 2009.

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.


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