Mitotic and interphase configurations of the model system chromosomes.

<p>(A) Initial mitotic-like arrangement, constituted by 6 copies of model human chromosome 19. Following ref. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003019#pcbi.1003019-Rosa1" target="_blank">[21]</a>, the chromatin fiber is helicoidally arranged into loops of each, and departing radially from a central axis. The six solenoidal arrangements were next placed in a random, but non-overlapping manner inside a cubic simulation box of side equal to and with periodic boundary conditions. (B) Chromosome spatial arrangement after short relaxation with a standard push-off protocol of MD time steps (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003019#s4" target="_blank">Materials and Methods</a>). (C) Interphase-like configuration obtained by evolving the initial mitotic configuration for MD time steps (approximately corresponding to hours in “real-time” <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003019#pcbi.1003019-Rosa1" target="_blank">[21]</a>). (<i>Inset</i>) The corresponding contact probabilities between <i>loci</i> of model interphase chromosomes decay as a power law of the genomic distance, , consistent with recent experimental observations <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003019#pcbi.1003019-LiebermanAiden1" target="_blank">[6]</a>,<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003019#pcbi.1003019-Rosa2" target="_blank">[29]</a>. In all panels, chromosome regions involved in the coregulatory network are highlighted in red.