The nuclear architecture of budding yeast and the mC-SAC model genome.

<p><b>(A)</b> Schematic representation of the nucleus and nuclear landmarks of budding yeast and their corresponding coordinates and dimensions (not to scale). <b>(B)</b> An example 3D structure of mC-SAC genome confined in the cell nucleus. <b>(C)</b> Correlation between genome-wide chromatin conformation capture interaction frequencies and interaction frequencies measured from the fully-constrained ensemble of model yeast genomes. <b>(D)</b> Heat map of interaction frequencies measured in the fully-constrained ensemble. Darker color indicates higher interaction frequency. <b>(E)</b> Heat map of interaction frequencies from the experimental measurements [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005658#pcbi.1005658.ref016" target="_blank">16</a>]. <b>(F)</b> Heat map of simulated interactions from the fully-constrained ensemble, with only interactions between restriction fragments of the genome-wide 3C experiment [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005658#pcbi.1005658.ref016" target="_blank">16</a>] are shown for direct comparison. <b>(G)</b> Heat map of interaction frequencies of the fully-constrained ensemble that are corrected after removal of expected interaction frequencies obtained from an ensemble generated using only nuclear confinement and excluded-volume as constraints. <b>(H)</b> Heat map of interaction frequencies of the genome-wide 3C experiments that are corrected after removal of expected interaction frequencies. <b>(I)</b> Correlation of interaction frequencies between genome-wide 3C data and from the fully-constrained ensemble, after removal of expected interactions as obtained from an ensemble generated using only nuclear confinement and excluded-volume as constraints.