Assessment of the structure population with independent experimental data not included as the input information in the calculations.

<p><b>(A)</b> Mean 3D distances for 18 pairs of loci calculated from structure population and determined by independent 3D FISH experiments (R<sup>2</sup> = 0.77)[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119672#pone.0119672.ref023" target="_blank">23</a>]. The mean distance between two loci is measured as the average distance between the two corresponding chromosome beads in all structures of the population. <b>(B)</b> Histogram of the distance distribution between locus chr2 (3094994bp to 3116383bp) and locus chr3 (1404306bp to 1441994bp) in the structure population and FISH experiments [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119672#pone.0119672.ref023" target="_blank">23</a>]. The correlation between the two histograms is calculated as the correlation of the pairwise frequency values between experiment and structure population, <i>r</i><sub><i>C</i></sub> = 0.93 (p-value<1E-8). <b>(C)</b> Spatial clustering of Pol-III transcribed genes (p-value < 1E-16 for both tRNA and 5srRNA). The histograms show the distribution of the mean pair distance ratio between a set of specific sites (e.g. Pol-III transcribed sites tRNA sites or 5sRNA sites) and all sites in the structures of the population. The distance ratio histograms are generated as follows: For a given structure in the population the mean pair distance between a set of specific loci (e.g. all early replication origins) is calculated. This distance is divided by the mean pair distance of all sites in the same structure to get a distance ratio. The distribution of the distance ratio is then obtained from all structures in the population. The vertical line represents the expected distance ratio if genes are randomly distributed. <b>(D)</b> Combined localization probability density (LPD) plot for the 2D distribution of all tRNA sites in fission yeast from our structure population (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119672#pone.0119672.s001" target="_blank">S1 Text</a>). The density is represented by the color ranging from blue to red. The plot shows that tRNA genes have the highest density close to SPB region. <b>(E)</b> Enrichment for chromatin—Man1 protein binding. (Left panel) Enrichment of Man1-binding signal from DamID experiments in the 100 beads that show the shortest average distance to the NE in the structure population. (Right panel) Man1-binding enrichment of randomly selected domains. The results show significantly higher Man1 enrichment in beads closest to NE compared to randomly selected beads (p-value<1E-6, Cohen’d = 0.66).</p>