Fission yeast genome structures calculation.

<p><b>(A)</b> Schematic view of fission yeast nuclear architecture and imposed geometric constraints. Centromeres are located within a sphere volume of radius 300 nm to ensure that they are close to the SPB. Telomeres are anchored to the NE and can freely move on the NE surface. rDNA genes are constrained to be on the nucleolar surface (right side). All non-rDNA genes are prevented to enter the nucleolus. All chromosomes are confined in a nucleus of radius 0.71 micron. <b>(B)</b> Snapshot of a genome structure illustrating the packing of the chromosomes in the nuclear volume. Different chromosome chains are depicted in different colors. The nucleolus volume is shown in silver. The spindle pole body is shown as a light green cylinder opposite to nucleolus. <b>(C,D,E)</b> Heatmaps of the genome-wide contact frequencies of the fission yeast from calculated structure populations (<b>C</b>), from experiment (<b>D</b>), and from a random control model with no geometric constraints applied (<b>E</b>). The resolution of the heatmaps is 96 kb per bin (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119672#pone.0119672.s001" target="_blank">S1 Text</a>). The color code ranges from white to red to represent frequencies from low to high. The telomere-telomere interactions are highlighted in a zoom-in box <b>(F)</b> Pearson correlation between contact frequency heat maps from experiment and structure populations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119672#pone.0119672.s001" target="_blank">S1 Text</a>). Correlation values are shown for intra-chromosomal and inter-chromosomal interactions separately. The experimental heat map is compared to several different structure populations generated with different amount of geometric constraints. Values for models C, R, N indicate structure populations that were generated only with centromeric constraints (C), rDNA constraints (R) and telomere anchoring constraints (N), respectively (Methods).