%0 Figure %A Gong, Ke %A Tjong, Harianto %A Jasmine Zhou, Xianghong %A Alber, Frank %D 2015 %T Assessment of the structure population with independent experimental data not included as the input information in the calculations. %U https://plos.figshare.com/articles/figure/_Assessment_of_the_structure_population_with_independent_experimental_data_not_included_as_the_input_information_in_the_calculations_/1351083 %R 10.1371/journal.pone.0119672.g002 %2 https://ndownloader.figshare.com/files/1982600 %K chromosome %K fission yeast genome %K Comparative 3 D Genome Structure Analysis %K yeast genome structures %K location %K 3 D %K chromatin interaction patterns %K gene %X

(A) Mean 3D distances for 18 pairs of loci calculated from structure population and determined by independent 3D FISH experiments (R2 = 0.77)[23]. 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) Histogram of the distance distribution between locus chr2 (3094994bp to 3116383bp) and locus chr3 (1404306bp to 1441994bp) in the structure population and FISH experiments [23]. The correlation between the two histograms is calculated as the correlation of the pairwise frequency values between experiment and structure population, rC = 0.93 (p-value<1E-8). (C) 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. (D) Combined localization probability density (LPD) plot for the 2D distribution of all tRNA sites in fission yeast from our structure population (S1 Text). 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. (E) 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).

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