Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model
Fig 3
Relationship between genomic and spatial positions of eight genes.
(A) The correlation between the relative positions of these genes measured by electron microscopy [6] (x-axis) and by fully-constrained ensemble (y-axis). (B) The relationship between the experimentally measured relative spatial positions of the important genes and their distance to the corresponding centromeres. The two locations of genes that correlate poorly are on Chr12 and telomere, which are subject to nucleolus and telomere attachment constraints. (C) The same relationship can be seen from computationally generated fully-constrained ensemble. (D) Heat map of interaction frequencies of Artificial Genome 1 (AG1) with 16 total chromosomes. (E) Heat map of interaction frequencies Artificial Genome 2 (AG2) with 12 total chromosomes. (F) The correlation between the relative position of the genes measured experimentally and measured from AG1 (blue) and AG2(red) ensembles. (G) The relationship between the relative positions of the genes measured from AG1 (blue) and AG2 (red) ensembles and their distances to the corresponding centromeres. The distances of these genes to their corresponding centromeres in artificial nuclei are different from each other and are all different from their corresponding distances in real yeast nuclei, as we assign random genomic coordinates to the centromeres in the artificial nuclei. (H) The correlation between the relative positions of the genes measured by electron microscopy [6] and by “with only centromere” ensemble. (I) The same correlation between the positions measured by electron microscopy [6] and in the “without centromere” ensemble.