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Fig. 4 | Genome Biology

Fig. 4

From: Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Fig. 4

Comparing model predictions to static experimental data. This figure compares predictions from our simulation with the parameters P = 69 nm, C = 50 bp/nm, W = 30 nm, L = 400 nm (“best model”, Table 1) to different experimental data. a predicted vs measured distance statistics between pairs of loci (Table 2, observables O1, O3–O7). Each of the 117 dots corresponds to a different pair of loci. Blue circles: distances between telomere 4R and other telomeres [50]; green circles: distances between telomere 10R and other telomeres [50]; red circles: distances between telomere 6R and other telomeres [50]. Blue squares: distances between pairs of loci on chromosome 4. Cyan diamonds: distances between SPB and telomeres [39]. Red diamonds: intrachromosomal distances for pairs of loci on chromosomes 6 and 14 [39]. Black squares: intrachromosomal distances for pairs of loci on chromosomes 4, 5, and 7 [51]. Red squares: distances between loci on chromosome 12 and the nucleolar center [64]. The Pearson correlation coefficient between predictions and measurements is r = 0.96 and the RMS error is 92 nm. b Predicted and measured median 2D distances between 12 pairs of loci on chromosome 4 as function of their genomic separation (in Kb). Diamonds show experimental measurements, solid curves are model predictions. Blue dots are for pairs of loci involving a pericentromeric locus (5 Kb from the centromere). Green and red dots are for pairs of loci involving a locus in the internal region of the chromosome arm (at 854 Kb and 1185 Kb from the centromere, respectively). The solid blue curve shows the predicted distance between the peri-centromeric locus and other loci on the same chromosome arm. The red curve shows the predicted distance between loci in the internal region of the chromosome arm. c Predicted vs. measured median angle (in degrees) between chromatin loci and the line joining the nuclear and nucleolar centers [31, 50]. Each dot corresponds to a single chromatin locus. The Pearson correlation between predictions and measurements is r = 0.92 and the RMS error is 9 degrees. df Genome-wide contact frequency matrices, binned at 30 Kb, as predicted by the model (d) or obtained from Hi-C experiments in [30] (e) and [62] (f). Bright pixels indicate high frequencies, dark pixels indicate low frequencies. A logarithmic scaling was applied to reveal lower frequency contact patterns

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