Figure 7

Prediction of UV dose-dependent threshold and validation results on wild type yeast cells at 20 J/m² and 30 J/m² UV doses. The figure shows the experimental measurements on WT cells irradiated at 20 J/m² UV dose (top part) and at 30 J/m² UV dose (bottom part), as well as the comparison with the corresponding simulation results. As the aim of these experiments was not to carry out a precise quantification of the PCNA ubiquitylated isoforms, but only to verify the prediction of computational analysis, they were conducted with a single repetition. (A-C) Comparison between the value of western blot quantification $\#{\text{PCNA}}_{\mathit{\text{exp}}}^{{\text{Ub}}_{\text{u}}}$ deriving from a single experiment, and the dynamics of mono-, di- and tri-ubiquitylated PCNA isoforms $\#{\text{PCNA}}_{\mathit{\text{sim}}}^{{\text{Ub}}_{\text{u}}}$ emerging from 100 independent stochastic simulations, executed starting from the same initial conditions (see Table 2 for molecular amounts and Table 3 for reaction constants), with an estimated number of DNA lesions equal to 4005 (A) and 6007 (C). Colored areas indicate the amplitude of stochastic fluctuations around the mean value $\mu \left(\#{\text{PCNA}}_{\mathit{\text{sim}}}^{{\text{Ub}}_{\text{u}}}\right)$. Data are plotted by using the units representation (see Additional file 5). (B-D) Comparison between the ratio of experimental ($÷{\text{PCNA}}_{\mathit{\text{exp}}}^{{\text{Ub}}_{\text{u}}}$, left bars) and simulated ($÷{\text{PCNA}}_{\mathit{\text{sim}}}^{{\text{Ub}}_{\text{u}}}$, right bars) ubiquitylated PCNA isoforms at every sampled time point. Mean and standard deviation bars of simulated results are plotted by using the normalized representation (see Additional file 5).