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Figure 3 | BMC Systems Biology

Figure 3

From: In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae

Figure 3

Comparison between experimental and simulation results of PCNA ubiquitylation dynamics obtained on wild type yeast cells at 10 J/m2 UV dose. The figure shows the experimental measurements on WT yeast cells irradiated at 10 J/m2 UV dose and the comparison with the corresponding simulation results. (A) Representative image of a western blot showing a time-course measurement of mono-, di- and tri-ubiquitylated PCNA isoforms (top part, denoted by α-Ub) and of non modified PCNA (bottom part, denoted by α-His), sampled from 0 to 5 h after UV irradiation. The experiment was repeated 3 times. (B) Average dynamics of mono-ubiquitylated PCNA (blue line) and of poly-ubiquitylated PCNA (orange line), obtained from 100 independent stochastic simulations, executed starting from the same initial conditions (see Table 2 for molecular amounts and Table 3 for reaction constants) and with an estimated number of DNA lesions equal to 2002. (C) Comparison between the mean dynamics of mono-, di- and tri-ubiquitylated PCNA isoforms emerging from 100 independent stochastic simulations, and the mean value of experimental data μ(# PCNA exp Ub u ), together with the respective standard deviation σ(# PCNA exp Ub u ). Colored areas indicate the amplitude of stochastic fluctuations around the mean value μ(# PCNA sim Ub u ). Data are plotted by using the units representation (see Additional file 5). (D) Comparison between the ratio of experimental (÷ PCNA exp Ub u , left bars) and simulated (÷ PCNA sim Ub u , right bars) ubiquitylated PCNA isoforms at every sampled time point where experimental measurements yield a detectable amount of modified PCNA. Mean and standard deviation bars of both experimental and simulated ratios are plotted by using the normalized representation (see Additional file 5).

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