Resolution:
## Figure 3.
Comparison between experimental and simulation results of PCNA ubiquitylation dynamics
obtained on wild type yeast cells at 10 J/m^{2} UV dose. The figure shows the experimental measurements on WT yeast cells irradiated at 10
J/m^{2} 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 , together with the respective standard deviation . Colored areas indicate the amplitude of stochastic fluctuations around the mean
value . Data are plotted by using the units representation (see Additional file 5). (D) Comparison between the ratio of experimental (, left bars) and simulated (, 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).
Amara |