Fig. 5. The impact of demethylation.
(A) Optimization of base methylation probability (kb) and demethylation probability (kD) parameters. The heatmap shows the sums of absolute differences between the mean fractions of H3K27me0, H3K27me1, H3K27me2, and H3K27me3 forecasted by the model and those measured by mass spectrometry in S2 and Kc cells for different combinations of kb and kD and S3 = 3.5. It indicates that parameter setting kb = 0.625 × 10−4 and kD = 0 (marked with dashed white box) result in predictions most closely resembling the experimental measurements (33). The fractions of variously methylated H3K27 positions predicted by the model were calculated based on 10 inspection rounds from 1000 parallel simulations. (B) The dynamics of H3K27 methylation states over time in a representative simulation with optimal parameters (S3 = 3.5, kb = 0.625 × 10−4, and kD = 0) after the replication ceased to happen.