Fig. 3: Effects of changing the concentrations of histone epigenetic remodelers on chromatin.

a Temporal kymograph of chromosome 19 of A375 cells when the ratio of methylation to acetylation is the same as the initial heterochromatin to euchromatin ratio. The epigenetic domains temporally maintain their genomic extent on the polymer to a large extent (~90% for a single simulation). b With increasing acetylation, the repressed domain sizes decrease, as observed through the simulation snapshots. This finding was further validated through the observed radius of gyration of the chromatin domains in c. For 3 (c), Violin plots show data distribution. The center line marks the median, the box bounds the interquartile range (25th–75th percentile), and the whiskers span the minima and maxima. Asterisks indicate statistical significance based on a two-sided t test: p < 0.05 (*), p < 0.01 (**), p < 0.001 (***), and p < 0.0001 (****). d Kymograph evolution exhibiting euchromatin domains spread out to neighboring genomic regions as the number of acetylated beads increased. About 75% of the regions maintain their epigenetic marks. e The pairwise distance map shows the spatial reconfiguration of the polymer upon acetylation. The lower triangle corresponds to the initial pairwise distance between the polymer beads, and the upper triangle corresponds to the final pairwise distance. Upon acetylation, major decompaction is observed at the boundaries of heterochromatin domains, as shown by the increasing pairwise distance in the green boxes.