Figure 4.

Role of nucleation in establishing and maintenance of epigenetic spreading for Scheme II in the SS regime. (Left) The state of each nucleosome in a trajectory, $⟨s_i⟩$ (Eq. 2 in section “methods”). The trajectory is divided into three parts with distinct simulation conditions, whose transition is marked by two horizontal lines. Initially, the simulation starts with the NS present. Subsequently, the NS is removed (marked by a red horizontal line). After removing the NS, a new steady state is achieved. Thereafter, we introduce DNA replication (marked by magenta horizontal line) by stochastically replacing approximately 50% of M marks with U marks, mimicking equal redistribution of parent histones to both strands upon replication. Replications are repeated every 150.6τ_r. (Right) The presence of epigenetic domains provided the fraction of trajectory in the marked state for each locus is > 0.5. The red curve is computed from the trajectory between the NS removal and DNA replication. The magenta curve is computed from the trajectory after the DNA replication. The horizontal dotted red line represents the 50% mark. k⁺/k⁻ = 10,000 and $k^{+}=0.01/{\tau }_r$. To see this figure in color, go online.