Fig. 4.

Schematic of active loop extrusion model and simulation snapshots. (A) Chromatin is discretized into loci with size b each representing $z$ base pairs. Cohesin domains bind to locus j and extrude away from one another with average curvilinear velocity $v_{\mathit{ex}}$ in units of the number of base pairs per unit time. Locus i is extruded at the time $t_i=z\left|j-i\right|/v_{\mathit{ex}}$. At time $z\left(\left|j-i\right|+s_{c,i}\right)/v_{\mathit{ex}}>t_i$, locus i is $s_{c,i}=v_{\mathit{ex}}\left(t-t_i\right)$ base pairs away from the cohesin. (B) Snapshots of a hybrid MD—MC simulation of a single active loop extrusion cycle when a single cohesin extrudes a single bead-spring polymer chain once. The snapshots are before extrusion starts with $D\approx 2$ (Left, blue) and after the cohesin reaches the chain ends (Right, green). Each bead represents 1 kbp of chromatin (see SI Appendix for details). The red beads indicate the cohesin binding site.