Figure 4.
Switching promotes intra-TAD contacts, but suppresses inter-TAD ones. (A) Overview: Simulations involved N = 2000 nonswitching (α = 0) or N = 2000 switching proteins (α = 0.0001 inverse Brownian times); for α = 0, half of the proteins are binding. In both cases, interaction energy and cutoff values were 4 kBT and 1.8σ. The fiber (length 15 Mbp) consisted of regularly interspersed segments containing runs of binding (blue) and nonbinding (black) beads (segment sizes 1.2 Mbp and 300 kbp, respectively). (B and C) Snapshots taken after 105 simulation units. Nonbinding (gray) and binding (red) proteins are shown. (D) Contact maps (averages from 10 simulations) for nonswitching (top-left triangle), and switching proteins (lower-right triangle). The scale (right) indicates contact frequencies. (E) The evolution of the ratio of nonlocal contacts over time. A local (nonlocal) contact is one between beads separated by less (more) than 1.2 Mbp along the fiber. Here the simulation was run for 105 simulation units with nonswitching proteins; switching was then turned on (α = 0.0001 inverse Brownian times) and the simulation was run for a further 105 simulation units. To see this figure in color, go online.