Fig. 6: Polymer simulations with sparse extruders recapitulate enhanced search time and moderate compaction.

A Procedure of simulation. B Schematic representation of chromatin chain looped by extruders, and the corresponding 1D arch diagram for a dense loop conformation (top) and sparse conformation (bottom). The average separation between loops d and loop size λ are depicted. Average search time (C) and distance (D) between two monomers separated by 360 kb (corresponding to the genomic separation of pair 4) with loop extrusion at v = 2 kb s⁻¹, shown for different values of loop size λ and loop separation d. Dashed lines indicate the experimentally measured search times in cells with condensin (−IAA, green) and without condensin (+IAA, gray), with shaded regions representing the corresponding 1.5 times the experimental error bars reported in Fig. 3. E The same simulation results as in (C, D), but with dot distance plotted against search time. Simulations where both the dot distance and search time fall within 1.5 times the experimental error are annotated. CFT (F) and average distance (G) for simulated trans pairs with best matching extrusion parameters. H Simulated contact frequency as a function of genomic distance with extrusion that matched experimental data (orange, green, purple) and without extrusion (red). I Ratio of simulated contact frequency (−extrusion divided by +extrusion) using the same parameters as in (H).