Fig 1.
(A) Parts of two different chromosome chains (blue and green). (B) Enlarged view around the the bases of the loops. Condensins (red and purple points) connect the bases of the loops (dashed lines) and attract each other in cis or in trans (dotted lines). The inter-condensin attraction is controlled by two parameters, Fcond and Δ, whereas the looping is controlled by Floop. (C) Example of initial configurations, where two chromosome chains (blue and green) are intermingled with each other. (D) Part of the initial configuration shown in panel C.
Table 1.
The radius of gyration, Rg, asphericity and overlap at initial configuration with each parameter set.
Fig 2.
(A) Asphericity as a function of the strength Fcond and the threshold distance Δ of inter-condensin attractions, with . (B) Asphericity as a function of the loop-holding force Floop under three pairs of different parameters of the attractions. (C) Chromosome monomer density as a function of the distance from condensin at the points D and E shown in panel A. (D–G) Example of the configurations observed at the end of the simulations at each point of D–G shown in panel A. The blue line is the chromosome and the red points are condensins. All simulations are performed employing a single chromosome condition with the number of monomers N = 5000 and the number of loops M = 100.
Fig 3.
(A) Time-course evolution of the asphericity, overlap, and trans-attraction. Configurations of the two chromosomes and distribution of condensins at t = 0.0 (B), 0.2 (C), and 1.0 (D). The blue and green lines represent two different chromosomes. The red and purple points are condensins bound to the blue and green chromosomes, respectively. The corresponding dynamics are shown in S1 Movie. Each chromosome has 5000 monomers and 100 loops. (Fcond, Δ, Floop) = (1.0, 1.0, 1.0).
Fig 4.
(A) Segregation speed as a function of the strength Fcond and threshold distance Δ of inter-condensin attractions. Floop = 1.0. (B) Segregation speed as a function of the loop-holding force Floop under three pairs of different parameters of inter-condensin attractions. (C) Segregation speed and the decay speed of trans-attractions as a function of Δ for Fcond = Floop = 1.0. (D–G) Example of configurations observed at the end of the simulations at each point of D–G shown in panel A. Each chromosome in all simulations has 5000 monomers and 100 loops.
Fig 5.
Correlation between the asphericity and segregation speed for various parameter sets of (Fcond, Δ, Floop).
The red plus symbols are the results for Δ < 2.5 and the blue crosses are the results for Δ > 2.5 (S1 Table in supplementary data for sets of detail parameter values).
Fig 6.
Configuration of chromosomes (blue and green lines) and distribution of condensins (red and purple points) at (Fcond, Δ, Floop) = (1.0, 2.0, 1.0) (A), (1.0, 1.0, 1.0) (B), and (1.0, 2.0, 0.2) (C). (D) Distribution of condensins on the plane perpendicular to the chromosome axis. The distributions are normalized at the origin. The other parameters are fixed to Fcond = Floop = 1.0.
Fig 7.
Schematic of the deterministic loop extrusion process.
The blue monomers and connecting springs represent a chromosome chain, and the red particles represent individual condensins. The arrows represent the time direction. The inset shows a series of processes that cross in a loop.