Extended Data Fig. 10: Polymer simulation of chromosomes.

a, Six chromosomes (50 Mb each) were initiated in a mitotic-like state with unit volume density. Row 1 and 3 show top views, row 2 and 4 show side views. In rows 1 and 2 six chromosomes are differentially colored; in rows 3 and 4 compartmental segments of A and B type chromatin are differentially colored with red for A and blue for B compartments. The initial expansion is very fast (column 2). However, once the chromosomes fill the nucleus uniformly, the subsequent dynamics is very slow and chromosomes retain their territoriality (note that times increase logarithmically). Nevertheless, due to attraction of B-type chromatin to the lamina, a radial structure emerges (rows 3 and 4). b, TLs are modeled by choosing a 300 kb segment on each chromosome 25.4 minutes after expansion and increasing the stiffness of the polymer fiber. The genes quickly expand on the order of minutes and are simulated for approximately 1.5 h. The measurements of inter-flank distances and Hi-C maps are performed using configurations sampled from the second half of this time interval. When genes are deactivated by removing the excess stiffness, they collapse back to the inactive state. c, Left: Hi-C of all 6 chromosomes shows their territoriality as patches. Second-left: A Hi-C contact map averaged over all 6 chromosomes exhibits the checkerboard pattern of a typical segregation of A- and B-type chromatin. The three rightmost graphs show zoomed views of modeled genes with stiffness profiles above the maps.