Fig. 6: Computer simulations of a polymer model showing that both intra- and extra-chromosomal interactions are required to establish the observed features of chromatin organization.

The simulated polymer contained 50 monomers representing the 50 TADs in Chr19. The monomers were assigned epigenetic scores based on the compartment scores of TADs in hepatocytes. a–c Simulations with only intra-chromosomal interactions between compartment-B TADs (B–B interaction). d–f Simulations with interactions between compartment-B TADs and interactions between compartment-A TADs (A–A interaction). g–i Simulations with A–A and B–B interactions as well as additional interactions of A/B TADs with extra-chromosomal components when the TADs were located at the chromosome surface (A–S and B–S interactions). a, d, g Traces of individual polymer conformations generated by the simulations. Red: compartment-A TADs. Blue: compartment-B TADs. b, e, h Polarization indices of the simulated chromosomes and the randomization controls. Dots, lines and boxes are defined as in Fig. 3e. Observation medians = 0.24 (b), 0.63 (e), 0.87 (h). Control medians = 0.36 (b), 0.39 (e), 0.32 (h). Data from 100 simulated chromosomes were used to generate each observation and control group in (b, e, h). c, f, i Chromosome surface ratios of TADs in the simulated chromosomes versus the compartment scores. Correlation coefficients were calculated for compartment-B TADs (blue) and compartment-A TADs (red) separately. The p values were calculated for Pearson’s correlation using a two-sided Student’s t distribution. No adjustment was made for multiple comparisons. Source data are provided as a Source data file.