Extended Data Figure 4. Compartment and insulation analysis for chromosome I in wild-type and DC mutant embryos. (see next page.).

a, ICE corrected chromatin interaction maps are shown for wild-type and DC mutant embryos for both 10 kb binned and 50 kb binned data across replicate 1, replicate 2, and the combined replicates. b, Insulation profiles are shown for each biological replicate (replicate 1, orange line; replicate 2, blue line) for 50 kb and 10 kb binned data in wild-type and DC mutant embryos. Insulation profiles are calculated using a 500 kb × 500 kb insulation square (10 bins × 10 bins for the 50 kb binned Hi-C data, and 50 bins × 50 bins for the 10 kb binned Hi-C data). The insulation profiles are consistent across replicates. Green tick marks, TAD boundaries identified using combined replicate data. c, Differential insulation plots derived from the insulation profiles calculated above (50 kb binned and 10 kb binned Hi-C data). d, 50 kb binned heatmap depicting the difference in chromatin interactions expressed as the difference in Z-scores between wild-type and DC mutant. e, Plot showing the compartment analysis calculated using the 50 kb binned wild-type Hi-C data. A/B compartment profile was determined by principle component analysis. First Eigen Vector value representing compartments (black) is plotted along the chromosome, revealing three zones for each autosome: two outer sections and the middle third of the chromosome. Positive Eigen1 signals represent the B (inactive compartment) and negative Eigen1 signals represent the A (active compartment). The compartments at chromosome ends display increased interactions with each other, both in cis and in trans (see Extended Data Fig. 1a). Also shown is the average binding of the lamin-associated protein LEM-2 along the chromosomes (grey). Overall compartmentalization correlates with LEM-2 binding, showing that compartments at both ends of chromosome I are located near the nuclear periphery.