Extended Figure 2. Three replicates of Hi-C analysis of G1 cells without and with IAA treatment.

(a) Hi-C interaction maps for three independent Hi-C experiments using G1-sorted cells treated with IAA as shown. Data for the 29–34 Mb regions of chromosome 14 is shown. (b) Insulation profiles for the same region as in (a). The blue, grey and red lines represent 0, 2 and 6hour IAA treatments, respectively. Blue arrow shows weakened insulation at boundaries (c). Aggregate Hi-C data at TAD boundaries that were identified in each replicate without IAA treatments. The numbers at the sides of the cross indicate the strength of boundary-anchored stripes using the mean values of interaction frequency within the white dashed boxes. (d). Aggregated Hi-C data at a set of 3169 loops identified in HCT116-RAD21-mAC cells with intact RAD21 identified by22. Plots at the bottom show average Hi-C signals along the dotted blue lines representing signals from the bottom-left corner to the top-right corner of the loop aggregated heatmaps shown in upper panels. (e). P(s) plots (upper panels) and derivative from P(s) plots (lower panels) for Hi-C data as indicated. The arrows on the derivative plots indicate cohesin loops. (f). Hi-C interaction maps for three independent Hi-C experiments using G1-sorted cells treated with IAA as shown. Data for the 18–107.3 Mb regions of chromosome 14 is shown. (g). E1 across the same region as in (f). Bottom panels, E1 for the 77.4-89Mb region is shown and the color assignments for the lines are the same as for the other panels. (h). Saddle plots for three independent Hi-C experiments using G1-sorted cells treated with IAA as shown. Saddle plots for each cell condition were calculated using the E1 calculated from the Hi-C data obtained with G1 cells grown without IAA treatments. The numbers indicate compartment strength.