Extended Data Figure 4. Increasing the resolution of Hi-C analysis increases the number of called TAD boundaries and alignment with replication domain boundaries.
a, Histograms of TAD sizes for original IMR90 calls (bottom, ref. 8) versus calls made using higher resolution IMR90 Hi-C data47 with 40 kb (middle) and 20 kb (top) directionality index bin sizes. b, An example region of the IMR90 replication timing profile (grey) is shown with TTR-present and TTR-absent replication domain boundaries indicated by vertical blue lines. Directionality index plots for each of the Hi-C data sets from panel a are shown across the same region with the 5′ TAD boundaries (start) indicated by solid red lines and the 3′ TAD boundaries (end) indicated by dotted black lines. c, Overlap of TAD boundaries using original or higher resolution data with TTR-present (black) or all (grey) replication domain boundaries (top left) is shown within 175 kb. The reciprocal comparison is shown below. The percentage of replication domain boundaries that overlap with TAD boundaries increases when additional TAD boundaries are identified using higher resolution data, while the percentage of TAD boundaries that overlap with replication domain boundaries is unchanged. The overlap in each case is significant (P < 10−77) relative to overlap with random positions (right).