Figure 2. Characterization of the IMR90 chromatin interactome.

a, Histogram showing the size distribution of all HindIII restriction fragments in human genome. The red curve plots the size distribution of all anchors used in this study. b, Size distribution of the genomic regions identified as interacting with all anchors. c, Distribution of genomic spans of all identified chromatin interactions. Histogram: frequency distribution; Red curve: cumulative fraction with increasing distances. d, Fraction of chromatin looping interactions that fall within the same topological domains is plotted as a function of genomic distance between the two interacting loci (red curve). Black curve: expected fraction calculated from random shuffling locations of topological domains (100 iterations, dashed error lines: s.d.). e, Average number of peaks identified for anchors with different cis-elements. f, Percentages of all interactions involving various types of cis-elements (either anchor or target peak has the elements). In e–f, Z-scores were calculated comparing the actual values to simulation by randomly shuffling the locations of cis-elements (100 iterations, two-side Z-test). * Z > 50, ** Z > 100, *** Z > 150. g, Box plot showing the distance distribution from different types of anchors to their targets. Median distances are also labeled. t-statistics are computed comparing log-transformed distance between each type of anchors to all anchors as control (dash horizontal line). * t > 20, ** t > 40, *** t > 80 (two-side t-test). h, Preferential interactions between different types of cis-elements. Heatmap shows the fold enrichment of different type of pair-wise combinations. p-values are computed using hypergeometric test and denoted in each cell.