Fig. 10

Comparison of interactions detected in CHi-C and Hi-C data. a Top panels: plots showing the read counts from bait–other end pairs within 750 kb (upstream and downstream) of three baits, containing the Pax6, Foxo4 and Tbx5 promoters (from left to right). Significant interactions detected by CHiCAGO (score ≥5) are shown in red, and sub-threshold interactions (3 ≤ score < 5) are shown in blue. Bottom panels: raw Hi-C matrices at 25-kb bin resolution within the corresponding 1.5-Mb regions. The bottom corners of the red lines indicate example bin pairs, within which significant interactions were detected in the CHi-C data. b Mapping of short-range (<1 Mb) CHi-C interactions within 25-kb interacting bins detected in the Hi-C data. Filled circles show the observed fraction of CHi-C interactions mapping within the Hi-C interacting bins; open circles show the expected fraction estimated by a permutation strategy accounting for genomic structure (see “Methods” for details). The standard deviations across 100 permutations are not shown as they are smaller than point size. c Mapping of long-range (>1 Mb) CHi-C interactions within 1-Mb interacting bins detected in the Hi-C data. Filled circles show the observed fraction of long-range cis- and trans-chromosomal interactions detected in the CHi-C data that map within the Hi-C interacting bins. Open circles show the expected fraction estimated by a permutation strategy accounting for genomic structure (see “Methods” for details). Error bars show standard deviation across 100 permutations. d The overlap of long-range (>5 Mb) interacting fragment pairs detected in CHi-C data (blue circles) and interacting 1-Mb bin pairs detected in the Hi-C data (black squares) on chromosomes 6 (left) and 11 (centre) and for trans-interactions between these chromosomes (right). All panels present pre-capture mESC Hi-C data from [4]