Extended Data Fig. 1: Enhancer capture Hi-C identifies enhancer-centric chromatin interactions in mouse embryonic tissues.

a, Unique on-target read counts for each library. The percentages above indicate the capture rates for each library. b, c, Principal component analysis and hierarchical clustering of all replicates based on the presence of peaks called by CHiCAGO in each replicate (considering peaks with valid di-tags on neighboring fragments). d, Significant enhancer-centric chromatin interactions identified in this study. The number on each link represents the number of fragments falling into different annotation categories and the width of links is proportional to the percentage (in the parentheses) of different kinds of interactions. Only interactions within 2 Mb are included. CTCF sites with ‘B’: CTCF sites at TAD boundary; Pc: polycomb; Enh: enhancers; Bait-Enh: baited enhancers; Pr: promoters. e, An average number of interactions detected per bait for different kinds of baits (promoter (n = 176), enhancer (n = 935) and negative control elements (n = 87)). Data are represented as mean ± s.e.m. f, Distribution of genomic distances between enhancers and the TSSs of interacting genes (black, frequencies; red, cumulative). g, Violin plots showing read counts on promoters of active genes that interact with enhancer baits (n = 541), promoter baits (n = 126) and control element baits (n = 25). The central horizontal lines are the median, with the boxes extending from the 25th to the 75th percentiles. The whiskers further extend by ±1.5 times the interquartile range from the limits of each box. h, Histogram showing the proportion of bait regions that interact with proximal genes and distal genes. i, Venn diagram showing the overlap between significant interactions called from enhancer baits and corresponding promoter baits. All P values were calculated by a two-sided Wilcox test and adjusted for multiple testing. j, Zoom-in view on Zic1/Zic4 locus for hs654 interaction profiles across 10 tissues. The average size for each pooled fragment is ~3 kb. FB, forebrain. MB, midbrain. HB, hindbrain. CF, face. HR, heart. FL, forelimb. HL, hindlimb. TK, trunk. TL, tail. NT, neural tube.