Fig. 4: Multi-enhancer hubs captured by single-cell high-resolution 3D genome structures.
a, Contact map of ensemble scMicro-C (top left) and bulk Micro-C (bottom right) at the EBF1 locus, accompanied by ChIP-seq signals of CTCF, H3K27ac, POLR2A and RAD21, and ABC model-predicted enhancers. b, Sorted scMicro-C contact profiles (n = 723) of the EBF1 gene with PES; the 5-kb bins covering the EBF1 TSS were used for this analysis. c, Schematic representation of the promoter and enhancers of the EBF1 gene selected for single-cell 3D genome structure analysis. d, Line plot showing the percentage of single-cell 3D chromatin structures with the proximity of corresponding E–P pairs. Six regions without stripes were used as controls. The dots indicate the median value, and the whiskers of control regions indicate the standard deviation. e, Top row, schematic representation of the E–P loops in each cell (columns). Middle row, representative single-cell 3D structure of the E–P loops. Bottom row, mean 3D distance matrices of single-cell structures, with the depicted loop indicated by a yellow circle. f, Bar plot of the percentage of cells (y axis) that have the indicated number of enhancer interactions with the promoter (x axis) at the EBF1 (blue) or control locus (red). For the EBF1 locus, the number of cells is indicated at the top of each bar. For control regions, the bar indicates the median value, and the error bar indicates the s.d. g, Representative single-cell 3D genome structures forming a multi-enhancer hub (red dashed circles) at EBF1. h, Mean 3D distance matrices measured from single-cell structures with the indicated number of enhancer loci interacting with EBF1 promoter from left to right, respectively. i, Boxplot of the radius of gyration (y-axis) of single-cell 3D genome structures with the indicated number of enhancer loci (x axis—n = 114, n = 66, n = 51, n = 44, n = 28, n = 8 for each group) interacting with the EBF1 promoter. Pairwise statistical tests showed statistical significance (P < 0.05, two-sided Wilcoxon rank sum exact test) for all pairs, except for 1–2 and 3–4. The six-enhancer group was excluded due to an insufficient number of single-cell structures. The centerline indicates the median, the box the 25% and 75% quantiles, and the whiskers the maximum and minimum values. ABC, activity-by-contact.
