Fig. 3: Cell-type-specific chromatin folding at the TAD-to-chromosome length scale.
From: Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
a Mean spatial distance matrix of the 50 TADs in hepatocytes. b Compartment scores of the 50 TADs in three cell types. c Fold increase of RNA copy number for each gene between each pair of cell types versus the change of compartment score of the gene region between the pair of cell types. Pie chart: Counts of data points with more than three-fold increase of expression. Orange: increase of compartment score. Green: decrease of compartment score. d (Top panel) Schematic illustration of the concept of compartment polarization. (Bottom panel) Spatial positions of compartment-B TADs (blue dots) and compartment-A TADs (red dots) in a copy of Chr19. The chromosome was rotated in space for better visualization of the polarized organization of A/B compartments. e Polarization indices of individual chromosomes in proerythroblasts. Observed values were compared with a randomization control, where we randomized the compartment assignments of TADs while maintaining the number of TADs in each compartment. Each dot corresponds to a single copy of Chr19. Data from 4830 chromosomes were used to generate each observation and control group in e. The red lines represent medians. The boxes show the 25% and 75% quantiles. ***p < 10−307 (two-sided Wilcoxon rank sum test; the exact p value is smaller than the smallest positive double precision floating-point number in MATLAB). Observation minimum, 25% quantile, median, 75% quantile, and maximum equal 0.02, 0.47, 0.59, 0.73, and 1, respectively. Control minimum, 25% quantile, median, 75% quantile, and maximum equal to 0.01, 0.27, 0.33, 0.41, and 1 respectively. Source data are provided as a Source data file.
