Fig. 3: 3D genome organization in islet β and α cell specification.
From: Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A
a Hierarchical genome architecture (compartment, contact domains and DNA Loops) near GCG locus in both α- and β-cells. b Scatterplot comparing the loop strength in α- and β-cells from DeepLoop analysis. Highlighted are the α- (n = 17,131) or β-cell (n = 19,733) specific loops. c The boxplots (median ± upper and lower quartiles) are showing the ATAC (n = 8761) intensity (top) and gene expression (n = 1080) (bottom) for regions with β-cell specific loops (left) and α-cell specific loops (right) (7410 ATAC peaks, and 843 genes). Statistical significance determined via two-sided Wilcox Test. *p-value < 0.05, **p-value < 0.005, ***p-value < 0.0005, upper and lower limits of boxes indicate interquartile ranges, center lines indicate median values, whiskers indicate values with a maximum of 1.5 times the interquartile range and outliers indicate values beyond 1.5 times the interquartile range. d The heatmap for 698 β-cell specifically expressed genes. Rows are categories of specificity. e Similar to (d), the heatmap for 546 α-cell specifically expressed genes. f Examples of β-cell-specific genes associated with β-cell-specific loops. Each locus includes contact heatmaps in α-cell and β-cell (left), the tracks for genes, compartments, ATAC and loop curves (right). g Similar to (f), examples of α-cell-specific genes with α-cell-specific loops.
