Extended Data Fig. 4. Linking gene expression and chromatin accessibility at the single-cell level.
a, Schematic diagram of linked accessible chromatin regions (ACRs) and a gene. An ACR and a gene are “linked” when there is a significant correlation between chromatin accessibility and mRNA expression across individual cells. b, Density plot showing the frequency of linkages at different distances from the transcription start sites (TSSs). c, Heatmap showing the linkage score (Pearson correlation coefficient between ACR count and mRNA expression) for genes that showed at least one significant link in at least one of the infection conditions or Mock. When a gene had multiple links, the maximum linkage score was shown. The sidebar shows the k-mean cluster annotation (the k value was determined by the elbow method). d, Expression of mRNA encoding VSP2, UGT85A1, and MAM1. e,f, Cluster-aggregated chromatin accessibility surrounding CBP60g (e) and AT1G56660 (f). Violin plots on the side show aggregated mRNA expression of each gene. Both genes were highly expressed in a cell-specific manner, but only CPB60g showed correlated (linked) chromatin accessibility patterns. g,h, Top motifs enriched in the promoter regions (2 kb upstream from the TSS) of defense genes (markers of immune-active mesophyll and epidermis clusters 3, 4, 7, 11, and 12) that are linked (g) and not linked (h).