Fig. 5: Lineage-specific enhancer-promoter interactions of core chondrogenic genes.

a-c hkmeans-clustered peak-to-gene link heatmaps displaying Z-score normalized peak accessibilities (left, ocher) and imputed target gene expression levels (right, gray) in single cells (columns). Cell clusters dominated by EC cells are highlighted in red (top). The top 40 peak-to-gene links are shown. Total numbers of identified peak-to-gene links per cluster are indicated by barplots on the right, cluster numbers (kX) on the left. d Venn diagram displaying the overlap of mesenchymal peak-to-gene link CREs across embryonic origins (top) and the overlap of target genes contained within these peak-to-gene links (bottom). e Average evolutionary conservation (calculated as phastCons scores) across CREs in peak-to-gene links shared amongst all embryonic origins (n = 40), shared by more than one embryonic origin (n = 886), and that are origin-specific ones (nasal n = 4396, somite n = 8452, and limb n = 6975). Boxplot center line = median, box limits = quartiles, and whiskers = 1.5× inter-quartile range. f Hierarchically clustered peak-to-gene link correlation heatmap of links identified at core chondrogenic genes across embryonic origins. Select target genes are indicated on the right.