Fig. 3: Trans- and cis-regulatory dynamics of skeletogenic convergence across three embryonic lineages.

tSNE representations of single-cell transcriptomes and co-embedded single-cell chromatin accessibilities (insets) for nasal (a), somite (b), and limb (c) origins. Superimposed on the single-cell transcriptomes are the pseudotime trajectories identified by slingshot, with the chondrogenic trajectories used for further analyses highlighted in red. Pseudotime progression is visualized by heatmaps on scRNA and scATAC data. '‘Fine'’ cluster annotations as in Fig. 1, with EC clusters highlighted in red. d–l Binned pseudobulk dynamics along chondrogenic pseudotime trajectories. d–f Z-score scaled expression dynamics along the chondrogenic pseudotime trajectories for chondrogenic modules (red) and common differentially expressed genes identified in all three embryonic origins (black). g–i Log-transformed expression dynamics of embryonic origin-specific transcription factors identified in nasal (magenta dotted line), somite (blue dotted line), and limb (yellow dotted line) samples. j–l Average normalized peak accessibility dynamics of embryonic origin-specific differentially accessible peaks (DAPs) identified in nasal (magenta dotted line), somite (blue dotted line), and limb (yellow dotted line) samples. Select DAP-adjacent genes are indicated on the right.