Delineating the early transcriptional specification of the mammalian trachea and esophagus

The genome-scale transcriptional programs that specify the mammalian trachea and esophagus are unknown. Though NKX2.1 and SOX2 are hypothesized to be co-repressive master regulators of tracheal and esophageal fates, this is untested at a whole transcriptomic scale and their downstream networks remain unidentified. By combining single cell RNA-sequencing with bulk RNA-sequencing of Nkx2.1 mutants and NKX2.1 ChIP-sequencing in mouse embryos, we delineate the NKX2.1 transcriptional program in trachea and esophagus specification, and reveal a previously unknown NKX2.1-independent transcriptional program. To decouple regulation of the NKX2.1 transcriptional program from regulation by SOX2, we interrogate the expression of our newly-identified tracheal and esophageal markers in Sox2/Nkx2.1 compound mutants. Finally, we discover that NKX2.1 binds directly to Shh and Wnt7b and regulates their expression to control mesenchymal specification to cartilage and smooth muscle, coupling epithelial ide...