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Though NKX2-1 and SOX2 are hypothesized to be co-repressive master regulators of tracheoesophageal 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 tracheoesophageal specification, and discover that the majority of the tracheal and esophageal transcriptome is NKX2-1 independent. To decouple the NKX2-1 transcriptional program from regulation by SOX2, we interrogate the expression of 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 identity with mesenchymal specification. These findings create a new framework for understanding early tracheoesophageal fate specification at the genome-wide level.<\/jats:p>","DOI":"10.7554\/elife.55526","type":"journal-article","created":{"date-parts":[[2020,6,8]],"date-time":"2020-06-08T20:00:19Z","timestamp":1591646419000},"source":"Crossref","is-referenced-by-count":38,"title":["Delineating the early transcriptional specification of the mammalian trachea and esophagus"],"prefix":"10.7554","volume":"9","author":[{"given":"Akela","family":"Kuwahara","sequence":"first","affiliation":[{"name":"Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States"},{"name":"Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States"},{"name":"Institute for Human Genetics, University of California San Francisco, San Francisco, United States"},{"name":"Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of 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