TY - JOUR TI - Delineating the early transcriptional specification of the mammalian trachea and esophagus AU - Kuwahara, Akela AU - Lewis, Ace E AU - Coombes, Coohleen AU - Leung, Fang-Shiuan AU - Percharde, Michelle AU - Bush, Jeffrey O A2 - Horsley, Valerie A2 - Morrisey, Edward E VL - 9 PY - 2020 DA - 2020/06/09 SP - e55526 C1 - eLife 2020;9:e55526 DO - 10.7554/eLife.55526 UR - https://doi.org/10.7554/eLife.55526 AB - 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 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. KW - trachea KW - esophagus KW - Nkx2-1 KW - Sox2 KW - tracheoesophageal fistula KW - lung JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -