Delineating the early transcriptional specification of the mammalian trachea and esophagus
Akela Kuwahara,
Ace E Lewis,
Coohleen Coombes,
Fang-Shiuan Leung,
Michelle Percharde,
Jeffrey O Bush
Affiliations
Akela Kuwahara
Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, United States; Developmental and Stem Cell Biology Graduate Program, University of California San Francisco, San Francisco, United States
Ace E Lewis
Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, United States
Coohleen Coombes
Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, United States; Department of Biology, San Francisco State University, San Francisco, United States
Fang-Shiuan Leung
Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, United States
Michelle Percharde
MRC London Institute of Medical Sciences (LMS), London, United Kingdom; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
Program in Craniofacial Biology, University of California San Francisco, San Francisco, United States; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, United States
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.
