RNA-seq of mouse mammary basal cells sorted from G0 and G1.

Molecular/cellular events that associate with epithelial-to-mesenchymal transition (EMT) are linked to acquisition of cancer stem cell traits, but whether EMT mechanisms regulate tissue epithelial cell fate and stem cell activity in vivo remains ambiguous. Using single-cell RNA sequencing, we detect heterogeneous EMT gene expression in stem cell-containing mammary basal/myoepithelial cells that normally possess both epithelial and smooth muscle characteristics. We show that EMT-inducing transcription factor Zeb1 is required within the mammary epithelium for ductal branching morphogenesis and regeneration, and that it promotes basal cell fate and regulates stem cell proliferation dynamics. We provide genetic and molecular evidence for EMT-dependent and -independent mechanisms of Zeb1 function, and show that Zeb1 cooperates with YAP to directly activate targets that inhibit Wnt signaling or control cell cycle. Together, our findings underscore Zeb1-mediated EMT control in governing mammary basal cell fate and proliferative activity, but with an interesting turn that involves mechanisms beyond EMT. RNA-seq experiments were performed using mouse mammary basal cells to identify genes that are differentially expressed between G0 and G1.