TY - JOUR TI - PI3K signaling specifies proximal-distal fate by driving a developmental gene regulatory network in SOX9+ mouse lung progenitors AU - Khattar, Divya AU - Fernandes, Sharlene AU - Snowball, John AU - Guo, Minzhe AU - Gillen, Matthew C AU - Jain, Suchi Singh AU - Sinner, Debora AU - Zacharias, William AU - Swarr, Daniel T A2 - Morrisey, Edward E VL - 11 PY - 2022 DA - 2022/08/17 SP - e67954 C1 - eLife 2022;11:e67954 DO - 10.7554/eLife.67954 UR - https://doi.org/10.7554/eLife.67954 AB - The tips of the developing respiratory buds are home to important progenitor cells marked by the expression of SOX9 and ID2. Early in embryonic development (prior to E13.5), SOX9+progenitors are multipotent, generating both airway and alveolar epithelium, but are selective progenitors of alveolar epithelial cells later in development. Transcription factors, including Sox9, Etv5, Irx, Mycn, and Foxp1/2 interact in complex gene regulatory networks to control proliferation and differentiation of SOX9+progenitors. Molecular mechanisms by which these transcription factors and other signaling pathways control chromatin state to establish and maintain cell-type identity are not well-defined. Herein, we analyze paired gene expression (RNA-Seq) and chromatin accessibility (ATAC-Seq) data from SOX9+ epithelial progenitor cells (EPCs) during embryonic development in Mus musculus. Widespread changes in chromatin accessibility were observed between E11.5 and E16.5, particularly at distal cis-regulatory elements (e.g. enhancers). Gene regulatory network (GRN) inference identified a common SOX9+ progenitor GRN, implicating phosphoinositide 3-kinase (PI3K) signaling in the developmental regulation of SOX9+ progenitor cells. Consistent with this model, conditional ablation of PI3K signaling in the developing lung epithelium in mouse resulted in an expansion of the SOX9+ EPC population and impaired airway epithelial cell differentiation. These data demonstrate that PI3K signaling is required for epithelial patterning during lung organogenesis, and emphasize the combinatorial power of paired RNA and ATAC seq in defining regulatory networks in development. KW - chromatin accessibility KW - lung development KW - ATAC-Seq KW - lung distal tip progenitor cells KW - epigenomics JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -