PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiations and Function [ATAC-seq]

Differential chromatin accessibility accompanies and mediates transcriptional control of diverse cell fates and their differentiation during embryogenesis. While the critical role of NKX2-1 and its transcritional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape to regulate NKX2-1 activites required for alveolar epithelial cell differentiation and function are not well understood. Herein, we demonstrate that the paird domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility required for NKX2-1 mediated AT1 and AT2 cell differentiation decisions during lung morphogenesis and for control of the induction of AT@ cell gene expression controlling alveolar function and ventilation at birth. PRDM3 and 16 were required for activation of AT2 cell-associated gene expression, enhancing chromatin accessibility at NKX2-1 transcriptional targets. NKX2-1, PRDM3, and PRDM16 bound together at cis-active DNA elements in AT2 and AT1 cell selective transcriptional target genes, including those critical for perinatal AT2 cell differentitaion, surfactant homeostasis, and innate host defense. Deletion of PRDM3/16 inhibited NKX2-1-dependent gene regulatory networks controlling surfactant lipid and protein production, resulting in respiratory failure at birth. NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by PRDM3/16. Overall design: Floxed alleles of Prdm16 and Prdm3 were knocked out using the sonic hedgehog CRE transgene. Lungs were harvested from fetal mice at E17.5 and EpCAM+ lung epithelial cells were isolated with microbeads. We investigated differential changes in chromatin accessibility between control mice and those lacking functional Prdm16 and Prdm3 genes in EpCAM+ sorted lung epithelial cells at the E17.5 timepoint.