PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function

Abstract

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 transcriptional targets in lung morphogenesis and pulmonary epithelial cell differentiation is increasingly known, mechanisms by which chromatin accessibility alters the epigenetic landscape and how NKX2-1 interacts with other co-activators required for alveolar epithelial cell differentiation and function are not well understood. Here, we demonstrate that the paired domain zinc finger transcriptional regulators PRDM3 and PRDM16 regulate chromatin accessibility to mediate cell differentiation decisions during lung morphogenesis. Combined deletion ofPrdm3andPrdm16in early lung endoderm caused perinatal lethality due to respiratory failure from loss of AT2 cell function.Prdm3/16deletion led to the accumulation of partially differentiated AT1 cells and loss of AT2 cells. Combination of single cell RNA-seq, bulk ATAC-seq, and CUT&RUN demonstrated that PRDM3 and PRDM16 enhanced chromatin accessibility at NKX2-1 transcriptional targets in peripheral epithelial cells, all three factors binding together at a multitude of cell-type specific cis-active DNA elements. Network analysis demonstrated that PRDM3/16 regulated genes critical for perinatal AT2 cell differentiation, surfactant homeostasis, and innate host defense. Lineage specific deletion of PRDM3/16 in AT2 cells led to lineage infidelity, with PRDM3/16 null cells acquiring partial AT1 fate. Together, these data demonstrate that NKX2-1-dependent regulation of alveolar epithelial cell differentiation is mediated by epigenomic modulation via PRDM3/16.Graphical AbstractModel of the role of PRMD3/16 in alveolar developmentPRMD3/16 participate in cell fate specification in the lung by modulating chromatin accessibility (top row) and by partnering with NKX2-1 and partner transcription factors to drive gene expression (second row) via a gene regulatory network required for terminal cell differentiation and surfactant expression in AT2 cells (third row). Loss of PRDM3/16 activity in lung endoderm leads to reduced AT2 quorum, failure of AT2 surfactant function, and transition to an immature AT1 phenotype (bottom panel).

The homeobox transcription factor Cux1 coordinates postnatal epithelial developmental timing but is dispensable for lung organogenesis and regeneration

“…TRN inferences thus provide a pathway to study specific, complex mechanisms predicted by large scale explorative studies in lung biology. Recent work from our group and others has demonstrated that TRN inference can identify unexpected functions of even well-described transcriptional regulators 11,68 . Fundamentally, however, all TRN inferences generate predictions that require functional validation.…”