Multiomic Profiling Reveals the Regulation of Many Immune-Related Genes by PU.1 in Porcine Alveolar Macrophages

Alveolar macrophages (AMs) play essential roles in maintaining homeostasis and immunity in the lung. The transcription factor PU.1, encoded by SPI1, is a core regulator in multiple immune cell lineages. However, its binding property and regulatory role in AMs remain unclear. The pig serves as an important livestock species and a valuable biomedical model. Using porcine AMs (PAMs) as a model, we combined gene knockdown experiments with multiomic profiling to elucidate the regulatory role of PU.1 in AMs. By integrating the RNA-seq data before and after SPI1 knockdown, we demonstrate that disruption of PU.1 impairs the expression of numerous immune-related genes, including many crucial for innate immune responses. We further employed CUT&Tag to characterize the genome-wide occupancy of PU.1 and the active histone modification H3K27ac, and found that PU.1 primarily binds active cis-regulatory elements (CREs), including a large proportion of enhancers derived from transposable elements. Moreover, integrative analysis identifies a set of CREs and their associated genes, which are putative direct targets of PU.1. Overall, this study provides novel insights into the regulatory role of PU.1 in AMs and extends our knowledge about this core regulator in the mammalian immune system.