Epigenetics and Transcriptomics Core

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ABSTRACT The function of the Epigenetics and Transcriptomics Core (Core B) is to identify the key gene networks and cis-regulatory mechanisms that define the pulmonary endothelium as an innate immune ‘organ’ during lung injury and repair. Core B will provide high-throughput production and optimal mining of genome-wide gene expression and chromatin datasets, for all three projects in this Program. The Core B leader has pioneered such approaches in stem cells and is now applying these analysis platforms to lung endothelial cells in a comprehensive and integrative manner. We have optimized the methods for several next generation sequencing approaches, including low cell number RNA-seq, ChIP-seq and ATAC-seq, and can effectively collect, manage, analyze, integrate, and interpret the generated data specifically in freshly isolated endothelial cells. By combining all four technologies we will develop a multi-dimensional view of the epigenetic programming of endothelial cells (EC) and reveal their modulatory interactions with circulating immune cells. On this basis, Core B will provide a foundation for the more specific and sophisticated needs of each individual project. Indeed, each project focuses on gene regulatory networks that are among the most robustly regulated across lung injury and repair models. Through the development and use of epigenetic and transcriptomic assays coupled with next generation sequencing, Core B will assist each Project in uncovering the molecular mechanisms and develop testable hypothesis about genes associated with EC innate immunity and their role in inflammatory response. These include the exploration of the epigenetic and transcriptomic changes that occur in response to endoplasmic reticulum localized Y143phosphorylated sphingosine 1 phosphate receptor 1 (S1PR1), as EC convert from an anti-inflammatory to an immune-active lineage in Project 1; delineate the cis-regulatory mechanisms and chromatin-based pathways that control the expression of ubiquitin E3 ligase CHFR in Project 2; and examine the role of epigenetic programs in the initiation of lung endothelial cell mitophagy and mitochondrial biogenesis as well as the downstream effectors of mitophagy-induced signals in Project 3. Ultimately, Core B represents a central conduit for genomic and bioinformatic flow of data for this PPG, providing data-generation, data-storage and data-sharing functions and therefore contributing significantly to further understanding the immune regulatory function of lung endothelium.