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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #381593

Research Project: Intestinal Microbial Ecology and Metagenomic Strategies to Reduce Antibiotic Resistance and Foodborne Pathogens

Location: Food Safety and Enteric Pathogens Research

Title: Integrative profiling of chromatin accessibility and gene expression elucidate specific transcriptional network in porcine neutrophils

item HERRERA-URIBE, JUBER - Iowa State University
item DAHARSH, LANCE - Iowa State University
item Byrne, Kristen
item LIU, HAIBO - Iowa State University
item Loving, Crystal
item TUGGLE, CRHISTOPHER - Iowa State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/15/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Pigs are an important component of global food security, and serve as a human biomedical model. Infectious diseases impact pig and human health and global food productivity. Components of the pig innate immune system, such as neutrophils, have not been fully described, and epigenetic mechanisms controlling gene expression remain unclear in pigs. We performed RNA- and assay for transposase-accessible chromatin (ATAC)- sequencing on two porcine neutrophil samples to characterize epigenetic regulation of gene expression in these differentiated cells. A deep neutrophil transcriptome detected expression of 10,974 genes. In comparison to previously reported RNA-seq data on eight sorted immune cell types from the same animals, we predicted 833 enriched (significantly higher and 2-fold higher than average across all other cell types) genes in neutrophils. The 833 gene list was significantly enriched for biological processes related to typical neutrophil functions using Gene Ontology and in comparison to human neutrophil RNA-seq data. ATAC-seq detected open chromatin (OP) regions from approximately 227 million total reads that identified on average 151,789 peaks located in intergenic (67 percent), intron (24 percent), promoter-TSS (6 percent), exon (3 percent) or TTS (1 percent) regions. OP regions whose signal is correlated with, and nearby to, genes with enriched neutrophil expression are being analyzed for sites predicted to be bound by transcription factors that could explain neutrophil-enriched expression patterns. The data reported here is the first integrative study of the epigenetics of porcine neutrophil gene expression and provide a valuable resource to elucidate neutrophil transcriptional regulatory networks.