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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 #400438

Research Project: Intestinal Microbial Ecology and Non-Antibiotic Strategies to Limit Shiga Toxin-Producing Escherichia coli (STEC) and Antimicrobial Resistance Transmission in Food Animals

Location: Food Safety and Enteric Pathogens Research

Title: Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils

item HERRERA-URIBE, JUBER - Iowa State University
item LIM, KYU-SANG - Iowa State University
item Byrne, Kristen
item DAHARSH, LANCE - Iowa State University
item LIU, HAIBO - Iowa State University
item VELLA, GIANNA - Iowa State University
item SCHROYEN, MARTINE - Universite De Liege
item KOLTES, JAMES - Iowa State University
item Loving, Crystal
item TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Neutrophils are vital components of the immune system for limiting pathogen invasion and proliferation, and tissue damage caused by pathogens. Surprisingly, the functional annotation of this immune cell type is still limited in pigs. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we compared the transcriptome of porcine neutrophils with eight porcine immune cell transcriptomes to identify a neutrophil enriched gene list within a neutrophil gene co-expression module. Second, we used ATAC-seq assay to profile for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for the neutrophil lineage commitment. We found chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells, including porcine neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and highly enriched genes in porcine neutrophils. In summary, we performed the first integrative analysis of the accessible chromatin regions and transcriptional data of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrate the utility of chromatin accessible regions to identify and enrich our understanding of cell-type specific transcriptional networks in neutrophils.