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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 #389564
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

Author
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 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: 1/12/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: As part of Functional Animal Genome Annotation of Animal Genomes, this study integrates epigenetic and transcriptomic profiling of pig neutrophils (PN) to identify the functional components of the pig immune system. Neutrophils are an innate immune cell type highly abundant in blood and are the best model for eukaryotic chemotaxic immune response. Yet, they have not been as well-studied as mononuclear cells. By combining Assay for Transposase Accessible Chromatin (ATAC-seq) and RNA sequencing (RNA-seq), we identified open chromatin regions (OCRs), and neutrophil specific genes (NSGs) using published transcriptomic data of eight other immune cell types (sorted monocytes/dendritic cells, T, B and NK cells) from the same animals. In total, 10,974 genes were detected by RNA-seq in PN and were used to create a co-expression network that generated a myeloid cluster shaped by 598 genes. Comparing transcriptomes between PN and sorted monocytes/dendritic cells, we identified 80 NSG within myeloid cluster, of which four were neutrophil specific transcription factors (NS-TF). ATAC-seq identified around 134,000 OCRs in porcine neutrophils, of which 57,567 were designated as consensus regions. TF binding motif analysis was performed using OCRs of NSGs (promoter regions ±3000 bp from Transcriptional-Start-Site). In total, 65 OCRs were found in 58 NSGs, identifying enriched motifs for GATA1, GFI1B and KLF5. A total of 52 NSGs were predicted to have motifs within their OCRs corresponding to these NS-TF. Altogether, our analysis revealed co-expressed and specific transcriptional patterns in PN, including TF predicted to bind to OCRs of predicted NSGs.