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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 #400441

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: Characterization and applications of advanced regulatory element annotation in circulating porcine immune cells

item CORBETT, RYAN - Iowa State University
item HERRERA-URIBE, JUBER - Iowa State University
item TENG, JINYAN - South China Agricultural University
item Byrne, Kristen
item LIU, HAIBO - Iowa State University
item LI, HOUCHENG - Michigan State University
item ZHANG, ZHE - South China Agricultural University
item KOLTES, JAMES - Iowa State University
item ERNST, CATHERINE - Michigan State University
item Loving, Crystal
item FANG, LINGHAO - Aarhus University
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: Quantitative genetics studies have revealed thousands of loci associated with complex immune traits in pig, but limited characterization of cis gene regulation has hindered identification of molecular mechanisms directly linking such genetic variants to altered phenotypes. We performed the first annotation of regulatory elements in nine porcine immune cell populations using ChIP-seq (H3K27ac, H3K27me3, H3K4me1, H3K4me3, CTCF) and ATAC-seq assays, and generated regulatory element maps across cell types. We utilized this regulatory data to further annotate 1) immune tissue cis-eQTL and 2) GWAS loci for immune capacity traits. We predicted 15 chromatin states from epigenomics datasets, including active and poised transcription start sites and enhancers, repressors, and insulators. We observed a high degree of cellular specificity among active enhancers, and predict cell-specific enhancers (csEnhs; N=53,974) to be important for respective cell functions based on 1) target gene enrichment for unique biological processes and 2) csEnh enrichment for immune cell transcription factor motifs. Clusters of enhancers exhibiting high activation signal were classified as super-enhancers N=140-843/cell type), and these were associated with high target transcript abundance that suggest their putative role as master cis-regulators of cell-specific gene expression. We observed a high degree of enrichment for active regulatory elements within cis-eQTL from 34 pig tissues and GWAS loci, with csEnhs showing strong enrichment for cis-eQTL in associated immune tissue types and for immunity trait GWAS SNPs. This project has provided a rich resource of functional elements in porcine immune cells that may prove valuable in future quantitative genetics and translational research studies.