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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 #395332

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: Integration of epigenomic and transcriptomic data to identify regulatory elements and networks controlling immune cell-type gene expression in the pig

item TUGGLE, CHRISTOPHER - Iowa State University
item CORBETTE, RYAN - Iowa State University
item YANG, PENGXIN - Iowa State University
item HERRERA-URIBE, JUBER - Iowa State University
item Byrne, Kristen
item Loving, Crystal

Submitted to: Annual International Conference on Intelligent Systems for Molecular Biology
Publication Type: Abstract Only
Publication Acceptance Date: 7/14/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The purpose of the Functional Annotation of ANimal Genomes (FAANG) project is to catalog RNA-expressing regions and regulatory elements (REs) in agriculturally important animals. Such annotation is needed to understand the biological effect of genetic variants associated with economic traits for genetic improvement. Further, there is interest in integrating such functional data across biological states and across species to improve our understanding of comparative biology and genomics. In the domestic pig, we have collected RNA and epigenomics data on >20 adult and fetal tissues as well as nine circulating immune cell populations. We will focus today on an analysis of recent immune cell transcriptomic and epigenomics data (ATACseq, DNA methylation, histone modifications) collected on these cell populations to identify novel cell type-specific REs. Integration of deep epigenomics data using ChromHMM to identify chromatin states in cell populations identifies potential REs across the pig genome. We are also using single-cell (sc) RNAseq and scATACseq data on circulating immune cells to identify such REs. Interestingly, analysis of open chromatin regions identified by scATACseq identify similar and potentially more discriminative cell types than does scRNAseq data. Integration of these data through correlation of RE activity with cell-type specific promoter element activity can predict putative regulatory networks controlling cell type-specific expression. Thus, these data are the foundation needed to create useful regulatory networks that map functional elements to the target genes they regulate. This regulatory information will add to the value of FAANG data for understanding the function of the genome and application to genetic improvement of domesticated animals.