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

Authors: HERRERA URIBE, JUBER - Iowa State University; LIM, KYU-SANG - Iowa State University; Byrne, Kristen; DAHARSH, LANCE - Iowa State University; LIU, HAIBO - Iowa State University; CORBETT, RYAN - Iowa State University; MARCO, GIANNA - Iowa State University; SCHROYEN, MARTINE - Iowa State University; KOLTES, JAMES - Iowa State University; Loving, Crystal; TUGGLE, CHRISTOPHER - Iowa State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2023
Publication Date: 5/23/2023
Citation: Herrera Uribe, J., Lim, K., Byrne, K.A., Daharsh, L., Liu, H., Corbett, R.J., Marco, G., Schroyen, M., Koltes, J.E., Loving, C.L., Tuggle, C.K. 2023. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Frontiers in Genetics. 14. Article 1107462. https://doi.org/10.3389/fgene.2023.1107462.
DOI: https://doi.org/10.3389/fgene.2023.1107462

Interpretive Summary: Pigs are an important protein source supporting global food security. A major goal of biological research is using genetic information, or genotype, to predict the complex physical composition of an individual or individual cells, or phenotype. Genome sequencing and cataloging genes expressed in immune cells is important in understanding genotype to phenotype, but it does not take into consideration the mechanisms that regulate gene expression. Many factors control gene expression, including accessibility to DNA and methylation of DNA, both of which alter the ability of proteins to access the DNA and initiate gene expression. Neutrophils are an important immune cell for combating disease, and little is known about factors controlling gene expression in neutrophils. Gene expression in neutrophils was inversely correlated with methylation rates at expected DNA locations, and was related to overall DNA accessibility. Gene transcription was also correlated with gene accessibility, indicating the relationship between the two. Overall, the results improve the functional annotation of the pig genome through identification of genes whose expression is likely controlled by DNA methylation and chromatin accessibility.

Technical Abstract: Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. 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 sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report 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 neutrophil lineage commitment and function. We identified 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 neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.