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- Title
Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils.
- Authors
Herrera-Uribe, Juber; Kyu-Sang Lim; Byrne, Kristen A.; Daharsh, Lance; Haibo Liu; Corbett, Ryan J.; Marco, Gianna; Schroyen, Martine; Koltes, James E.; Loving, Crystal L.; Tuggle, Christopher K.
- 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 listwithin a detected neutrophil co-expressionmodule. 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.
- Subjects
GENE regulatory networks; GENE expression profiling; NEUTROPHILS; CHROMATIN; TRANSCRIPTION factors; RNA sequencing
- Publication
Frontiers in Genetics, 2023, p1
- ISSN
1664-8021
- Publication type
Article
- DOI
10.3389/fgene.2023.1107462