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

Frontiers in Genetics

Genetics

Christopher K. Tuggle¹  Haibo Liu¹  Ryan J. Corbett¹  Gianna Marco¹  Lance Daharsh¹  Martine Schroyen¹  Juber Herrera-Uribe¹  James E. Koltes¹  Kyu-Sang Lim²  Kristen A. Byrne³  Crystal L. Loving³ 

[1] Department of Animal Science, Iowa State University, Ames, IA, United States;Department of Animal Science, Iowa State University, Ames, IA, United States;Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea;USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States;

关键词: pig;    transcriptome;    bulk-RNA-seq;    co-expressed genes;    transcription factor (TF);    gene regulation;    immune cells;    ATAC-seq;   

DOI  :  10.3389/fgene.2023.1107462

 received in 2022-11-24, accepted in 2023-04-27,  发布年份 2023

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

Unknown   
Copyright © 2023 Herrera-Uribe, Lim, Byrne, Daharsh, Liu, Corbett, Marco, Schroyen, Koltes, Loving and Tuggle.