Integrative methylome and transcriptome analysis of porcine abdominal fat indicates changes in fat metabolism and immune responses during different development

Fat is involved in synthesizing fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. The samples were collected from the porcine abdominal fat of different developmental stages (10 and 26 weeks of age). Then, the samples were sequenced using MBD-seq and RNA-seq for profiling DNA methylation and RNA expression. In 26 weeks of age pigs, differentially methylated genes (DMGs) and differentially expressed genes (DEGs) were identified as 2,251 and 5,768, compared with 10 weeks of age pigs, respectively. Gene functional analysis was performed using GO and KEGG databases. In functional analysis results of DMGs and DEGs, immune responses such as chemokine signaling pathways, B cell receptor signaling pathways, and lipid metabolism terms such as PPAR signaling pathways and fatty acid degradation were identified. It is thought that there is an influence between DNA methylation and gene expression through changes in genes with similar functions. The effects of DNA methylation on gene expression were investigated using cis-regulation and trans-regulation analysis to integrate and interpret different molecular layers. In the cis-regulation analysis using 629 overlapping genes between DEGs and DMGs, immune response functions were identified, while in trans-regulation analysis through the TF-target gene network, the co-expression network of lipid metabolism-related functions was distinguished. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging. Lay Summary Fat is involved in the synthesis of new fatty acids (FAs), FA circulation, and lipid metabolism. Various genetic studies have been conducted on porcine fat but understanding the growth and specific adipose tissue is insufficient. The purpose of this study is to investigate the epigenetic difference in abdominal fat according to the growth of porcine. Modifications in DNA methylation and expression values were confirmed epigenetically with growth. Changed genes in each DNA and RNA showed identical trends in the function of immune response and lipid metabolism. The effects of DNA methylation on gene expression were investigated using cis-regulation (functional enrichment analysis of overlapping genes) and trans-regulation (transcription factor and target gene networking) analysis to integrate and interpret different molecular layers. Our research provides an understanding of the underlying mechanisms for epigenetic regulation in porcine abdominal fat with aging.

Automated summary

Fat is involved in the synthesis of fatty acids, circulation of fatty acids, and lipid metabolism. This study aimed to investigate the epigenetic differences in abdominal fat during the growth of pigs. The results showed changes in DNA methylation and gene expression with growth. Genes that were differentially methylated or expressed were found to be involved in immune response and lipid metabolism. The effects of DNA methylation on gene expression were analyzed through cis-regulation and trans-regulation analysis. This research provides insights into the underlying mechanisms of epigenetic regulation in porcine abdominal fat during aging.