Genome-Level Analysis of the Methylation Patterns of Differentially Expressed Genes Among Neocortex, Liver, Muscle, Spleen and a Macrophage Cell Line in Pigs

DNA methylation plays an important role in the epigenetic regulation of gene expression. Although a few DNA methylation profiling studies of swine genome which is one of important biomedical model for human diseases have been reported, the available data is still limited. We tried to study methylation patterns of diverse pig tissues as a study of the International Swine Methylome Consortium to generate the swine reference methylome map in order to extensively evaluate the methylation profile of the pig genome at a single base resolution. We generated and analyzed the DNA methylome profiles of the five different tissues and a cell line originated from pig. On average, 39.85% and 62.1% of cytosine and guanine dinucleotides (CpGs) of CpG islands and 2 kb upstream of transcription start sites were covered, respectively. We detected a low rate (an average of 1.67%) of non-CpG methylation in the six samples except for the neocortex (2.3%). The observed global CpG methylation patterns of pigs indicated high similarity to other mammals including humans. The percentage of CpG methylation associated with gene features was similar among the tissues but not for a 3D4/2 cell line. In addition, we analyzed the correlation between the levels of DNA methylation and differences in gene expression among neocortex, liver, muscle, spleen and a macrophage cell line. Observed patterns of differentially methylated cytosine (DMC) were compared among different tissues. Our results provide essential information for future studies of the swine epigenome.