Global CpG Methylation Patterns of Pigs Shows High Similarity to Other Mammals Including Humans

DNA methylation is a major component of the epigenetic regulation of gene expression in the mammalian genome. Although a few genome-wide DNA methylation profiling studies have been reported in pigs, the available data is still quite limited, especially for tissue diversity and detailed analysis. In order to estimate the efficiency of reduced representation bisulfite sequencing (RRBS) for the porcine genome, we carried out in silico analysis of the pig reference genome and compared the methylation associated genome parameters to those of humans, mice and zebra fish in which the genome level RRBS analysis results are available. Subsequently, we experimentally generated the DNA methylation profiles of the neocortex, olfactory epithelium, spleen, liver and muscle tissues and a pulmonary alveolar macrophage (PAM; 3D4/2) cell line using RRBS. On average, 3.92 Gb of clean reads were analyzed from each of the six samples. The results showed that 42.82% to 45.71% and 4.85% to 5.07% of detected cytosine and guanine dinucleotides (CpG) were located in CpG islands (CGI) and 2 kb upstream of transcription start sites (TSS), respectively. We observed 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 such as humans and mice. The general characteristics of the methylation pattern of the pig genome by RRBS analysis in this study were consistent to the results of another recent pig genome RRBS study. In addition, we analyzed the correlation between the levels of DNA methylation and gene expression among neocortex, liver, muscle, spleen and a macrophage cell line. Observed patterns of differentially methylated cytosine (DMC) were compared among different tissues. These results should serve as a basic framework to establish the complete porcine methylome map and to understand the effect of DNA methylation on gene expression and phenotypic differences.