Genome-Wide DNA Methylation Profile of the Muscle (longissimus dorsi) Tissue in Swine

DNA methylation has been suggested to play a major role in regulating expression of metabolic traits. The objective of this study was to identify and characterize genome-wide DNA methylation in the muscle (longissimus dorsi) of pigs. The longissimus dorsi tissue samples were taken from eight Duroc gilt after slaughtered. The methylated DNA immunoprecipitation (MeDIP) assay was performed with the extracted genomic DNA by the 36 bp single-end sequencing using Illumina Genome Analyzer II. After a quality control process, the sequence reads were aligned to the pig reference genome build Sscrofa_10.2, and the genomic methylated regions were identified by the MACS tool. A total of 6.16 Gb MeDIP-seq data were aligned on the reference genome. The highest density of DNA methylation was observed in the chromosome 10 while the lowest in the chromosome 12. The methylated regions common in all eight samples were only 1.1% of the total. Subsequent analysis was conducted with these overlapped methylation peaks. A major portion of the methylation peaks were present in the repeat regions (60.3%), followed by CpGs (20.9%). Within the repeat regions, we observed relatively high levels of methylation in simple repeat (43.9%) and LINE (20.5%). On the other hand, the least number of methylation peaks was contained in exon (0.8%), followed by promoters (1.2%). The data have been visualized using a GBrowse platform providing an overview of global DNA methylation profile of the muscle (longissimus dorsi) of pigs. Further research on their biological consequence is guaranteed.