Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing

The first ovulation marks ovarian and sexual maturation in female mammals. Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing (RRBS). We extracted the genomic DNA from the ovaries of three Landrace × Yorkshire crossbred gilts aged 6 months, digested them with MspI, and selected the 110–220 bp digested fragments to build the libraries. Then, we sequenced the libraries through PE100 on an Illumina HiSeq 2500 platform using RRBS operating standards. We frequently found hypermethylation occurring in regions of low gene abundance, while hypomethylation was generally found in regions of high gene abundance. We found a negative correlation between DNA methylation around transcriptional start sites and CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5′ and 3′ flanking regions. The DNA methylation patterns of low and high CpG content promoter genes differed significantly.