Profiling the Genome-Wide DNA Methylation Pattern of Porcine Ovary

The first ovulation marks ovarian maturation and sex in female mammals. Substantial evidence shows that DNA methylation regulates the initiation of ovarian and sexual maturation. We aimed to choose the proper fragment sizes to built the porcine reduced representation (RR) genome and perform reduced representation bisulphite sequencing (RRBS) on porcine ovary to analyze its DNA methylome.

Based on our analysis of the porcine genome digested by MspI with different sequencing strategies in silico, the segments of 110-220 bp were used to build the porcine RR genome. The porcine RR genome showed enrichment at CpG sites. Next, we performed RRBS on porcine ovaries (n=3) to evaluate their genome-wide DNA methylation profiles. We frequently found hypermethylation occurred in regions of low gene abundance, while hypomethylation generally in regions of high gene abundance. The CpG content was highest at transcription start site (TSS), thereafter decreasing sharply within 2 kb around TSS. There was a negative correlation between the methylation levels around TSS and the CpG content. For all porcine genes, the methylaiton level of gene body was higher than that of neighbouring flanking regions, with an abrupt increase from the TSS to transcription end site (TES) and a decline after TES.

Analysis of the three porcine ovaries indicated that RRBS had the potential to provide methylation atlases for clearly documenting the changes occurring during the process of sexual maturation, as well as the basic epigenetic mechanisms of reproductive systems.