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

Abstract

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. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own 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 pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome.

Genome-wide analysis of DNA Methylation profiles on sheep ovaries associated with prolificacy using whole-genome Bisulfite sequencing

“…Non-CpG information was also obtained in the present study, CAG was the most common sequence motif in the CHG mC sites, as also found in other studies [ 26 ], and the sequence motif in CHH differed between the two groups. The methylation levels near the TSS were the lowest of all the gene functional regions, which was consistent with the results found in pig ovaries by RRBS [ 27 ]. Most hypermethylation CGI (over 68%) were located in distal intergenic regions, while only 1.5% were in UTR.…”

“…Evidence has revealed that ovarian maturation is regulated by DNA methylation [ 5 , 6 ]. By profiling the methylome of porcine ovaries, researchers examined the methylation changes during the process of sexual and ovarian maturation in pigs [ 7 ]. Similar studies also found that DNA methylation alterations influenced gene expression profiles in the goat hypothalamus during the onset of puberty [ 8 ].…”

Whole-Genome Methylation Analysis Reveals Epigenetic Variation in Cloned and Donor Pigs

“…In our study, the DMRs (CP vs DP) suffered more hypomethylation (391/775 DMRs) than hypermethylation (384/ 775 DMRs) in the ear, suggested the DNA methylation status in the DMRs altered and phenotype changed in cloned pig, this was consistent with the DNA methylation context of skeletal muscle in abnormal and normal cloned pig . Therefore, the methylation context of the ear and blood were different, which was consistent with the results of the DNA methylation in the ovary and intestine of pigs (Yuan et al, 2016). Furthermore, the average sequencing depth was more than 25X, the methylation conversion of reads with a coverage of >10X were more than 87.82% and >74.93% of bases were aligned to the reference genome.…”

Exogenous adrenocorticotropic hormone affects genome‐wide DNA methylation and transcriptome of corpus luteum in sows

“…DNA methylation is an epigenetic mechanism that regulates gene expression in response to environmental stimuli (39,41). Although the genome-wide DNA methylation patterns of many tissues have been reported (42)(43)(44), the methylation maps in CL remain largely undetermined. In this study, we systematically investigated the global methylation patterns of CLs in sows.…”