DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta

Abstract

Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG) and larger (LLG) litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1) was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows.

Sperm DNA Hypomethylation Proximal to Reproduction Pathway Genes in Maturing Elite Norwegian Red Bulls

“…The distribution of DMRs demonstrated here showed that the majority lay within intergenic regions and regions outside CpG Islands/CpG shores. Similar trends have been reported in boar (Hwang et al, 2017;Khezri et al, 2019) and bull (Jiang et al, 2018;Perrier et al, 2018) sperm DNA. Previous research has shown that CpG Islands and CpG shores, in parallel with promoters, play an important role in regulation of transcription (Deaton and Bird, 2011;Long et al, 2017).…”

Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit

“…As the DNA methylation status of the promoter and gene body regions could affect gene expression thorough changes in the chromatin structure or transcription efficiency [ 45 , 46 , 47 ], we compared the genome-wide methylation patterns of the control and sense-/antisense tomato fruit to identify the DMRs and investigated the biological functions of the DMRs and DEGs using the GO and KEGG analysis. Forty-three DEGs were found, of which 26 were upregulated and 17 were downregulated in the Sense_vs_Antisense group.…”

DNA methylation pattern of the goat <i>PITX1</i> gene and its effects on milk performance

“…Recently an increasing number of studies have demonstrated that nutritional or environmental changes contribute to changes in inheritable epigenetic modifications, such as DNA methylation (Lan et al, 2013a;Chavatte-Palmer et al, 2018;Kwan et al, 2018;Yuan et al, 2018). As one of the most important and common types of epigenetic modification, DNA methylation plays a significant role in regulating biological processes such as milk production and organ development (Hwang et al, 2017;Fleming et al, 2018;Jessop et al, 2018). In recent years, gene methylation involved in vital biological functions has been wellstudied in animals (Ibeagha-Awemu and Zhao, 2015).…”