DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta.
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 accor...
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Public Library of Science (PLoS)
2017-01-01
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| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184539&type=printable |
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| author | Jung Hye Hwang Sang Mi An Seulgi Kwon Da Hye Park Tae Wan Kim Deok Gyeong Kang Go Eun Yu Il-Suk Kim Hwa Chun Park Jeongim Ha Chul Wook Kim |
| author_facet | Jung Hye Hwang Sang Mi An Seulgi Kwon Da Hye Park Tae Wan Kim Deok Gyeong Kang Go Eun Yu Il-Suk Kim Hwa Chun Park Jeongim Ha Chul Wook Kim |
| author_sort | Jung Hye Hwang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-850261c71e9e410ca89bda4ef0ec7a92 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-850261c71e9e410ca89bda4ef0ec7a922025-08-20T03:04:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01129e018453910.1371/journal.pone.0184539DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta.Jung Hye HwangSang Mi AnSeulgi KwonDa Hye ParkTae Wan KimDeok Gyeong KangGo Eun YuIl-Suk KimHwa Chun ParkJeongim HaChul Wook KimIncreasing 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184539&type=printable |
| spellingShingle | Jung Hye Hwang Sang Mi An Seulgi Kwon Da Hye Park Tae Wan Kim Deok Gyeong Kang Go Eun Yu Il-Suk Kim Hwa Chun Park Jeongim Ha Chul Wook Kim DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. PLoS ONE |
| title | DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. |
| title_full | DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. |
| title_fullStr | DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. |
| title_full_unstemmed | DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. |
| title_short | DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. |
| title_sort | dna methylation patterns and gene expression associated with litter size in berkshire pig placenta |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0184539&type=printable |
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