Profiling the Genome-wide DNA Methylation Pattern of Porcine Ovaries Using Reduced Representation Bisulfite Sequencing

Overview

Journal Sci Rep

Specialty Science

Date 2016 Feb 26

PMID 26912189

Citations 24

Authors

Xiao-Long Yuan

Ning Gao

Yan Xing

Hai-Bin Zhang

Ai-Ling Zhang

Jing Liu

Jin-Long He

Yuan Xu

Wen-Mian Lin

Zan-Mou Chen

Hao Zhang

Zhe Zhang

Jia-Qi Li

Affiliations

Soon will be listed here.

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.

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References

Ball M, Li J, Gao Y, Lee J, LeProust E, Park I . Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol. 2009; 27(4):361-8. PMC: 3566772. DOI: 10.1038/nbt.1533. View

Gu H, Bock C, Mikkelsen T, Jager N, Smith Z, Tomazou E . Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010; 7(2):133-6. PMC: 2860480. DOI: 10.1038/nmeth.1414. View

Groenen M, Archibald A, Uenishi H, Tuggle C, Takeuchi Y, Rothschild M . Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 2012; 491(7424):393-8. PMC: 3566564. DOI: 10.1038/nature11622. View

Li M, Tian S, Jin L, Zhou G, Li Y, Zhang Y . Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. Nat Genet. 2013; 45(12):1431-8. DOI: 10.1038/ng.2811. View

Chatterjee A, Rodger E, Stockwell P, Weeks R, Morison I . Technical considerations for reduced representation bisulfite sequencing with multiplexed libraries. J Biomed Biotechnol. 2012; 2012:741542. PMC: 3495292. DOI: 10.1155/2012/741542. View

Nagarajan A, Roden C, Wajapeyee N . Reduced representation bisulfite sequencing to identify global alteration of DNA methylation. Methods Mol Biol. 2014; 1176:23-31. DOI: 10.1007/978-1-4939-0992-6_3. View

Wang L, Sun J, Wu H, Liu S, Wang J, Wu B . Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies. J Biotechnol. 2011; 157(1):1-6. DOI: 10.1016/j.jbiotec.2011.06.034. View

Gao F, Zhang J, Jiang P, Gong D, Wang J, Xia Y . Marked methylation changes in intestinal genes during the perinatal period of preterm neonates. BMC Genomics. 2014; 15:716. PMC: 4153944. DOI: 10.1186/1471-2164-15-716. View

Illingworth R, Gruenewald-Schneider U, Webb S, Kerr A, James K, Turner D . Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet. 2010; 6(9):e1001134. PMC: 2944787. DOI: 10.1371/journal.pgen.1001134. View

10.

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong C . Dynamic changes in the human methylome during differentiation. Genome Res. 2010; 20(3):320-31. PMC: 2840979. DOI: 10.1101/gr.101907.109. View

11.

Hunter M . Oocyte maturation and ovum quality in pigs. Rev Reprod. 2000; 5(2):122-30. DOI: 10.1530/ror.0.0050122. View

12.

Krueger F, Andrews S . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011; 27(11):1571-2. PMC: 3102221. DOI: 10.1093/bioinformatics/btr167. View

13.

Rishi V, Bhattacharya P, Chatterjee R, Rozenberg J, Zhao J, Glass K . CpG methylation of half-CRE sequences creates C/EBPalpha binding sites that activate some tissue-specific genes. Proc Natl Acad Sci U S A. 2010; 107(47):20311-6. PMC: 2996703. DOI: 10.1073/pnas.1008688107. View

14.

Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y . The DNA methylation landscape of human early embryos. Nature. 2014; 511(7511):606-10. DOI: 10.1038/nature13544. View

15.

Maunakea A, Nagarajan R, Bilenky M, Ballinger T, DSouza C, Fouse S . Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010; 466(7303):253-7. PMC: 3998662. DOI: 10.1038/nature09165. View

16.

Sang Q, Li X, Wang H, Wang H, Zhang S, Feng R . Quantitative methylation level of the EPHX1 promoter in peripheral blood DNA is associated with polycystic ovary syndrome. PLoS One. 2014; 9(2):e88013. PMC: 3914883. DOI: 10.1371/journal.pone.0088013. View

17.

Pei L, Choi J, Liu J, Lee E, McCarthy B, Wilson J . Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics. 2012; 7(6):567-78. PMC: 3398986. DOI: 10.4161/epi.20237. View

18.

Couldrey C, Brauning R, Bracegirdle J, MacLean P, Henderson H, McEwan J . Genome-wide DNA methylation patterns and transcription analysis in sheep muscle. PLoS One. 2014; 9(7):e101853. PMC: 4092064. DOI: 10.1371/journal.pone.0101853. View

19.

Saxonov S, Berg P, Brutlag D . A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A. 2006; 103(5):1412-7. PMC: 1345710. DOI: 10.1073/pnas.0510310103. View

20.

Smith Z, Chan M, Mikkelsen T, Gu H, Gnirke A, Regev A . A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012; 484(7394):339-44. PMC: 3331945. DOI: 10.1038/nature10960. View