Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

  • Cao, Yang ;
  • Jin, Hai-Guo ;
  • Ma, Hui-Hai ;
  • Zhao, Zhi-Hui
  • Received : 2017.02.28
  • Accepted : 2017.06.08
  • Published : 2017.11.01


Objective: The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper${\times}$Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods: Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results: 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypomethylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion: In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.


DNA Methylation;Small Tailed Han Sheep;Dorper${\times}$Small Tailed Han Crossbred Sheep;Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq);Longissimus Dorsi Muscle


  1. Cheng P. Livestock breeds of China. FAO Animal Production and Health Paper. Rome, Italy: Food and Agriculture Organization of the United Nations; 1985. p. 46.
  2. Cloete SWP, Snyman MA, Herselman MJ. Productive performance of Dorper sheep. Small Rumin Res 2000;36:119-35.
  3. Walling GA, Visscher PM, Wilson AD, et al. Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations. J Anim Sci 2004;82:2234-45.
  4. Zhang L, Liu J, Zhao F, et al. Genome-wide association studies for growth and meat production traits in sheep. PLoS One 2013;8:e66569.
  5. Courtier B, Heard E, Avner P. Xce haplotypes show modified methylation in a region of the active X chromosome lying 3' to Xist. Proc Natl Acad Sci USA 1995;92:3531-5.
  6. Sasaki H, Allen ND, Surani MA. DNA methylation and genomic imprinting in mammals. In: Jost JP, Saluz HP, editors. DNA methylation. Basel, Switzerland: Birkhauser. EXS 1993;64:469-86.
  7. Siegfried Z, Eden S, Mendelsohn M, et al. DNA methylation represses transcription in vivo. Nat Genet 1999;22:203-6.
  8. Gim JA, Hong CP, Kim DS, et al. Genome-wide analysis of DNA methylation before-and after exercise in the thoroughbred horse with MeDIP-Seq. Mol Cells 2015;38:210-20.
  9. Hu Y, Xu H, Li Z, et al. Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers. PLoS One 2013:8:e56411.
  10. Jin L, Jiang Z, Xia Y, et al. Genome-wide DNA methylation changes in skeletal muscle between young and middle-aged pigs. BMC Genomics 2014;15:653.
  11. Li N, Ye M, Li Y, et al. Whole genome DNA methylation analysis based on high throughput sequencing technology. Methods 2010;52:203-12.
  12. Li H, Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25:1754-60.
  13. Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008;9:R137.
  14. Kadarmideen HN. Biochemical, ECF18R, and RYR1 gene polymorphisms and their associations with osteochondral diseases and production traits in pigs. Biochem Genet 2008;46:41-53.
  15. Fan YY, Fu GW, Fu CZ, Zan LS, Tian WQ. A missense mutant of the PPAR-gamma gene associated with carcass and meat quality traits in Chinese cattle breeds. Genet Mol Res 2012;11:3781-8.
  16. Jin S, Chen S, Li H, et al. Polymorphisms in the transforming growth factor beta3 gene and their associations with feed efficiency in chickens. Poult Sci 2013;92:1745-9.
  17. Lee SH, Gondro C, Werf J, et al. Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle). BMC Genomics 2010;11:623.
  18. Mao M, Thedens DR, Chang B, et al. The podosomal-adaptor protein SH3PXD2B is essential for normal postnatal development. Mamm Genome 2009;20:462-75.
  19. Widmann P, Nuernberg K, Kuehn C, et al. Association of an ACSL1 gene variant with polyunsaturated fatty acids in bovine skeletal muscle. BMC Genet 2011;12:96.
  20. Couldrey C, Brauning R, Bracegirdle J, et al. Genome-wide DNA methylation patterns and transcription analysis in sheep muscle. PLoS One 2014;9:e101853.
  21. Li Q, Li N, Hu X, et al. Genome-wide mapping of DNA methylation in chicken. PLoS One 2011;6:e19428.
  22. Huang YZ, Sun JJ, Zhang LZ, et al. Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep 2014;4:6546.
  23. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff, S. Genomewide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2007;39:61-9.
  24. Hon GC, Hawkins RD, Caballero OL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012;22:246-58.
  25. Farmer LJ, Perry GC, Lewis PD, et al. Responses of two genotypes of chicken to the diets and stocking densities of conventional UK and Label Rouge production systems-II. Sensory attributes. Meat Sci 1997;47:77-93.
  26. Song F, Smith JF, Kimura MT, et al. Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci USA 2005;102:3336-41.
  27. Fernandezborja M. A tale of three GTPases and a RIN in endothelial cell adhesion. Cell Res 2012;22:1426.
  28. Stratz P, Wellmann R, Preuss S, Wimmers K, Bennewitz J. Genomewide association analysis for growth, muscularity and meat quality in Pietrain pigs. Anim Genet 2014;45:350-6.
  29. Sanders EJ, Wride MA. Roles for growth and differentiation factors in avian embryonic development. Poult Sci 1997;76:111-7.
  30. Lu Y, Chen S, Yang N. Expression and methylation of FGF2, TGF-beta and their downstream mediators during different developmental stages of leg muscles in chicken. PLoS One 2013;8:e79495.
  31. Shao X, Wang M, Wei X, et al. Peroxisome Proliferator-Activated Receptor-gamma: master regulator of adipogenesis and obesity. Curr Stem Cell Res Ther 2015;11:282-9.