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Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

  • Gim, Jeong-An (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Hong, Chang Pyo (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Kim, Dae-Soo (Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Moon, Jae-Woo (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Choi, Yuri (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Eo, Jungwoo (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Kwon, Yun-Jeong (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Lee, Ja-Rang (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Jung, Yi-Deun (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Bae, Jin-Han (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Choi, Bong-Hwan (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Ko, Junsu (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Song, Sanghoon (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Ahn, Kung (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Ha, Hong-Seok (Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey) ;
  • Yang, Young Mok (Department of Pathology, School of Medicine, and Institute of Biomedical Science and Technology, Konkuk University) ;
  • Lee, Hak-Kyo (Department of Biotechnology, Hankyong National University) ;
  • Park, Kyung-Do (Department of Biotechnology, Hankyong National University) ;
  • Do, Kyoung-Tag (Department of Equine Sciences, Sorabol College) ;
  • Han, Kyudong (Department of Nanobiomedical Science and WCU Research Center, Dankook University) ;
  • Yi, Joo Mi (Research Center, Dongnam Institute of Radiological and Medical Science (DIRAMS)) ;
  • Cha, Hee-Jae (Department of Parasitology and Genetics, Kosin University College of Medicine) ;
  • Ayarpadikannan, Selvam (Department of Biological Sciences, College of Natural Sciences, Pusan National University) ;
  • Cho, Byung-Wook (Department of Animal Science, College of Life Sciences, Pusan National University) ;
  • Bhak, Jong (TBI, Theragen BiO Institute, TheragenEtex) ;
  • Kim, Heui-Soo (Department of Biological Sciences, College of Natural Sciences, Pusan National University)
  • Received : 2014.05.26
  • Accepted : 2014.11.21
  • Published : 2015.03.31

Abstract

Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethy-lated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.

Keywords

DNA methylation;exercise;MeDIP-Seq;thoroughbred horse;transposable elements

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