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Open Access Highly Accessed Research article

Genome-wide analysis of DNA methylation patterns in horse

Ja-Rang Lee1, Chang Pyo Hong2, Jae-Woo Moon2, Yi-Deun Jung1, Dae-Soo Kim3, Tae-Hyung Kim2, Jeong-An Gim1, Jin-Han Bae1, Yuri Choi1, Jungwoo Eo1, Yun-Jeong Kwon1, Sanghoon Song2, Junsu Ko2, Young Mok Yang4, Hak-Kyo Lee5, Kyung-Do Park5, Kung Ahn2, Kyoung-Tag Do5, Hong-Seok Ha6, Kyudong Han7, Joo Mi Yi8, Hee-Jae Cha9, Byung-Wook Cho1, Jong Bhak2* and Heui-Soo Kim1*

Author Affiliations

1 Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea

2 TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea

3 Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea

4 Department of Pathology, School of Medicine, Institute of Biomedical Science and Technology, Konkuk University, Seoul 143-701, Republic of Korea

5 Department of Biotechnology, Hankyong National University, Anseong 456-749, Republic of Korea

6 Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, 145 Bevier Rd, Piscataway, NJ 08854, USA

7 Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea

8 Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Jwadong-gil 40, Jangan-eup, Gijang-gun, Busan 619-950, Republic of Korea

9 Department of Parasitology and Genetics, Kosin University College of Medicine, Busan 602-703, Republic of Korea

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BMC Genomics 2014, 15:598  doi:10.1186/1471-2164-15-598

Published: 15 July 2014



DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.


We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.


We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

Thoroughbred horse; Jeju horse; Genome-wide DNA methylation; Differential methylated region (DMR); MeDIP-seq