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Home / Equine Research Bank / BMC Genomics / Genome-wide analysis of DNA methylation patterns in horse.
BMC genomics2014; 15(1); 598; doi: 10.1186/1471-2164-15-598

Genome-wide analysis of DNA methylation patterns in horse.

Abstract: 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. Results: 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. Conclusions: 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.
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Publication Date: 2014-07-15 PubMed ID: 25027854PubMed Central: PMC4117963DOI: 10.1186/1471-2164-15-598Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article presents the first genome-wide DNA methylation data in horses, specifically in two breeds – thoroughbred and Jeju. The study provides insight into DNA methylation distribution across different tissues and identifies differentially methylated genomic regions between the two breeds.

Background and Objectives

  • The DNA methylation is a crucial process that aids in the regulation of biological processes and contributes to changes in an organism’s phenotype. Despite its significance, there is limited understanding about DNA methylation patterns in horses.
  • The study’s main aim is to offer the first comprehensive analysis of the DNA methylation landscape in horses, with a particular focus on two breeds: Thoroughbred (TH) and Jeju (JH), an indigenous Korean breed.

Methodology

  • The study utilized methyl-DNA immunoprecipitation sequencing to observe the DNA methylation characteristics in the skeletal muscle, heart, lung, and cerebrum tissues of TH and JH horses.
  • Further, the study investigates DNA methylation alterations in different genomic regions, including the promoter region, coding DNA sequence (CDS) region, and repeat elements such as long interspersed nuclear elements, short interspersed nuclear elements, and long terminal repeat elements.

Results and Findings

  • The analysis revealed that the overall methylation density was lowest in the promoter region, while the density within the CDS region was highest.
  • Among the repeat elements, long interspersed nuclear elements demonstrated a relatively high methylation density compared to the other two types of elements.
  • Furthermore, the research also succeeded in identifying differential methylated regions by comparing corresponding tissues from TH and JH. The results showed that the gene body regions had a high methylation density.

Conclusion

  • The research paper presents the first DNA methylation landscape of the horse, with particular reference to thoroughbred and Jeju breed.
  • The identified differentially methylated genomic regions (DMRs) between the two breeds provide a significant contribution to the understanding of horse epigenetics and may aid future biological function analyses.

Cite This Article

APA
Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K, Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS. (2014). Genome-wide analysis of DNA methylation patterns in horse. BMC Genomics, 15(1), 598. https://doi.org/10.1186/1471-2164-15-598

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 15
Issue: 1
Pages: 598
PII: 598

Researcher Affiliations

Lee, Ja-Rang
    Hong, Chang Pyo
      Moon, Jae-Woo
        Jung, Yi-Deun
          Kim, Dae-Soo
            Kim, Tae-Hyung
              Gim, Jeong-An
                Bae, Jin-Han
                  Choi, Yuri
                    Eo, Jungwoo
                      Kwon, Yun-Jeong
                        Song, Sanghoon
                          Ko, Junsu
                            Yang, Young Mok
                              Lee, Hak-Kyo
                                Park, Kyung-Do
                                  Ahn, Kung
                                    Do, Kyoung-Tag
                                      Ha, Hong-Seok
                                        Han, Kyudong
                                          Yi, Joo Mi
                                            Cha, Hee-Jae
                                              Cho, Byung-Wook
                                                Bhak, Jong
                                                • Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea. jongbhak@genomics.org.
                                                Kim, Heui-Soo

                                                  MeSH Terms

                                                  • Animals
                                                  • Cerebrum / metabolism
                                                  • Computational Biology
                                                  • CpG Islands
                                                  • DNA / genetics
                                                  • DNA / metabolism
                                                  • DNA Methylation
                                                  • Genome
                                                  • Horses / genetics
                                                  • Lung / metabolism
                                                  • Muscle, Skeletal / metabolism
                                                  • Myocardium / metabolism
                                                  • Sequence Analysis, DNA

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