Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq

Jeong An Gim; Chang Pyo Hong; Dae Soo Kim; Jae Woo Moon; Yuri Choi; Jungwoo Eo; Yun Jeong Kwon; Ja Rang Lee; Yi Deun Jung; Jin Han Bae; Bong Hwan Choi; Junsu Ko; Sanghoon Song; Kung Ahn; Hong Seok Ha; Young Mok Yang; Hak Kyo Lee; Kyung Do Park; Kyoung Tag Do; Kyudong Han; Joo Mi Yi; Hee Jae Cha; Selvam Ayarpadikannan; Byung Wook Cho; Jong Bhak; Heui Soo Kim

doi:10.14348/molcells.2015.2138

Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq

Jeong An Gim
, Chang Pyo Hong
, Dae Soo Kim
, Jae Woo Moon
, Yuri Choi
, Jungwoo Eo
, Yun Jeong Kwon
, Ja Rang Lee
, Yi Deun Jung
, Jin Han Bae
, Bong Hwan Choi
, Junsu Ko
, Sanghoon Song
, Kung Ahn
, Hong Seok Ha
, Young Mok Yang
, Hak Kyo Lee
, Kyung Do Park
, Kyoung Tag Do
, Kyudong Han

Joo Mi Yi, Hee Jae Cha, Selvam Ayarpadikannan, Byung Wook Cho, Jong Bhak^*, Heui Soo Kim

^*Corresponding author for this work

Department of Animal Biotechnology

Pusan National University
TBI
Korea Research Institute of Bioscience and Biotechnology
Rural Development Administration
Rutgers - The State University of New Jersey, New Brunswick
Konkuk University
Hankyong National University
Sorabol College
Dankook University
Dongnam Institute of Radiological and Medical Science (DIRAMS)
Kosin University
Ulsan National Institute of Science and Technology

Research output: Contribution to journal › Journal article › peer-review

29 Scopus citations

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 hypo- methylated 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.

Original language	English
Pages (from-to)	210-220
Number of pages	11
Journal	Molecules and Cells
Volume	38
Issue number	3
DOIs	https://doi.org/10.14348/molcells.2015.2138
State	Published - 2015

Keywords

DNA methylation
Exercise
MeDIP-Seq
Thoroughbred horse
Transposable elements

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10.14348/molcells.2015.2138

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Gim, J. A., Hong, C. P., Kim, D. S., Moon, J. W., Choi, Y., Eo, J., Kwon, Y. J., Lee, J. R., Jung, Y. D., Bae, J. H., Choi, B. H., Ko, J., Song, S., Ahn, K., Ha, H. S., Yang, Y. M., Lee, H. K., Park, K. D., Do, K. T., ... Kim, H. S. (2015). Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq. Molecules and Cells, 38(3), 210-220. https://doi.org/10.14348/molcells.2015.2138

@article{2d0b2cbd775d4588ba72eeaf0cf5b3b3,

title = "Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq",

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 hypo- methylated 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",

author = "Gim, \{Jeong An\} and Hong, \{Chang Pyo\} and Kim, \{Dae Soo\} and Moon, \{Jae Woo\} and Yuri Choi and Jungwoo Eo and Kwon, \{Yun Jeong\} and Lee, \{Ja Rang\} and Jung, \{Yi Deun\} and Bae, \{Jin Han\} and Choi, \{Bong Hwan\} and Junsu Ko and Sanghoon Song and Kung Ahn and Ha, \{Hong Seok\} and Yang, \{Young Mok\} and Lee, \{Hak Kyo\} and Park, \{Kyung Do\} and Do, \{Kyoung Tag\} and Kyudong Han and Yi, \{Joo Mi\} and Cha, \{Hee Jae\} and Selvam Ayarpadikannan and Cho, \{Byung Wook\} and Jong Bhak and Kim, \{Heui Soo\}",

note = "Publisher Copyright: {\textcopyright} 2014 The Korean Society for Molecular and Cellular Biology.",

year = "2015",

doi = "10.14348/molcells.2015.2138",

language = "English",

volume = "38",

pages = "210--220",

journal = "Molecules and Cells",

issn = "1016-8478",

number = "3",

}

Gim, JA, Hong, CP, Kim, DS, Moon, JW, Choi, Y, Eo, J, Kwon, YJ, Lee, JR, Jung, YD, Bae, JH, Choi, BH, Ko, J, Song, S, Ahn, K, Ha, HS, Yang, YM, Lee, HK, Park, KD, Do, KT, Han, K, Yi, JM, Cha, HJ, Ayarpadikannan, S, Cho, BW, Bhak, J & Kim, HS 2015, 'Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq', Molecules and Cells, vol. 38, no. 3, pp. 210-220. https://doi.org/10.14348/molcells.2015.2138

TY - JOUR

T1 - Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq

AU - Gim, Jeong An

AU - Hong, Chang Pyo

AU - Kim, Dae Soo

AU - Moon, Jae Woo

AU - Choi, Yuri

AU - Eo, Jungwoo

AU - Kwon, Yun Jeong

AU - Lee, Ja Rang

AU - Jung, Yi Deun

AU - Bae, Jin Han

AU - Choi, Bong Hwan

AU - Ko, Junsu

AU - Song, Sanghoon

AU - Ahn, Kung

AU - Ha, Hong Seok

AU - Yang, Young Mok

AU - Lee, Hak Kyo

AU - Park, Kyung Do

AU - Do, Kyoung Tag

AU - Han, Kyudong

AU - Yi, Joo Mi

AU - Cha, Hee Jae

AU - Ayarpadikannan, Selvam

AU - Cho, Byung Wook

AU - Bhak, Jong

AU - Kim, Heui Soo

PY - 2015

Y1 - 2015

N2 - 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 hypo- methylated 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.

AB - 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 hypo- methylated 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.

KW - DNA methylation

KW - Exercise

KW - MeDIP-Seq

KW - Thoroughbred horse

KW - Transposable elements

UR - https://www.scopus.com/pages/publications/84935691832

U2 - 10.14348/molcells.2015.2138

DO - 10.14348/molcells.2015.2138

M3 - Journal article

C2 - 25666347

AN - SCOPUS:84935691832

SN - 1016-8478

VL - 38

SP - 210

EP - 220

JO - Molecules and Cells

JF - Molecules and Cells

IS - 3

ER -

Genome-wide analysis of DNA methylation before- and after exercise in the thoroughbred horse with MeDIP-seq

Abstract

Keywords

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