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. Genome-wide analysis of DNA methylation patterns in horse.
BMC Genomics 2014;
15:598. [PMID:
25027854 PMCID:
PMC4117963 DOI:
10.1186/1471-2164-15-598]
[Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 07/07/2014] [Indexed: 12/23/2022] Open
Abstract
Background
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.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-598) contains supplementary material, which is available to authorized users.
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