Abstract
BackgroundDNA 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.ResultsWe 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.ConclusionsWe 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 materialThe online version of this article (doi:10.1186/1471-2164-15-598) contains supplementary material, which is available to authorized users.
Highlights
DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms
The degree of methylation was high in the intergenic regions containing repeats, followed by the intron and coding sequence (CDS) regions in both TH and Jeju horse (JH) (Table 1)
In comparison with most of the repetitive elements, long interactive nuclear elements (LINE), short interactive nuclear elements (SINE), and long terminal repeat (LTR) elements exhibited a high level of methylation density in both TH and JH (Figure 1C, D)
Summary
DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. The regulation and characteristics of the DNA methylation still remain enigmatic, the importance of it has been demonstrated in many biological processes such as gene expression regulation, genomic imprinting, X chromosome inactivation, maintenance of genomic stability by transposon silencing. It has been implicated in the development of diseases such as cancer [1,2,3,4,5,6,7]. There is insufficient evidence indicating that methylation differences exist at subspecies or breeds level
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