Genome-wide analysis of DNA methylation patterns in horse

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.

Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

“…This high methylation density in exons has already been observed in horse, rat and human [17, 24, 25]. However, the high density of methylation in promoter regions seen in the present study was unexpected.…”

Genome-wide analysis of salinity-stress induced DNA methylation alterations in cotton (Gossypium hirsutum L.) using the Me-DIP sequencing technology

“…The repeat elements showed a high methylation density, while the CDS and intron elements showed a relatively low methylation density. The results of this study were similar to those of the previous studies performed on other species, including plants and animals (Zhang et al, 2006;Yan et al, 2010;Li et al, 2011;Lee et al, 2014).…”

HEpD: A database describing epigenetic differences between Thoroughbred and Jeju horses

“…By using this method, users can retrieve the methylation state of specific regions in horse genome, then apply to design primer sets for bisulfite sequencing. We confirmed tissue-specific regions revealed in the previous study by this method (Lee et al, 2014), and this database provides similar methylation patterns (Fig. S1).…”

“…We performed methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-Seq) in four tissues (cerebrum, lung, heart, and skeletal muscle) derived from genomic DNA from each individual of Thoroughbred and Jeju horses (Lee et al, 2014) (Table S1). All animal protocols (ethical procedures and scientific care) used in this study were reviewed and approved by the Pusan National University-Institutional Animal Care and Use Committee (PNU-IACUC; Approval Number PNU-2013-0411).…”