Abstract
BackgroundDNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored.ResultsGenome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq). Analysis of DNA methylation patterns indicate that the majority of methylation peaks found within genes are located gene body regions, for both organs. Analysis of the distribution of methylated sites per chromosome showed that chromosome X had the lowest number of methylation peaks. The X chromosome has one of the highest percentages of methylated CpG islands in both organs, and approximately 50% of the CpG islands in the goat epigenome are methylated in hypothalamus and ovary. Organ-specific Differentially Methylated Genes (DMGs) were correlated with the expression levels.ConclusionsThe comparison between transcriptome and methylome in hypothalamus and ovary showed that a higher level of methylation is not accompanied by a higher gene suppression. The genome-wide DNA methylation map for two goat organs produced here is a valuable starting point for studying the involvement of epigenetic modifications in regulating goat reproduction performance.
Highlights
DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and in biological processes and in determining phenotypic plasticity in organisms
Mapping of DNA methylation in Saanen goats Methyl binding domain sequencing was performed on two reproduction-associated organs of three Saanen goats
A clonal fraction of sequence reads was removed from each sample, resulting in 65.7% uniquely mapped reads for the hypothalamus and 71.1% for the ovary, with a high quality read alignment against the goat reference genome version 1.0 (2.64 Gb)
Summary
DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and in biological processes and in determining phenotypic plasticity in organisms. Genome-wide DNA methylation studies of many livestock species have been recently reported [13,14,15,16,17]. These studies used several methods to explore tissue specific methylation associated with economically important traits. Phenotypic variation in economically important traits, such as lipid synthesis, milk production, growth and development, that are not explained by genetics could be influenced by epigenetic factors, such as the wide spectrum of methylation levels and patterns seen in livestock [19]
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