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

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3866-4) contains supplementary material, which is available to authorized users.

Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling

“…These observations are consistent with previous studies on gene methylation status in other livestock species, including goats [ 32 ], horses [ 33 ] and cattle [ 19 ]. Similar patterns were observed in a very recent goat study [ 32 ], in which the distribution of methylated residues was higher in gene bodies than upstream regions in caprine hypothalamus and ovary tissues. In the present study, CpG islands and CGI shores showed a higher CGI and CGI methylation densities than gene bodies and promoter regions, respectively.…”

“…In the present study, CpG islands and CGI shores showed a higher CGI and CGI methylation densities than gene bodies and promoter regions, respectively. These data are also consistent with the findings in a study of caprine hypothalamus and ovary tissues, which reported that approximately 50% of the CGIs in are methylated [ 32 ]. Although there were no apparent CG methylation differences between the groups, the overall methylation level (including mCHG and mCHH) of the telogen group was higher than that of the anagen group.…”

DNA methylation and histone acetylation are involved in Wnt10b expression during the secondary hair follicle cycle in Angora rabbits

“…The results revealed that 45 CpG sites were hypomethylated or virtually unmethylated during the SHF cycle. Our findings are supported by previous studies in other livestock species reporting that gene bodies (exons and introns) exhibit the highest levels of CG methylation relative to gene promoters in skin tissue during anagen or telogen (Frattini et al., 2017; Lee et al., 2014).…”

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“…beads) twice 69 . The methods described below have been reproduced in part from Frattini et al 2017 70 . RNA-Seq libraries were generated using the Illumina TruSeq RNA Sample Preparation v2 Kit but with one-half of the recommended reagent volumes.…”