The analysis of the methylome of Capra hircus

Methylation at the carbon 5 position of cytosine residues is among the best studied epigenetic modification, and a fundamental layer of cellular differentiation through the control of transcriptional potential. DNA methylation patterns can be inherited and influenced by environment, diet and aging, and disrupted in diseases. Complete DNA methylomes for several organisms are now available, helping to clarify the evolutionary story of this epigenetic mark and its distribution in key genomic elements. At the present, methylome of the domestic goat, Capra hircus is unexplored, and hence to contribute information on epigenetic modification in the species, we analyzed the methylome of two tissues, ovary and hypothalamus, from 3 adult Saanen goats. DNA methylation patterns are increasingly studied using high throughput sequencing methods. In order to evaluate differentially methylated region, we used Methylated DNA binding domain sequencing (MBD-seq), with enrichment of methylated DNA fragments and next generation sequencing (NGS - Hiseq 2000 Illumina). We produced least 23 million reads per sample, which were aligned to the goat reference genome with a minimum success rate of 97.5%. Further analyses were performed to identify peaks corresponding to hyper-methylated regions. Matching the methylation pattern of hypothalamus versus ovaries of the three goats under study we found 4687 methylated fragments showing significant differences (P < 0.001) between tissues. Chromosomes 19 and 23 showed the highest density of methylated fragment, respectively every 0.56 Mb and 0.52 Mb in ovaries. Chromosomes 19 and 25 had the highest density of methylated fragment in the hypothalamus, every 0.58 Mb for both the chromosomes. The chromosome with least methylated fragments was the X, with a statistically significant (P < 0.001) methylated fragment every 9.38 Mb in the ovaries and 6.42 Mb in the hypothalamus. This is the first work dealing with methylome in Capra hircus: the outcoming pioneering preliminary results could be helpful for a deeper comprehension of the complex epigenetic machinery.