One of the key determinants in the control of gene expression in mammals, and the most common covalent modification of DNA in eukaryotes, is methylation at the carbon 5 of cytosine residues. DNA methylation patterns can be inherited and influenced by environment, diet and aging, and disrupted in diseases. Although methylomes from several issues were investigated in some species, goats are still unexplored. We analysed the methylome of hypothalamus and ovary from 3 adult Saanen goats, trying to take the first steps on the potential epigenetic involvement in goat biology. In order to evaluate differentially methylated regions, 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 at least 20 million reads per sample, covering an average of about 30% of the goat genome. Further analyses were performed to identify peaks corresponding to hyper-methylated regions. Chromosomes 12 and 20 showed the lowest density of methylated fragments on both issues, while chromosomes 18 and 19 the highest. We also investigated methylation distribution in the different genomic regions: promoter, intron, exon, downstream of gene, distal and intergenic. Introns showed the highest methylation frequency on both hypothalamus (34.6% on the total of the region detected) and ovary (39.1%). Matching the methylation pattern of hypothalamus versus ovaries of the three goats under study we looked for the biological and molecular pathways involving genes with issue-specific methylation peaks. Pathways with the highest p-values (P < 0.001) affect RNA binding in ovary, and regulation of the immune system processes in hypothalamus. This is the first work dealing with a global methylation pattern in Capra hircus: our pioneering results could be helpful for a deeper comprehension of the complex epigenetic machinery in this species.
DNA Methylation Pattern of Hypothalamus and Ovary in Capra Hircus
E Capra;S Chessa;B Castiglioni;A Stella;G Pagnacco
2015-01-01
Abstract
One of the key determinants in the control of gene expression in mammals, and the most common covalent modification of DNA in eukaryotes, is methylation at the carbon 5 of cytosine residues. DNA methylation patterns can be inherited and influenced by environment, diet and aging, and disrupted in diseases. Although methylomes from several issues were investigated in some species, goats are still unexplored. We analysed the methylome of hypothalamus and ovary from 3 adult Saanen goats, trying to take the first steps on the potential epigenetic involvement in goat biology. In order to evaluate differentially methylated regions, 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 at least 20 million reads per sample, covering an average of about 30% of the goat genome. Further analyses were performed to identify peaks corresponding to hyper-methylated regions. Chromosomes 12 and 20 showed the lowest density of methylated fragments on both issues, while chromosomes 18 and 19 the highest. We also investigated methylation distribution in the different genomic regions: promoter, intron, exon, downstream of gene, distal and intergenic. Introns showed the highest methylation frequency on both hypothalamus (34.6% on the total of the region detected) and ovary (39.1%). Matching the methylation pattern of hypothalamus versus ovaries of the three goats under study we looked for the biological and molecular pathways involving genes with issue-specific methylation peaks. Pathways with the highest p-values (P < 0.001) affect RNA binding in ovary, and regulation of the immune system processes in hypothalamus. This is the first work dealing with a global methylation pattern in Capra hircus: our pioneering results could be helpful for a deeper comprehension of the complex epigenetic machinery in this species.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
