Abstract
BackgroundDNA methylation is an important epigenetic modification that is essential for epigenetic gene regulation in development and disease. To date, the genome-wide DNA methylation maps of many organisms have been reported, but the methylation pattern of cattle remains unknown.ResultsWe showed the genome-wide DNA methylation map in placental tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq). In cattle, the methylation levels in the gene body are relatively high, whereas the promoter remains hypomethylated. We obtained thousands of highly methylated regions (HMRs), methylated CpG islands, and methylated genes from bovine placenta. DNA methylation levels around the transcription start sites of genes are negatively correlated with the gene expression level. However, the relationship between gene-body DNA methylation and gene expression is non-monotonic. Moderately expressed genes generally have the highest levels of gene-body DNA methylation, whereas the highly, and lowly expressed genes, as well as silent genes, show moderate DNA methylation levels. Genes with the highest expression show the lowest DNA methylation levels.ConclusionsWe have generated the genome-wide mapping of DNA methylation in cattle for the first time, and our results can be used for future studies on epigenetic gene regulation in cattle. This study contributes to the knowledge on epigenetics in cattle.
Highlights
DNA methylation is an important epigenetic modification that is essential for epigenetic gene regulation in development and disease
DNA methylation preferentially occurs at the 5′ position of cytosine in CpG dinucleotides, which are mostly found in clusters known as CpG islands (CGIs) [1]
Global mapping of DNA methylation in cattle To study the global mapping of DNA methylation in cattle, we generated a total of 8.1 Gb MeDIP-seq data from two placental samples, including 81,632,654 (SCNT) and 83,673,470 raw reads
Summary
DNA methylation is an important epigenetic modification that is essential for epigenetic gene regulation in development and disease. DNA methylation, a major epigenetic modification of the genome found in most eukaryotes, is essential for normal development and crucial in many biological processes, such as gene expression regulation, genomic imprinting, X-chromosome inactivation, suppression of repetitive elements, and carcinogenesis. The expression and DNA methylation levels of several imprinted genes were aberrant in the placenta of deceased cloned calves [22]. The principal cause of the developmental abnormalities of the fetus and placenta in cloned animals is aberrant epigenetic nuclear reprogramming of the donor somatic cell, which involves various epigenetic modifications.
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