Open Access Research article

Genome-wide analysis of DNA methylation in bovine placentas

Jianmin Su12, Yongsheng Wang12, Xupeng Xing12, Jun Liu12 and Yong Zhang12*

Author Affiliations

1 College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, PR China

2 Key Laboratory of Animal Bio-Technology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, PR China

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BMC Genomics 2014, 15:12  doi:10.1186/1471-2164-15-12

Published: 8 January 2014

Abstract

Background

DNA 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.

Results

We 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.

Conclusions

We 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.