DNA Methylation Patterns in Two Porcine Tissues

While many studies suggest an essential role of DNA methylation in various biological processes, the analysis of methylation status of normal tissues could provide further insight into the molecular basis of tissue differentiation as well as improve our understanding of how normal DNA methylation patterns affect global gene expression.

We established a genome-wide high resolution map of methylation (BS-seq) in porcine liver and brain tissues and integrated these data with expression data (RNA-seq) of the same samples. The overall CpG methylation level of the porcine genome was 61% in liver and 66% in brain tissue. Higher methylation level was observed in gene body regions especially near the transcription termination site (TTS) as compared to promoter region and the neighboring transcription start site (TSS). Surprisingly, the number of non-CG sites is three times higher than the number of methylated cytosines in CHG and CHH context in brain relative to liver. Our results demonstrate that the methylation level of promoters is negatively correlated with gene expression. We also investigated the correlation between methylation and gene expression around TSS and TTS (± 5kb) for both tissues and found that CpG methylation around the TSS is negatively associated with gene expression while methylation near the TTS is positively correlated. The integration of whole genome methylation and global expression profiles provides a promising tool to study the regulation of gene expression by methylation.