The Enrichment and Regulation of High-methylated CpG sites in CGI Border in ARPE-19 [MNase-seq]

Stable maintenance of cytosine methylation is essential for mammalian biological processes such as gene transcription. To investigate the relationship of stably high methylation sites with gene expression, we cultured the ARPE-19 for lasting 10 generations and performed reduced representation bisulfite sequencing (RRBS) to obtain the highly methylated sites. Then we analyzed the characters of highly methylated sites and detected the transcription level of the cells. After filtered the low methylated CpG island (CGI), we found that highly methylated CpG sites had a preference for CGI boundary. In the promoter CGI, only in the condition as the gene expression is inhibited and the promoter CGI is at a high methylation level, a significant enrichment of the highly methylated sites is observed in the promoter CGI boundary. Our results showed that the enrichment of high methylation sites at the boundary of the CGI in the promoter region would have a significant inhibitory effect on the gene expression. In summary, we provide new insights into the regulatory mechanisms of DNA methylation. Overall design: MNase-seq was used to detect the nucleosome occupancy.