Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters

Abstract

The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X–linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing. About half of all human genes contain a CpG-rich region called a “CpG island” in the 5′ area, often encompassing the promoter and transcription start site of the associated gene. DNA methylation was initially suggested to control tissue-specific gene expression in mammalian cells, but most promoter region CpG islands were found to be unmethylated regardless of tissue specificity of expression. In this study, we discovered an exceptional subset of autosomal genes associated with dense promoter CpG islands that is methylated in normal tissues. We observed tissue-specific gene silencing correlated with hypermethylation in this class of genes, and provided evidence for a direct role of methylation in maintaining the silencing state. Furthermore, we identified five sequence motifs significantly enriched in this class of genes, suggesting the influence of cis-regulatory elements on the establishment and/or stability of DNA methylation. Together, these results provide important new insights into the role of CpG island methylation in normal development and differentiation.