A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

Abstract

CpG islands (CGIs) are dense clusters of CpG sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack of cytosine methylation, we devised a CGI enrichment method based on nonmethylated CpG affinity chromatography. The resulting library was sequenced to define a novel human blood CGI set that includes many that are not detected by current algorithms. Approximately half of CGIs were associated with annotated gene transcription start sites, the remainder being intra- or intergenic. Using an array representing over 17,000 CGIs, we established that 6%–8% of CGIs are methylated in genomic DNA of human blood, brain, muscle, and spleen. Inter- and intragenic CGIs are preferentially susceptible to methylation. CGIs showing tissue-specific methylation were overrepresented at numerous genetic loci that are essential for development, including HOX and PAX family members. The findings enable a comprehensive analysis of the roles played by CGI methylation in normal and diseased human tissues.

Author Summary

The human genome contains about 22,000 genes, each encoding one of the proteins required for human life. A particular cell type (e.g., blood, skin, etc.) expresses a specific subset of protein genes and silences the remainder. To shed light on the mechanisms that cause genes to be activated or shut down, we studied DNA sequences called “CpG islands” (CGIs). These sequences are found at over half of all human genes and can exist in either the active or silent state depending on the presence or absence of methyl groups on the DNA. We devised a method for purifying all CGIs and showed that, unexpectedly, only half occur at the beginning of genes near the promoter, the rest occurring within or between genes. Notably, methylation of CGIs causes stable gene silencing. We tested 17,000 CGIs in four human tissues and found that 6%–8% were methylated in each. Genes whose protein products play an essential role during embryonic development were preferentially methylated, suggesting that gene expression during development could be regulated by CGI methylation.

Abstract

CpG island methylation, an epigenetic phenomenon usually associated with abnormality in disease, is little characterised in the context of "normal" human cells. Here we highlight tissue-specific CpG Island methylation, which frequently associates with developmental genes.