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.
Highlights
DNA methylation in the mammalian genome arises due to covalent addition of a methyl group to the 59 position of cytosine in the context of the palindromic dinucleotide, CpG
To shed light on the mechanisms that cause genes to be activated or shut down, we studied DNA sequences called ‘‘CpG islands’’ (CGIs)
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
Summary
DNA methylation in the mammalian genome arises due to covalent addition of a methyl group to the 59 position of cytosine in the context of the palindromic dinucleotide, CpG. The pattern of CpG methylation in the human genome distinguishes two fractions with distinct properties: a major fraction (;98%), in which CpGs are relatively infrequent (on average 1 per 100 bp) but highly methylated (approximately 80% of all CpG sites), and a minor fraction (,2%) that comprises short stretches of DNA (;1,000 bp) in which CpG is frequent (;1 per 10 bp) and methylation-free The latter are known as CpG islands (CGIs) and they frequently colocalise with the transcription start sites (TSSs) of genes [3,4]. Demethylation of endogenous methylated CGIs using DNA methytransferase inhibitors can restore expression of the gene [6] These findings demonstrate that dense CpG methylation prevents expression of CGI promoters. Several additional candidates for CGI methylation in normal tissues have been reported [11,12], and the number of cases has recently grown due to large-scale bisulfite sequencing [13] and analysis of promoter methylation using microarrays [14]
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