Figure 1. Three-dimensional structure of a double-stranded DNA fragment containing four methylated CpG dinucleotides. The methyl groups of the complementary methylated CpGs protrude into the major groove of the DNA molecule.

Figure 2. Examples of human genes with and without CpG islands. The diagrams show the distribution of CpGs across the 5¢ end of four human genes. The -globin and the aldose reductase (ADO) genes are associated with CpG islands, as is clearly shown by the high density of CpG dinucleotides around their 5¢ ends. In contrast, the frequency of CpGs at the 5¢ ends of the -globin and the 5-aminolevulinate synthase 2 (5-ALAS) genes is similar to the genome average. Vertical lines indicate CpGs. Boxes represent exons and arrows show the transcription initiation site. Only exon 1 of the ADO and 5-ALAS genes is shown.

Figure 3. Schematic representation of the chromatin structure of a CpG island. Vertical lines indicate CpGs. Most CpGs outside the islands are methylated (indicated by a black dot), while CpGs within the island remain nonmethylated. Transcription initiation from a nucleosome-free gap is indicated with an arrow. HS: sites of hypersensitivity to DNAase; MeCP: methyl CpG-binding protein; MBD: methyl CpG-binding domain.