CpG islands as gene markers in the human genome.

CpG islands are short, dispersed regions of unmethylated DNA with a high frequency of CpG dinucleotides relative to the bulk genome. We have analyzed 375 genes and 58 pseudogenes from the human entries in the EMBL Database for the presence of CpG islands. All 240 islands identified are associated with genes, and almost all cover at least a part of one exon; i.e., they are useful landmarks in the genome for identifying genes. More than half of the genes analyzed were associated with islands. All housekeeping and widely expressed genes have a CpG island covering the transcription start, whereas 40% of the genes with a tissue-specific or limited expression are associated with islands. In this latter group of genes, the position of the islands was not biased toward the 5' end of the transcription unit.