Purification of CpG islands using a methylated DNA binding column

CpG islands are short stretches of DNA containing a high density of non–methylated CpG dinucleotides, predominantly associated with coding regions. We have constructed an affinity matrix that contains the methyl–CpG binding domain from the rat chromosomal protein MeCP2, attached to a solid support. A column containing the matrix fractionates DNA according to its degree of CpG methylation, strongly retaining those sequences that are highly methylated. Using this column, we have developed a procedure for bulk isolation of CpG islands from human genomic DNA. As CpG islands overlap with approximately 60% of human genes, the resulting CpG island library can be used to isolate full–length cDNAs and to place genes on genomic maps.