Genomic microarrays

A number of genomic microarray platforms have become available in recent years. It is important to distinguish between microarrays that have a spotted selection of genomic sequences and those with a broad representation of the entire genome. Several microarrays have been designed for CGH measurements. In this case, large-insert genomic clones, such as bacterial artificial chromosomes (BACs), are used for array spots (10). Although this type of microarray can be used in the ChIP-on-chip technique, the large size of the BAC clones makes it difficult to identify the target sequence of the nuclear factor. Once a positive spot has been identified, additional studies would be necessary to map the target sequence at a higher resolution within the BAC clone.

An interesting specialized genomic microarray, designed by Tim Huang (11), consists of a library of CpG island clones. This microarray has been used in combination with a method known as differential methylation hybridization. Linker-ligated genomic DNA is digested with a methylation-sensitive restriction enzyme, amplified by PCR, and hybridized to the array. Many CpG islands become methylated in cancer and are thereby protected from methylation-sensitive restriction cleavage and so can be amplified by

PCR, producing array-hybridization signals (12, 13). Since CpG islands generally coincide with the promoter of many genes, a CpG island micro-array can be useful for investigating the binding sites at the regulatory regions of CpG-island-containing genes (14). We have recently used Tim Huang's CpG-island microarray to reveal novel targets of methyl-CpG binding domain (MBD) proteins in cancer (15).

Finally, there are several promoter-based microarrays. Although this type of microarray is obviously of great interest for its potential use for studying the binding of factors to regulatory regions, it must be remembered that the entire human genome is not represented on the microarray.

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