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Scientists use targeted methylation and microarrays to map locations of DNA binding proteins
By Bijal P. Trivedi

The binding of proteins to DNA controls many essential functions in cells, from switching genes on and off to repairing DNA to packaging DNA into chromosomes. Identifying binding sites in the genome is difficult and laborious. Now, American and Dutch researchers have used DNA microarrays, or gene chips, to simultaneously tag and map the location in the genome of hundreds of these binding sites. The team proposes that similar studies on a genome-wide scale will broaden our understanding of how genes are regulated.

Bas van Steensel, of the University of Amsterdam, and colleagues tested their strategy in the fruit fly Drosophila melanogaster by pinpointing the binding sites of the three fly proteins—HP-1, GAF and Sir2—that bind DNA. The researchers found that each protein bound to a distinct set of genes.

HP-1 bound to a handful of genes previously identified as binding targets. This protein also bound to 13 transposons, or stretches of DNA that 'jump' throughout the genome. HP-1 may be some sort of defense mechanism that prevents transposons from wandering, the researchers say.

The GAF protein bound more than 100 different locations in the genome, most commonly at repetitive DNA sequences in the regulatory regions of genes. The third protein, Sir2, can silence genes in yeast, but it appears to have a different role in Drosophila. The genes it targeted were active.

The microarray used in the study contained only 300 Drosophila cDNAs and some random sequences from around the genome. Larger arrays with genomic DNA could provide a more detailed picture of how enhancer and promoter regions influence the activity of genes, the researchers write in Nature Genetics.

The new method involves tethering to a binding protein an enzyme that leaves a chemical tag near the binding site. The enzyme is called DNA adenine methyltransferase, and is affectionately known as 'Dam.' The protein transports Dam to the binding site, where it attaches molecules called methyl groups to the DNA. These segments are labeled with a fluorescent dye and read by DNA microarrays, providing researchers with the location in the genome of each methyl group, and thus each binding site.

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van Steensel, B. et al. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-308 (March 2001).

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