In the January 25 Nature, Iyer et al. describe an elegant technique to identify transcriptional target genes throughout the genome (Nature 2001, 409:533-538). They combined chromatin immunoprecipitation (ChIP) with microarray analysis (DNA chips) to probe individual protein-genome interactions. The technique involved cross-linking, immunoprecipitation, PCR amplification and fluorescent labeling, followed by hybridization to microarrarys containing genomic DNA. They searched the yeast genome for intergenic regions that contained functional binding sites for the cell cycle transcription factors SBF (Swi6/Swi4) and MBF (Swi6/Mbp1). They identified 183 SBF-regulated genes, many of which are involved in budding or cell wall biogenesis. The 98 potential MBF target genes include those implicated in DNA replication, recombination and repair. And 43 loci appear to be targets of both factors. This is a powerful technique for identifying common and distinct targets of related transcription factors.

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