Many methods have been developed to identify genomic targets of DNA-binding factors. Here we outline and discuss our adaptation of the chromatin immunoprecipitation (ChIP) assay to a high-throughput microarray based method for discovering genomic regions occupied by human DNA-binding proteins. Others, primarily using yeast model systems, have also explored the use of coupled chromatin immunoprecipitation and microarrays to identify large sets of binding sites of DNAbinding proteins. For example, binding sites for yeast transcriptional regulators such as SBF, MBF, Gal4, Ste12 and Rap1 have been identified. Other studies have focused on chromatin remodeling factors, such as components of the RSC complex and components of the DNA replication machinery, such as ORC and MCMs.

In certain cases, the investigators have monitored all intergenic regions and/or known promoters in the yeast genome. In other cases, the authors have taken advantage of the relatively small size of the yeast genome to spot probes which span the entire genome (both intergenic regions and open reading frames) onto a microarray. A recent, Herculean effort by Lee et al.7 has utilized ChIPs and microarrays to identify the global binding locations of the majority of known yeast transcription factors and used the resulting data along with data from mRNA expression array analysis to define the regulatory networks that exist in yeast.