Microarray technology coupled with chromatin iminunoprecipitation (ChIP) will be used for the genome wide mapping of bZIP protein DNA-binding sites in Saccharomyces cerevisiae. bZIP proteins display distinct DNA-binding characteristics (specific binding to ATF/CREB, AP-l, or YAP sites) in vitro. It is unclear how these specificities are borne out in vivo, on the genomic scale. A modest number of bZIP-regulated genes have been identified, likely representing a small fraction of the total bZIP target genes. Whole-genome binding site maps for several bZIP derivatives will be generated, allowing for the identification of strong candidate genes for regulation by the specific factors in question. This will also contribute to the understanding of bZIP protein DNA-binding characteristics and requirements. Binding patterns will be evaluated in appropriate mutant genetic backgrounds to study positive or negative interplay between bZIP family members. Chimeric bZLP derivatives will be produced, and their genomic DNA-binding patterns will be evaluated to determine which protein features contribute to DNA-binding specificity, and in what way. Natural bZIP protein levels will be perturbed to evaluate the extent to which genomic distributions are sensitive to protein concentration. This will provide additional insight into the DNA determinants that direct specific levels of bZIP-protein affinity for particular DNA sites.
