Genome-wide location and function of DNA binding proteins

Understanding how DNA binding proteins control global gene expression and c hromosomal maintenance requires knowledge of the chromosomal Locations at w hich these proteins function in vivo. We developed a microarray method that reveals the genome-wide Location of DNA-bound proteins and used this metho d to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activ ators and reveal previously unknown functions for Gal4 and Ste12. Genome-wi de Location analysis will facilitate investigation of gene regulatory netwo rks, gene function, and genome maintenance.