To whom correspondence should be addressed. Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. 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 activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.
Many proteins bind to specific sites in the genome to regulate genome expression and maintenance.
The reprogramming of gene expression that occurs as cells move through the cell cycle, or when cells sense changes in their environment, is effected in part by changes in the DNA binding status of transcriptional activators. Our understanding of these proteins and their functions is limited by our knowledge of their binding sites in the genome. Briefly, cells were fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest were enriched by immunoprecipitation with a specific antibody. The genome-wide location profiling method.