DISSECTING THE REGULATORY CIRCUITRY OF A EUKARYOTIC GENOME

Genome-wide expression analysis was used to identify genes whose expre ssion depends on the functions of key components of the transcription initiation machinery in yeast. Components of the RNA polymerase II hol oenzyme, the general transcription factor TFIID, and the SAGA chromati n modification complex were found to have roles in expression of disti nct sets of genes. The results reveal an unanticipated level of regula tion which is superimposed on that due to gene-specific transcription factors, a novel mechanism for coordinate regulation of specific sets of genes when cells encounter limiting nutrients, and evidence that th e ultimate targets of signal transduction pathways can be identified w ithin the initiation apparatus.