Genome-wide expression and location profiling in Saccharomyces cerevisiae : experimental and graphical analysis

Abstract

Genome-wide expression analysis was used to identify genes whose expression depends on the functions of key components of the transcription initiation machinery in yeast. Components of the RNA polymerase II holoenzyme, the general transcription factor TFIID, and the SAGA chromatin modification complex were found to have roles in expression of distinct sets of genes. The results reveal an unanticipated level of regulation which is superimposed on that due to gene-specific transcription factors, a novel mechanism for co-ordinate regulation of specific sets of genes when cells encounter limiting nutrients, and evidence that the ultimate targets of signal transduction pathways can be identified within the initiation apparatus. Understanding how DNA-binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations where these proteins function in vivo. We developed a microarray method that reveals the genome wide location of DNA-bound proteins and used this method 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 Ga14 as cells respond to changes in carbon source, and by Thi2 in the absence or presence of thiarnin. The results identify pathways that are coordinately regulated by these regulators and reveal novel functions for these regulators. Understanding a transcriptional network such as these will be useful in constructing a cellular regulatory network map. The use of microarray technology has created new challenges in data analysis for biologists. Visual displays can greatly facilitate the analysis and communication of large quantities of data. We have created a Graphical Display Suite (GDS) that consists of a collection of tools to assist in the visualization of data from genome-wide experiments in S. cerevisiae. The ODS is web-accessible, easy to use, and additional components can easily be incorporated into its interface. This suite of tools has proven to be useful in revealing important biological insights.