Defining the Role of Multiple Mechanisms in Tup1-mediated Repression in Saccharomyces Cerevisiae

Book excerpt: Eukaryotic transcription is a highly regulated cellular process that represents the balance of positive and negative factors acting on the promoter of a given gene. In Saccharomyces cerevisiae , the Tup1-Sn6 repressor complex negatively influences the expression of approximately five percent of all genes. Functional homologs of this complex exist in other organisms, and a better understanding of the functions of Tup1 in yeast will provide us with insight into the broader questions of how transcriptional repression is regulated across species and the consequences of its misregulation. Most of the targets of Tup1-mediated repression have been identified, but the means by which Tup1 inhibits transcription of these target genes is not entirely clear. To explore this question, we focused on two proteins know to be involved in Tup1-mediated repression--Hda1, a histone deacetylase, and Srb10, a cyclin-dependent kinase associated with the Mediator complex. We disrupted each of these genes separately and in combination and compared the effects of the disruptions on Tup1-regulated genes using a statistical analysis of microarray data. We saw a strong overlap between the genes derepressed in an hda1DELTA strain and the set of Tup1-regulated genes and a smaller but still significant intersection between the mutant srb10 and tup1DELTA datasets. Tup1-regulated genes can be divided into subclasses based on their requirements for Hda1 and/or Srb10 function for full repression. However, the magnitudes of the derepression defect in these mechanistic disruptions are rarely as severe as that of a tup1DELTA strain. We also showed that there was not a strict correlation between the loss of Hda1 deacetylation function and a loss transcriptional repression. These data imply that there are multiple and overlapping mechanisms that contribute to full Tup1-mediated repression and that often several of these mechanisms are acting at a given promoter to repress transcription. We also tried to better understand the mechanisms of Tup1-mediated repression by analyzing the functions of Tup1 itself. We mutagenized a surface of Tup1 conserved among metazoan homologs and measured the effects of the mutants on Tup1-mediated repression by microarray analysis. The mutant alleles represented a range of deficiencies in repression, with the strongest mutant affecting about half of Tup1-regulated genes. For one set of Tup1-regulated genes, some of the point mutants disrupted the recruitment of Tup1 to regulated promoters; however, for the majority of Tup1-repressed genes, the mutant proteins are properly recruited but cannot repress transcription. These point mutants of Tup1 demonstrate that the conserved surface of Tup1 is important for two different aspects of Tup1-mediated repression--recruitment to repressed promoters and the active repression of transcription.