Investigating Gene Regulation by the Tup1-Cyc8 (Ssn6) Complex in the yeast Saccharomyces cerevisiae

Abstract

The Tup1-Cyc8 (Ssn6) co-repressor complex is a powerful epigenetic regulator of genes in the yeast Saccharomyces cerevisiae. The highly conserved complex brings about a repressive chromatin structure at regulatory regions of its target genes or prevents the recruitment of the factors needed for activation of transcription. The FLO family of genes are repressed by the Tup1-Cyc8 complex, these genes encode the proteins required for flocculation, a stress response in yeast where the cells aggregate, or form flocs, to protect cells within the floc. Interestingly each mutant strain (tup1, cyc8 and tup1 cyc8) has a distinct flocculant phenotype. The tup1 strain displays large, dense flocs compared to smaller, more dispersed flocs associated with the cyc8 strain, whereas the tup1 cyc8 strain displays an intermediate flocculant phenotype. RT-qPCR showed that FLO1, considered to be the dominant member of this family of genes, is highly de-repressed in the tup1 and tup1 cyc8 deletion strains. This suggests that Tup1 makes the dominant contribution to repression of this gene. However, this pattern is not seen at all target genes. The results of RNA-Sequencing show a core set of 429 genes significantly upregulated in all three mutant strains. These genes, on average, show the highest de-repression in the cyc8 and tup1 cyc8 mutant strains. Indicating that Cyc8 makes the dominant contribution to repression at the majority of target genes. Together these results indicate that each of the subunits of the Tup1-Cyc8 complex may be dominant in bringing about repression at different sets of genes.