Distinct phenotypes and transcriptomes of tup1 and cyc8 mutants suggest novel roles for TUP1 and CYC8 in Saccharomyces cerevisiae

Abstract

The Tup1-Cyc8 (Ssn6) co-repressor complex is a regulator of gene transcription in the yeast Saccharomyces cerevisiae. This project provides insights into the distinct roles of Tup1p and Cyc8p in gene repression, identifies core sets of genes regulated by the Tup1-Cyc8 complex, and demonstrates the influence of flocculation on gene regulation. Flocculation is a stress response whereby cells aggregate. The FLO family of genes, which encode proteins involved in flocculation, are repressed by the Tup1-Cyc8 complex.

Each mutant strain (tup1, cyc8 and tup1 cyc8) had a distinct flocculant phenotype and RNA-Seq analysis showed that different genes were upregulated in each of the mutant strains. However, a group of 429 genes were at least twofold upregulated in all three mutant strains compared to wt. Most of the 429 commonly upregulated genes showed the highest upregulation in the cyc8 and tup1 cyc8 mutant strains, indicating that CYC8 made the dominant contribution to repression at most Tup1-Cyc8 target genes. Conversely, a group of 40 genes showed relatively high upregulation in both the tup1 and tup1 cyc8 mutant strains. FLO1, a member of the FLO family of genes, was part of this set of 40 genes, which were enriched within regions of the genome that are heavily regulated by the deacetylase, HDA1. Hda1p has been shown to interact with Tup1p, and in a hda1 cyc8 mutant strain repression of FLO1 was abolished. This indicates that TUP1 dependent recruitment of Hda1p provided a major contribution to repression of FLO1.

The Anchor Away (AA) technique allows for a target nuclear protein to be conditionally sequestered to the cytoplasm. Using a Cyc8-AA strain I investigated if flocculation influences gene transcription. I compared the transcriptomes of a flocculant and non-flocculant Cyc8-AA strain. Flocculation influenced the regulation of 344 genes, whereas a set of 477 genes showed changes in gene expression that were not affected by flocculation. Therefore, this set of 477 genes were regulated solely by the Tup1-Cyc8 complex.