Promoter-dependent Roles for the Srb10 Cyclin-dependent Kinase and the Hda1 Deacetylase in Tup1-mediated Repression inSaccharomyces cerevisiae

Abstract

The Tup1-Ssn6 complex has been well characterized as a Saccharomyces cerevisiae general transcriptional repressor with functionally conserved homologues in metazoans. These homologues are essential for cell differentiation and many other developmental processes. The mechanism of repression of all of these proteins remains poorly understood. Srb10 (a cyclin-dependent kinase associated with the Mediator complex) and Hda1 (a class I histone deacetylase) have each been implicated in Tup1-mediated repression. We present a statistically based genome-wide analysis that reveals that Hda1 partially represses roughly 30% of Tup1-repressed genes, whereas Srb10 kinase activity contributes to the repression of ϳ15% of Tup1-repressed genes. These effects only partially overlap, suggesting that different Tup1-repression mechanisms predominate at different promoters. We also demonstrate a distinction between histone deacetylation and transcriptional repression. In an HDA1 deletion, many Tup1-repressed genes are hyperacetylated at lysine 18 of histone H3, yet are not derepressed, indicating deacetylation alone is not sufficient to repress most Tup1-controlled genes. In a strain lacking both Srb10 and Hda1 functions, more than half of the Tup1-repressed genes are still repressed, suggesting that Tup1-mediated repression occurs by multiple, partially overlapping mechanisms, at least one of which is unknown. INTRODUCTIONThe Tup1-Ssn6 complex is a general transcriptional repressor in Saccharomyces cerevisisae that controls a diverse set of genes generally characterized as being important for adaptation to nonstandard growth. Homologues of Tup1 have been identified in several other organisms (for example, unc-37 in Caenorhabditis elegans, Groucho in Drosophila, and TLE proteins in humans), and their repression functions are essential for embryonic development, cell differentiation, neurogenesis, and other developmental processes (Pflugrad et al., 1997;Fisher and Caudy, 1998;Levanon et al., 1998;Grbavec et al., 1999). Consequently, a better understanding of the mechanism of Tup1-mediated repression in yeast should illuminate this same process and its wide-ranging downstream consequences in other organisms. The Tup1-Ssn6 complex does not itself bind DNA but is recruited to target promoters through an association with sequence-specific DNA binding proteins; however, the crucial question of how transcriptional repression is established once this event occurs has not been clearly answered.Two models for Tup1-mediated repression are supported by a number of earlier observations. One proposes that Tup1 produces a transcriptionally repressed chromatin state by recruiting histone deacetylases (HDACs). Hda1, a class I HDAC, has emerged as the most likely deacetylase to be acting with Tup1. Hda1 binds to Tup1 in vitro and an HDA1 deletion results in hyperacetylation of histones at several Tup1-controlled genes (Wu et al., 2001). Hyperacetylation of Tup1-repressed genes also is seen when Tup1 is deleted (Bone and Roth, 2001;Davie et al., 2002). ...

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

“…and ergosterol biosynthesis (erg2 and erg3). Interestingly, single deletions in SSN6, RPD3, or TUP1-components of a well-characterized transcriptional silencing complexresulted in the differential expression of .180 genes (Smith and Johnson 2000;Green and Johnson 2004), many of which were also differentially expressed in PSY3642. Motif enrichments in the promoters of upregulated genes implicated transcription factors associated with several biological processes ( Figure 3B).…”

A chromatin-mediated mechanism for specification of conditional transcription factor targets

“…Hda1 is a class 2 histone deacetylase required for repression of a subset of Tup1-repressed genes 23 . To determine whether recruitment of Hda1 is required for Tup1's role in restricting Rap1 targets, we tested Rap1 localization in an hda1Δ strain.…”

“…To corroborate these results, we used existing data 23,28 to ask if the mRNA expression of lowglucose targets was affected in tup1Δ, isw2Δ, or hda1Δ strains. Expression of low-glucose targets was increased in tup1Δ and hda1Δ, but not in isw2Δ strains, whereas the expression of static targets was unaffected by these mutations ( Figure 3D).…”

Transcriptional activating regions target attached substrates to a cyclin-dependent kinase

“…Thus, a series of phosphorylations would be triggered by the kind of binding reaction we have described as transcription is activated. In addition to its positive role in gene activation (2,(5)(6)(7)20), Srb10͞11 has also been characterized as required for efficient repression by Tup1͞Ssn6, a protein complex that is recruited to and works at many yeast genes (12,(21)(22)(23)(24)(25). Suggestions as to the mechanism of this effect have been proposed, but the matter has not been fully resolved (1,3,8,21,22).…”