The Transcriptional Coactivators SAGA, SWI/SNF, and Mediator Make Distinct Contributions to Activation of Glucose-repressed Genes

Abstract

The paradigm of activation via ordered recruitment has evolved into a complicated picture as the influence of coactivators and chromatin structures on gene regulation becomes understood. We present here a comprehensive study of many elements of activation of ADH2 and FBP1, two glucose-regulated genes. We identify SWI/SNF as the major chromatin-remodeling complex at these genes, whereas SAGA (Spt-AdaGcn5-acetyltransferase complex) is required for stable recruitment of other coactivators. Mediator plays a crucial role in expression of both genes but does not affect chromatin remodeling. We found that Adr1 bound unaided by coactivators to ADH2, but Cat8 binding depended on coactivators at FBP1. Taken together, our results suggest that commonly regulated genes share many aspects of activation, but that gene-specific regulators or elements of promoter architecture may account for small differences in the mechanism of activation. Finally, we found that activator overexpression can compensate for the loss of SWI/SNF but not for the loss of SAGA.The paradigm of eukaryotic gene activation centers on activators recognizing and binding to unique sequences of DNA and then recruiting coactivators and the transcription machinery (1). The order of recruitment events has been determined for several yeast genes, including HO (2), PHO5 (3-6), and the GAL genes (7-9). Based on these and other studies, the idea of activation has evolved beyond simple ordered recruitment.One of the reasons for this evolving picture of activation is the finding that many coactivator complexes can play multiple roles. For example SAGA 4 functions as a histone-acetyltransferase (HAT) at the HO promoter (10), but it is required for a non-HAT function at the GAL1 promoter (7). In cases such as these, knowing the order in which SAGA arrives at a promoter is insufficient for understanding its role in activation. The dual nature of coactivators emphasizes the need to look not only at their recruitment to the promoter, but also at the functional consequences of this recruitment. Glucose-regulated genes, under the control of Snf1, the homolog of the mammalian AMP-activated kinase, provide a model for such comprehensive studies. In response to glucose starvation, ϳ200 genes are activated by Snf1, many of which depend on the transcription factors Adr1 and Cat8 (11). Previous work in our laboratory has established that SAGA, SWI/SNF, and Mediator are recruited by these two activators upon derepression (12). However, the specific roles of these coactivators and their interactions at these genes remain undetermined.This subset of genes allowed us to address several factors that may influence the mechanisms of activation. First, we focused on two genes, ADH2 and FBP1, which have differential dependences on both the activators Adr1 and Cat8 (13), and on the repressor Mig1 (14), allowing us to determine if trends were regulator-specific. Second, these promoters have established chromatin structures providing a basis for examining the impact of promoter architecture o...

Genome-wide cooperation by HAT Gcn5, remodeler SWI/SNF, and chaperone Ydj1 in promoter nucleosome eviction and transcriptional activation

“…Hyperacetylated histones promote recruitment of SWI/SNF in vitro (Hassan et al 2002), consistent with the requirement for both Gcn5, the HAT subunit in SAGA, and Snf2 for nucleosome remodeling at ADH2 (Verdone et al 2002;Biddick et al 2008) and PHO8 (Gregory et al 1999). Gcn5 and Snf2 also promote remodeling at PHO5 under suboptimal induction conditions (Barbaric et al 2007), although Pho4 binding at PHO5 is impaired in snf2Δ and gcn5Δ cells under certain conditions (Adkins et al 2007).…”

Activation of a Poised RNAPII-Dependent Promoter Requires Both SAGA and Mediator

“…Although we found that Mediator occupies the CYC1 promoter only after activation, the Mediator complex has a well-established role in RNAPII recruitment (Biddick et al 2008;Esnault et al 2008). To rule out the possibility that Mediator influences recruitment of RNAPII to the CYC1 promoter, chromatin immunoprecipitation of RNAPII was performed in the med18D and med19D strains.…”

The AMP-activated Protein Kinase Snf1 Regulates Transcription Factor Binding, RNA Polymerase II Activity, and mRNA Stability of Glucose-repressed Genes in Saccharomyces cerevisiae

“…Relief from glucose repression (derepression) is accompanied by promoter binding of Adr1 in a Snf1-dependent fashion (31) and requires Snf1-dependent histone H3 hyperacetylation of promoter nucleosomes (20,32). Chromatin remodeling precedes and is required for gene activation and requires Snf1, Adr1, and Cat8, which recruit the Swi/Snf chromatin remodeling complex as well as the SAGA (Spt-Ada-Gcn5 acetyltransferase), and NuA4 histone acetyltransferase complexes (33,34). Impaired histone deacetylase activity or deletion of the histone H3 or histone H4 tail allows Adr1 binding and preinitiation complex (PIC) formation in the presence of glucose (32,35,36).…”