SWI/SNF Binding to the HO Promoter Requires Histone Acetylation and Stimulates TATA-Binding Protein Recruitment

Abstract

We use chromatin immunoprecipitation assays to show that the Gcn5 histone acetyltransferase in SAGA is required for SWI/SNF association with the HO promoter and that binding of SWI/SNF and SAGA are interdependent. Previous results showed that SWI/SNF binding to HO was Gcn5 independent, but that work used a strain with a mutation in the Ash1 daughter-specific repressor of HO expression. Here, we show that Ash1 functions as a repressor that inhibits SWI/SNF binding and that Gcn5 is required to overcome Ash1 repression in mother cells to allow HO transcription. Thus, Gcn5 facilitates SWI/SNF binding by antagonizing Ash1. Similarly, a mutation in SIN3, like an ash1 mutation, allows both HO expression and SWI/SNF binding in the absence of Gcn5. Although Ash1 has recently been identified in a Sin3-Rpd3 complex, our genetic analysis shows that Ash1 and Sin3 have distinct functions in regulating HO. Analysis of mutant strains shows that SWI/SNF binding and HO expression are correlated and regulated by histone acetylation. The defect in HO expression caused by a mutant SWI/SNF with a Swi2(E834K) substitution can be partially suppressed by ash1 or spt3 mutation or by a gain-of-function V71E substitution in the TATA-binding protein (TBP). Spt3 inhibits TBP binding at HO, and genetic analysis suggests that Spt3 and TBP(V71E) act in the same pathway, distinct from that of Ash1. We have detected SWI/SNF binding at the HO TATA region, and our results suggest that SWI/SNF, either directly or indirectly, facilitates TBP binding at HO.The Saccharomyces cerevisiae HO gene encodes an endonuclease that initiates mating-type switching in haploid yeast cells, and the gene is governed by complex transcriptional regulation (for reviews, see references 22, 41, and 62). The gene is expressed only during the late G 1 phase of the cell cycle, and only in mother cells, one of the two progeny after mitotic division. The Ash1 repressor protein is required for this asymmetric expression, as HO is expressed in both mother and daughter cells in an ash1 mutant (14, 76).Chromatin structure plays an important role in transcriptional regulation, including at HO. There are two major classes of chromatin-modifying factors that alleviate the repressive effects of chromatin, the ATP-dependent chromatin-remodeling factors, such as SWI/SNF, and histone acetyltransferases (HATs) that covalently modify the N-terminal tails of histones by acetylation (84). Recent work has shown that transcription factors recruit chromatin-modifying factors to promoters and that at some promoters, the concerted action of chromatinremodeling and HAT complexes is required for gene activation (61). It has been shown for a number of promoters that sequence-specific DNA-binding proteins recruit chromatin remodelers and HATs in a temporal order.Sequential recruitment of transcription factors was first shown at the HO gene (25). HO contains two defined upstream promoter regions, URS1 and URS2, which contain recognition sites for the Swi5 and SBF sequence-specific DNA-binding factors,...

Chromatin and Transcription in Yeast

“…As several different activators can recruit Swi/Snf, the nature of the activator-Swi/Snf interaction is of interest; studies have shown that two or three Swi/Snf subunits can participate in recruitment (Neely et al 2002;Prochasson et al 2003;Ferreira et al 2009). Once at a promoter, the association of Swi/Snf is stabilized by the Snf2 bromodomain (Hassan et al 2001(Hassan et al , 2002, which binds acetylated histone tails (Dhalluin et al 1999); this represents an example of cooperation between Gcn5 histone acetylation and Swi/Snf and is consistent with reports that Swi/Snf association is Gcn5 dependent (Govind et al 2005;Mitra et al 2006). Although Swi/Snf acts at 59 regulatory regions to remodel or evict nucleosomes, it also appears to have a role in elongation in both yeast (Schwabish and Struhl 2007) and mammalian cells (Sullivan et al 2001;Corey et al 2003).…”

“…For example, when snf2D is combined with gcn5D (GCN5 encodes the histone acetyltransferase within SAGA), the double mutants are either inviable (Pollard and Peterson 1997) or extremely sick (Roberts and Winston 1997). There is strong evidence that both Swi/Snf chromatin-remodeling activity and Gcn5 histone-modifying activity function at an overlapping set of genes, including SUC2 (Sudarsanam et al 1999), HO (Cosma et al 1999;Mitra et al 2006), PHO5 (Barbaric et al 2007), GAL1 (Biggar and Crabtree 1999), and Gcn4-activated genes (Govind et al 2005). Other combinations also function together, such as Swi/Snf and Asf1 (Gkikopoulos et al 2009).…”

The SAGA continues: expanding the cellular role of a transcriptional co-activator complex

“…Notably, this effect is only seen in the presence of acetyl-CoA; thus the interaction between SAGA and chromatin is stabilized by its own HAT activity. Additionally, acetylation of chromatin by SAGA stabilizes the SWI/SNF chromatin remodeling complex, further contributing to a transcriptionally active chromatin environment (Hassan et al, 2002;Mitra et al, 2006). The function of the Spt7 bromodomain remains unknown; perhaps, it further stabilizes SAGA at gene promoters by binding acetylated proteins other than histones that are involved in transcription initiation.…”

Characterization of New Spt3 and TATA-Binding Protein Mutants of Saccharomyces cerevisiae: Spt3–TBP Allele-Specific Interactions and Bypass of Spt8

“…In other cases, Spt3 and Spt8 have been shown to play the opposite role, by inhibiting TBP-TATA interactions (Belotserkovskaya et al 2000;Yu et al 2003). The factors that determine positive vs. negative regulation by Spt3 and Spt8 are not currently understood, although the factors Swi/Snf or yFACT may play a role (Biswas 1 et al 2005;Mitra et al 2006). In addition to controlling the level of TBP-TATA interaction, Spt3 and Spt8 have been implicated in recruiting Mot1 to activate transcription by a mechanism independent of TBP recruitment (Topalidou et al 2004;Van Oevelen et al 2005).…”