The Saccharomyces cerevisiae Histone Chaperone Rtt106 Mediates the Cell Cycle Recruitment of SWI/SNF and RSC to the HIR-Dependent Histone Genes

Abstract

BackgroundIn Saccharomyces cerevisiae, three out of the four histone gene pairs (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2) are regulated by the HIR co-repressor complex. The histone chaperone Rtt106 has recently been shown to be present at these histone gene loci throughout the cell cycle in a HIR- and Asf1-dependent manner and involved in their transcriptional repression. The SWI/SNF and RSC chromatin remodeling complexes are both recruited to the HIR-dependent histone genes; SWI/SNF is required for their activation in S phase, whereas RSC is implicated in their repression outside of S phase. Even though their presence at the histone genes is dependent on the HIR complex, their specific recruitment has not been well characterized. In this study we focused on characterizing the role played by the histone chaperone Rtt106 in the cell cycle-dependent recruitment of SWI/SNF and RSC complexes to the histone genes.Methodology/Principal FindingsUsing GST pull-down and co-immunoprecipitation assays, we showed that Rtt106 physically interacts with both the SWI/SNF and RSC complexes in vitro and in vivo. We then investigated the function of this interaction with respect to the recruitment of these complexes to HIR-dependent histone genes. Using chromatin immunoprecipitation assays (ChIP), we found that Rtt106 is important for the recruitment of both SWI/SNF and RSC complexes to the HIR-dependent histone genes. Furthermore, using synchronized cell cultures, we showed by ChIP assays that the Rtt106-dependent SWI/SNF recruitment to these histone gene loci is cell cycle regulated and restricted to late G1 phase just before the peak of histone gene expression in S phase.Conclusions/SignificanceOverall, these data strongly suggest that the interaction between the histone chaperone Rtt106 and both the SWI/SNF and RSC chromatin remodeling complexes is important for the cell cycle regulated recruitment of these two complexes to the HIR-dependent histone genes.

Regulation of Histone Gene Expression in Budding Yeast

“…However, RSC binding correlates with repression of the histone genes (Ng et al 2002), whereas SWI/SNF binding correlates with their activation (Dimova et al 1999;Ferreira et al 2011) (Figure 4). Much evidence indicates that these complexes are recruited to promoters by sequence-specific transcription factors, but this paradigm is challenged by the fact that RSC contains two sequence-specific DNA-binding factors, Rsc3 and Rsc30 (Badis et al 2008).…”

“…Rtt106 was identified as a repressor of HTA1 expression in a genetic screen, which also identified two other histone chaperones as repressors: the HIR complex and Asf1 (Fillingham et al 2009). Thus, three different histone chaperones are involved, although physical interactions between all of them have been reported in vitro and in vivo (Sutton et al 2001;Green et al 2005;Fillingham et al 2009;Ferreira et al 2011), suggesting that they might act together, with apparently redundant functions. The HTA1-HTB1 promoter is more depleted of nucleosomes in rtt106D and hir1D cells than in wild-type cells, suggesting that these chaperones might facilitate assembly of nucleosomes on the histone promoters, which then repress transcription (Fillingham et al 2009).…”

“…Thus, SWI/SNF binding correlates with activation, and RSC binding correlates with repression. ChIP data for TFIIB and RSC were adapted from Ng et al (2002); data for SWI/SNF and HTA1 expression were adapted from Ferreira et al (2011). Note that, although these experiments were done in two different laboratories, the times between the first and second cell-cycle peaks are very similar, and so a direct comparison is reasonable.…”

“…A reasonable model is that the histone chaperones (the HIR complex, Asf1, and Rtt106) assemble nucleosomes on the histone promoters toward the end of S phase (Fillingham et al 2009) and that these nucleosomes are then positioned appropriately for repression by the RSC complex, perhaps targeted by Rsc3 or Rsc30. It has been hypothesized that, in late G1, the HIR complex is converted from a corepressor into a co-activator (Dimova et al 1999) and that then it cooperates with Asf1 and Rtt106 to recruit the SWI/SNF complex (Dimova et al 1999;Ferreira et al 2011). This might involve the Rtt109-Vps75 HAT complex because Rtt109 interacts with Asf1 (Tsubota et al 2007).…”

Direct Interplay among Histones, Histone Chaperones, and a Chromatin Boundary Protein in the Control of Histone Gene Expression

“…Asf1 copurifies with the HIR complex (21), and in asf1⌬ cells, Rtt106 localization is reduced, leading to inappropriate histone expression outside S phase (51, 53). Although these data suggest that Asf1 plays a direct role in histone gene regulation, whether Asf1 localizes to histone gene promoters as a member of the HIR:Rtt106 regulatory complex was unclear.During late G 1 , histone gene repression is alleviated by the dissociation of the RSC complex and by the Rtt106-dependent recruitment of the SWI/SNF chromatin-remodeling complex (8,15). SWI/SNF promotes active transcription, perhaps by exposing the upstream activating sequences (UAS) to the cell cycle-regulated transcription factors Spt10 and SBF (9,12,58).…”