A Region of the Nucleosome Required for Multiple Types of Transcriptional Silencing in Saccharomyces cerevisiae

Abstract

Extended heterochromatin domains, which are repressive to transcription and help define centromeres and telomeres, are formed through specific interactions between silencing proteins and nucleosomes. This study reveals that in Saccharomyces cerevisiae, the same nucleosomal surface is critical for the formation of multiple types of heterochromatin, but not for local repression mediated by a related transcriptional repressor. Thus, this region of the nucleosome may be generally important to long-range silencing. In S. cerevisiae, the Sir proteins perform long-range silencing, whereas the Sum1 complex acts locally to repress specific genes. A mutant form of Sum1p, Sum1-1p, achieves silencing in the absence of Sir proteins. A genetic screen identified mutations in histones H3 and H4 that disrupt Sum1-1 silencing and fall in regions of the nucleosome previously known to disrupt Sir silencing and rDNA silencing. In contrast, no mutations were identified that disrupt wild-type Sum1 repression. Mutations that disrupt silencing fall in two regions of the nucleosome, the tip of the H3 tail and a surface of the nucleosomal core (LRS domain) and the adjacent base of the H4 tail. The LRS/H4 tail region interacts with the Sir3p bromo-adjacent homology (BAH) domain to facilitate Sir silencing. By analogy, this study is consistent with the LRS/H4 tail region interacting with Orc1p, a paralog of Sir3p, to facilitate Sum1-1 silencing. Thus, the LRS/H4 tail region of the nucleosome may be relatively accessible and facilitate interactions between silencing proteins and nucleosomes to stabilize long-range silencing.T HE formation of silenced chromatin, or heterochromatin, in eukaryotes is important for proper gene regulation and chromosome stability and helps define centromeres and telomeres. One interesting property of heterochromatin is its capacity to spread along a chromosome to form an extended, repressive domain. This spreading is enabled by specific interactions between silencing proteins and nucleosomes. Consequently, particular surfaces on the nucleosome can be critical to the assembly of heterochromatin. This study reveals that in the budding yeast Saccharomyces cerevisiae, the same nucleosomal surface is critical for the formation of three types of silenced chromatin, mediated by the Sir, RENT, or Sum1-1 complexes, suggesting that this region of the nucleosome may be generally important to long-range silencing.In S. cerevisiae, silenced chromatin domains associated with Sir proteins are found at the cryptic mating-type loci HMLa and HMRa and subtelomeric regions (Rusche et al. 2003). A distinct form of silencing occurs in the rDNA repeats and is mediated by the RENT complex. Strains lacking Sir2p, Sir3p, or Sir4p lose silencing at the mating-type loci and consequently express both a and a mating-type information, resulting in the loss of cell-type identity and an inability to mate. Interestingly, silencing and mating can be restored by the SUM1-1 mutation, which was originally identified as a suppressor of a sir2...

The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae

“…These features convert the Sum1-1/Rfm1/Hst1 complex from a shortrange repressor of specific promoters to a complex that can bind silencers and spread long-range repression to the promoters of the mating-type genes at the HM loci. Spreading is in many ways analogous to the behavior of the Sir2/3/4 complex (e.g., H4K16 is deacetylated) yet in other ways distinct (e.g., unstable and nonheritable repression) (Rusche and Rine 2001;Sutton et al 2001;Lynch et al 2005;Valenzuela et al 2006;Prescott et al 2011). In this context, it should also be mentioned that Sum1 normally associates with the HML-E silencer at a 10-bp site called D2, where it is required for silencing under weakened conditions (see Figure 3; Irlbacher et al 2005).…”

Regulation of telomere silencing by the core histones–autophagy–Sir2 axis

“…These 15 histone residues localize at three primary structure clusters: five histone residues (H3R2, H3K4, H3T6, H3K14, H3R17) localize on the H3 N-terminal tail; the second cluster is composed of H3R40, H4K44, H3R49, H3K56, and H4L37; the third cluster consists of H4R55, H3R69, H3R72, H3D77, and H3Q85 ( Fig S5J ). Among these mutations, four histone mutants (H3R2A, H3K4A, H3K14A, and H3R72G) have been shown to regulate telomere silencing ( Park et al, 2002 ; Thompson et al, 2003 ; Kirmizis et al, 2007 ; Prescott et al, 2011 ). H3D77N mutation has been reported to suppress the telomere silencing defects caused by Sir3 BAH domain ( Sampath et al, 2009 ).…”

Repression of Middle Sporulation Genes in Saccharomyces cerevisiae by the Sum1-Rfm1-Hst1 Complex Is Maintained by Set1 and H3K4 Methylation

“…However, our data suggest that histone methylation at H3K4 also promotes Sum1 binding to middle sporulation loci, indicating that there are additional chromatin elements that contribute to properly localizing this transcription factor. Although a previous screen of histone residues required for Sum1 -mediated repression did not uncover a specific role for H3K4, this residue was not tested in isolation and specific reporter genes were used, which may not reflect all middle sporulation genes ( Prescott et al 2011 ). Interestingly, however, Set1 was required for gene silencing mediated by a gain-of-function mutant in SUM1 , known as SUM1 -1 , although this appeared to be independent of Sum1 -1 recruitment to silent regions ( Prescott et al 2011 ).…”