Academic journal article Genetics

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

Academic journal article Genetics

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

Article excerpt

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.

THE 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 Suml-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 HMLα and HMRα 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 sir2A mutation (Klar et al 1985). The SUM1-1 mutation results from a single-amino-acid change (Chi and Shore 1996), which enables the Suml repressor that normally does not spread to form an extended silenced domain (Rusche and Rine 2001; Sutton et al 2001). The ability of mutant Sum1-1p to spread suggests that Sum1-1p or an associated protein interacts with nucleosomes and raises the question of whether the wild-type, nonspreading Sum1 complex also interacts with nucleosomes. To address these issues, we identified histone residues important for silencing mediated by the mutant Sum1-1 complex and the wild-type Sum1 complex.

Sir silencing at the cryptic mating-type loci is initiated at the flanking E and I silencers, which contain binding sites for the origin recognition complex (ORC) and the transcription factors Raplp and Abflp. These factors recruit the Sir proteins. Orel p, the largest subunit of ORC, interacts directly with Siri p, stabilizing the Sir proteins at the silencer (Triolo and Sternglanz 1996; Gardner et al 1999). …

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