Academic journal article Genetics

Promoter Strength Influences the S Phase Requirement for Establishment of Silencing at the Saccharomyces Cerevisiae Silent Mating Type Loci

Academic journal article Genetics

Promoter Strength Influences the S Phase Requirement for Establishment of Silencing at the Saccharomyces Cerevisiae Silent Mating Type Loci

Article excerpt

ABSTRACT

In Saccharomyces cerevisiae, the two cryptic mating type loci, HML and HMR, are transcriptionally silent. Previous studies on the establishment of silencing at HMR identified a requirement for passage through S phase. However, the underlying mechanism for this requirement is still unknown. In contrast to HMR, we found that substantial silencing of HML could be established without passage through S phase. To understand this difference, we analyzed several chimeric HM loci and found that promoter strength determined the S phase requirement. To silence a locus with a strong promoter such as the a1/a2 promoter required passage through S phase while HM loci with weaker promoters such as the α1/α2 or TRP1 promoter did not show this requirement. Thus, transcriptional activity counteracts the establishment of silencing but can be overcome by passage through S phase.

EPIGENETIC silencing refers to a transcriptionally inactive state and its heritable transmission. It involves the formation, maintenance, and inheritance of a specialized, constitutively compact chromatin structure, termed heterochromatin. This kind of transcriptional silencing plays an important role in establishing and maintaining distinct patterns of gene expression in genetically identical cells during growth and differentiation. Examples of transcriptional silencing include the inactive mammalian X chromosome, position effect variegation in Drosophila melanogaster, and the cryptic mating-type loci in fission and budding yeasts (Rusche et al. 2003; Probst et al. 2009).

In the budding yeast Saccharomyces cerevisiae, the MAT locus encodes transcriptional regulatory proteins that are responsible for the differences between the two mating types. HML and HMR harbor cryptic copies of the mating type information genes, a and a, respectively. Transcriptional silencing at these loci relies on cisregulatory DNA elements called silencers and on a number of trans -acting gene products. Previous studies revealed that establishment of silencing involves a series of protein-DNA and protein-protein interactions (reviewed inGasser and Cockell 2001; Rusche et al. 2003; Fox and Mcconnell 2005). The silencer elements flanking the HM loci recruit the DNA binding proteins Rap1, Abf1, and ORC, which in turn recruit the silent information regulator (Sir) proteins, Sir1, Sir2, Sir3, and Sir4. A Sir2-Sir3-Sir4 complex spreads from the silencers into nearby nucleosomes (Hoppe et al. 2002; Rusche et al. 2002; Liou et al. 2005; Rudner et al. 2005). This spreading requires Sir2, which deacetylates histone H4 K16, thereby creating a binding site for Sir3 and Sir4 and hence the Sir2/3/4 complex (Carmen et al. 2002; Liou et al. 2005). Multiple rounds of deacetylation by Sir2 allow the Sir complex to spread to adjacent nucleosomes, thus creating a stretch of silent chromatin.

To investigate the establishment of silencing and its relationship to the cell cycle, previous studies utilized conditional or inducible alleles of the Sir proteins to create a transition from Sir- to Sir1 and then examined the establishment of silencing (Miller and Nasmyth 1984; Fox et al. 1997; Kirchmaier and Rine 2001; Li et al. 2001; Lau et al. 2002; Martins-Taylor et al. 2004; Kirchmaier and Rine 2006; Xu et al. 2006; Wang et al. 2008; Osborne et al. 2009). For example, in a classic study, Miller and Nasmyth (1984) used a sir3 temperature-sensitive allele (sir3-8) and shifted cells from a nonpermissive temperature to a permissive temperature to follow the establishment of silencing as functional Sir3 protein became available. This strain contained a-information at both HML and HMR cassettes while MAT was deleted, so that it could be arrested in G1 phase by a-factor at either temperature. Therefore, the establishment of silencing at HML and HMR could not be distinguished in this strain. They tested the establishment of silencing under two conditions, arresting in G1 phase or released for cell-cycle progression. …

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