Individual Subunits of the Ssn6-Tup11/12 Corepressor Are Selectively Required for Repression of Different Target Genes

Abstract

The Saccharomyces cerevisiae Ssn6 and Tup1 proteins form a corepressor complex that is recruited to target genes by DNA-bound repressor proteins. Repression occurs via several mechanisms, including interaction with hypoacetylated N termini of histones, recruitment of histone deacetylases (HDACs), and interactions with the RNA polymerase II holoenzyme. The distantly related fission yeast, Schizosaccharomyces pombe, has two partially redundant Tup1-like proteins that are dispensable during normal growth. In contrast, we show that Ssn6 is an essential protein in S. pombe, suggesting a function that is independent of Tup11 and Tup12. Consistently, the group of genes that requires Ssn6 for their regulation overlaps but is distinct from the group of genes that depend on Tup11 or Tup12. Global chip-on-chip analysis shows that Ssn6 is almost invariably found in the same genomic locations as Tup11 and/or Tup12. All three corepressor subunits are generally bound to genes that are selectively regulated by Ssn6 or Tup11/12, and thus, the subunit specificity is probably manifested in the context of a corepressor complex containing all three subunits. The corepressor binds to both the intergenic and coding regions of genes, but differential localization of the corepressor within genes does not appear to account for the selective dependence of target genes on the Ssn6 or Tup11/12 subunits. Ssn6, Tup11, and Tup12 are preferentially found at genomic locations at which histones are deacetylated, primarily by the Clr6 class I HDAC. Clr6 is also important for the repression of corepressor target genes. Interestingly, a subset of corepressor target genes, including direct target genes affected by Ssn6 overexpression, is associated with the function of class II (Clr3) and III (Hst4 and Sir2) HDACs.

SUPPLEMENTAL MATERIAL

We thank Akihisa Matsuyama and Minoru Yoshida at the Chemical Genetics Laboratory, Riken, Saitama, Japan, for providing plasmids for expression of the Ssn6 protein. We also thank members of the Wright and Ekwall groups for valuable discussions and advice on the manuscript.

DNA microarray slides were scanned at the KI-CHIP core facility at the Karolinska Institute, which is supported by the Wallenberg Foundation. Affymetrics tiling arrays were hybridized and scanned at BEA Bioinformatics and Expression Analysis Core Facility, Karolinska Institute.

This research was funded by project grants from the Swedish Research Council and the Foundation for Strategic Research. A.P.H.W. is a senior investigator financed by the Swedish Research Council. K.E. is a Royal Swedish Academy of Sciences research fellow supported by the Knut and Alice Wallenberg foundation, Swedish Cancer Society, and the Swedish Research Council.