The Saccharomyces cerevisiae Tup1 protein is a member of a family of WD repeat containing proteins that are involved in repression of transcription. Tup1, along with the Ssn6 protein, represses a wide variety of genes in yeast including cell type-specific and glucose-repressed genes. Tup1 and Ssn6 are recruited to these specific gene sets by interaction with sequence-specific DNA binding proteins. In this work, a protein complex containing Ssn6 and Tup1 was purified to determine its composition. The size of the complex is estimated to be 440 kDa. Tup1 and Ssn6, which are both phosphoproteins, are the only proteins present in stoichiometric amounts in the complex. We also demonstrate that this purified complex represses transcription in an in vitro assay.The Tup1 protein of Saccharomyces cerevisiae is one of a family of repressor proteins that contain -transducin or WD repeats. The majority of the WD repeat containing proteins are homologs of -transducin and are known to function in signal transduction pathways within the cytoplasm. However, an increasing number of WD repeat proteins have been identified that are nuclear localized and function in the repression of transcription. These include Tup1, Hir1, and Met30 in S. cerevisiae; SCON2 in Neurospora crassa; extra sex combs and groucho in Drosophila; COP1 in Arabidopsis thaliana; and HIRA and the family of TLE proteins in humans (1-10). These WD repeat repressor proteins turn off a wide variety of genes, including those involved in segmentation, sex determination, and neurogenesis (controlled by groucho) and those involved in photomorphogenesis (controlled by COP1) (7, 11). The HIRA protein has been implicated in the human developmental disease DiGeorge syndrome (8,9).Of these WD repeat repressor proteins, Tup1 is the best characterized. Tup1 along with another protein, Ssn6, is required for the repression of at least five sets of genes in yeast, including the glucose-repressed genes, genes regulated by the presence of oxygen (hypoxic genes), the a-specific and haploidspecific genes, and a set of genes induced by DNA damage (12-16). A deletion of SSN6 or TUP1 results in the constitutive expression of all of these genes sets. Tup1 and Ssn6 are recruited to these specific gene sets by interaction with sequencespecific DNA binding proteins. In the case of the a-specific and haploid-specific genes in yeast, the homeodomain protein ␣2 binds to sequences (operators) located upstream of each gene in the set and recruits Ssn6 and Tup1 by direct interaction with each of these proteins (for review, see Ref. 17).Tup1 and Ssn6 interact directly in vitro and are found associated in a large complex in yeast extracts estimated at 1.2 MDa (18). The size of this complex suggests that it consists of many protein subunits. Genetic experiments have implicated a number of additional proteins in the Ssn6-Tup1 repression pathway including Rox3, Sin4, Srb8, Srb9, Srb10,. Each of these proteins is required for full repression of transcription by Tup1 and Ssn6 in vivo. To determine the...