Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome

Transcription regulation in eukaryotes involves rapid recruitment and proper assembly of transcription factors at gene promoters. To determine the dynamics of the transcription machinery on DNA, we used a differential chromatin immunoprecipitation procedure coupled to whole-genome microarray detection in Saccharomyces cerevisiae. We find that TATA-binding protein (TBP) turnover is low at RNA polymerase I (Pol I) promoters. Whereas RNA polymerase III (Pol III) promoters represent an intermediate case, TBP turnover is high at RNA polymerase II (Pol II) promoters. Within these promoters, the highest turnover correlates with binding of the Spt-Ada-Gcn5 acetyltransferase complex (SAGA) coactivator, Mot1p dependence and presence of a canonical TATA box. In contrast, slow turnover Pol II promoters depend on TFIID and on the gene-specific factor, Rap1p. Together this shows that TBP turnover is regulated by protein factors rather than DNA sequence and argues that TBP turnover is an important determinant in regulating gene expression.