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

• Published in: Nature structural & molecular biology Vol. 16; no. 10; pp. 1043 - 1048
• Main Authors: Timmers, H Th Marc, van Werven, Folkert J, van Teeffelen, Hetty A A M, Holstege, Frank C P
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.10.2009; Nature Publishing Group
• Subjects: Biochemistry; Biological Microscopy; Biomedical and Life Sciences; Chromatin; Chromatin Immunoprecipitation; Deoxyribonucleic acid; DNA; DNA binding proteins; DNA, Ribosomal - genetics; Gene Expression Regulation, Fungal; Genetic aspects; Genome, Fungal - genetics; Genomics; Life Sciences; Membrane Biology; Molecular biology; Physiological aspects; Promoter Regions, Genetic; Promoters (Genetics); Protein Structure; RNA polymerase; RNA Polymerase I - genetics; RNA Polymerase II - genetics; RNA Polymerase III - genetics; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Sequence Analysis, DNA; TATA-Box Binding Protein - genetics; Time Factors; Transcription Factors - metabolism; Transcription, Genetic; Yeast; Yeast fungi; Yeasts; United States
• ISSN: 1545-9993; 1545-9985
• DOI: 10.1038/nsmb.1674

Transcription initiation involves recruitment of key factors to promoters. Yeast TATA-binding protein (TBP) turnover is now examined genome-wide and genes transcribed by the three RNA polymerases found to have distinct signatures. Further analyses suggest that TBP dynamics, rather than DNA sequence affinity per se , is key to gene expression. 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.