Core promoter elements and TAFs contribute to the diversity of transcriptional activation in vertebrates.

Gene-specific transcriptional activation is a multistep process that requires numerous protein factors and DNA elements, including enhancers and the core promoter. To investigate the roles of core promoter elements in transcriptional activation in vertebrates, we examined expression and factor occupancy on representative promoters in chicken DT40 cells containing a conditional TATA binding protein (TBP)-associated factor 9 allele (TAF9). Characterized core elements, including TATA box-flanking regions and the downstream promoter element, were found to play significant roles in determining promoter strength, response to activators, and factor occupancy and recruitment. The requirement for TAF9 was found to be highly promoter specific, and TAF9 dependence and promoter occupancy were not always correlated. We also describe contrasting examples of factor recruitment and activation mechanisms at different promoters, highlighted by the nearly opposite mechanisms utilized by the simian virus 40 enhancer and p53. With the core promoters analyzed, the former functions by facilitating RNA polymerase II (RNAP II) recruitment to a preassembled TBP/TFIIB-containing scaffold and p53 strongly recruits TBP and TFIIB while RNAP II levels remain modest. Taken together, our results illustrate both the important roles of core promoter elements and the remarkable diversity that characterizes transcriptional activation mechanisms in vertebrates.