The stability of the TFIIA-TBP-DNA complex is dependent on the sequence ofthe TATAAA element

To determine the mechanistic differences between canonical and noncanonical TATA elements, we compared the functional activity of two sequences: TATAA A (canonical) and CATAAA (noncanonical). The TATAAA element can support hig h levels of transcription in vivo, whereas the CATAAA element is severely d efective for this function.. This dramatic functional difference is not lik ely to be due to a difference in TBP (TATA-binding protein) binding efficie ncy because protein-DNA complex studies in vitro indicate little difference between the two DNA sequences in the formation and stability of the TBP-DN A complex. In addition, the binding and stability of the TFIIB-TBP-DNA comp lex is similar for the two elements. In striking contrast, the TFIIA-TBP-DN A complex is significantly less stable on the CATAAA element when compared with the TATAAA element. A role for TFIIA in distinguishing between TATAAA and CATAAA in vivo was tested by fusing. a subunit of TFIIA to TBP. We foun d that fusion of TFIIA to TBP dramatically increases transcription from CAT AAA, in yeast cells. Taken together, these results indicate that the stabil ity of the TFIIA-TBP complex depends strongly on the sequence of the core p romoter element and that the TFIIA-TBP complex plays an important function in recognizing optimal promoters in vivo.