To reveal mechanistic differences in transcription initiation between variant TATA elements, in vivo and in vitro assays of the functional activity of 14 different sequences were compared. Variant elements exhibited particular degrees of activation in vivo but universally were unable to support the -fold activation observed for an element consisting of TATAAA. Each element was classified by its functional activity for in vitro interaction with TATA-binding protein (TBP), TFIIA, and TFIIB. Certain off-consensus TATA elements form poor binding sites for TBP and this compromised interaction interferes with higher order complex formation with TFIIA and/or TFIIB. Other elements are only modestly decreased for TBP binding but dramatically affected for higher order complex formation. Another distinct category is comprised of two elements (CATAAA and TATAAG), which are not affected in the initial formation of the TBP, TFIIA-TBP, or TFIIB-TBP complexes. However, CATAAA and TATAAG are unable to form a stable TFIIA-TBP-DNA complex in vitro. Moreover, fusion of TFIIA to TBP specifically restores activity from these two elements in vivo. Taken together, these results indicate that the interplay between the sequence of the TATA element and the components of the general transcription machinery can lead to variations in the formation of functional complexes and/or the stability of these complexes. These differences offer distinct opportunities for an organism to exploit diverse steps in the regulation of gene expression depending on the precise TATA element sequence at a given gene.Initiation of transcription by RNA polymerase II is the major site for regulation of eukaryotic gene expression during cell cycle progression, development, and physiological induction (1). Increased gene expression is mediated by activator proteins that bind regulatory sequences in the promoter and, either directly or indirectly, facilitate recruitment of the general transcription factors assembled near the initiation site at the core promoter (2). TATA-binding protein (TBP) 3 specifically recognizes and binds to the TATA sequence of the core promoter allowing for the nucleation of other general transcription factors including TFIIA, -B, -E, -F, -H, -J, and polymerase II (for reviews, see Refs. 3 and 4). Although high affinity binding sites have been identified for yeast TBP (5-7), and computational studies indicate that TATA(A/T)A(A/T)(A/G) is commonly found at TBP-dependent promoters in yeast (8), a wide variety of off-consensus elements have been shown to exhibit transcriptional activity. Indeed, these alterations from the consensus sequence are not passive players in gene regulation but can contribute to the proper expression of a given gene. For example, activation by E1A of the human hsp70 promoter is highly dependent on the sequence of the TATA element: substitution of the hsp70 TATA (TATAA) with the SV40 early promoter TATA (TATTTAT) results in loss of induction by E1A but not by heat shock (9). In addition, an off-consensus TATA element is...