Transcription is centrally involved in an array of biological processes, which include growth, development, and response to external stimuli. In eukaryotes, protein-coding genes are transcribed by the RNA polymerase II transcriptional machinery, which comprises RNA polymerase II and other factors that are required for basal and regulated transcription. Transcription by RNA polymerase II is directed by cis-acting DNA sequences that typically consist of a core promoter along with regulatory elements, such as enhancers, that contain binding sites for sequence-specific transcriptional activator and/or repressor proteins. Thus, the study of both the trans-acting protein factors and the cis-acting DNA elements is necessary to gain a better understanding of the fundamental mechanisms by which genes are transcribed (for recent reviews, see Bjorkland and Kim 1996; Burley and Roeder 1996; Orphanides et al. 1996; Roeder 1996; Verrijzer and Tjian 1996; Ptashne and Gann 1997; Sauer and Tjian 1997; Smale 1997; Tansey and Herr 1997). The key DNA element that is essential for transcription by RNA polymerase II is the core promoter—the DNA sequences, which encompass the transcription start site (within about −40 to +40 relative to the +1 start site) and are sufficient to direct the accurate initiation of transcription. Two important core promoter motifs are the TATA box and the initiator (Inr) (Fig. (Fig.1).1). The TATA box is an A/T-rich sequence that is located ∼25–30 nucleotides upstream of the RNA start site of many, but not all, promoters. It is recognized by the TATA box-binding polypeptide (TBP), which is a component of the multisubunit TFIID complex. The Inr encompasses the RNA start site, and like the TATA box, it is also present in many, but not all, core promoters (Smale and Baltimore 1989; Smale 1994, 1997). Inr elements have been characterized in various TATA-less and TATA-containing promoters, and the Inr consensus sequence is Py-Py-A+1-N-T/A-Py-Py (where A+1 is the transcription start site) in mammalian genes (Smale and Baltimore 1989; Bucher 1990; Javahery et al. 1994) and T-C-A+1-G/T-T-T/C in Drosophila genes (Hultmark et al. 1986; Purnell et al. 1994; Arkhipova 1995). Figure 1 The TATA box, Inr, and DPE are core promoter elements. The consensus sequences and locations of the TATA box, Inr, and DPE motifs are indicated. The TATA box and DPE appear to be functionally redundant, and promoters generally do not contain ... Many promoters contain functionally important sequences that are downstream of the transcription start site. Such downstream promoter sequences have been found in TATA-containing promoters (see, e.g., Lewis and Manley 1985; Nakatani et al. 1990; Lee et al. 1992; Emanuel and Gilmour 1993; Purnell and Gilmour 1993), as well as in TATA-less promoters (see, e.g., Biggin and Tjian 1988; Perkins et al. 1988; Soeller et al. 1988; Smale and Baltimore 1989; Jarrell and Meselson 1991; Contursi et al. 1995; Minchiotti et al. 1997). It appears that many of these downstream promoter sequences are involved in basal transcription, but it is also important to consider that some downstream promoter sequences might be binding sites for sequence-specific transcriptional activators. In the analysis of the interaction of purified TFIID with TATA-less promoters, a conserved downstream core promoter element was found to be required for the sequence-specific binding of TFIID to a subset of TATA-less promoters (Burke and Kadonaga 1996). This motif was termed the downstream promoter element (DPE). The DPE is a distinct 7-nucleotide element that is located at about +30 (typically, from +28 to +34) relative to the transcription start site (Fig. (Fig.1).1). It is present in many, but not all, promoters and is bound by TFIID but not by TBP. In addition, nearly all of the promoters that have been found to contain DPE-like sequences are TATA-less promoters. Modification of the DPE by clustered point mutagenesis was found to cause a decrease in the binding of purified TFIID to the promoter as well as an 8- to 100-fold reduction in basal transcriptional activity in vitro. Mutational analysis of the Inr and DPE motifs revealed that the DPE acts in conjunction with the Inr to provide a binding site for TFIID in the absence of a TATA box. Interestingly, the loss of transcriptional activity upon disruption of the TATA box in a TATA-containing promoter could be recovered by the insertion of a DPE at a downstream position (+28 to +34) in the defective promoter. Thus, the DPE appears to be a functionally important, conserved downstream core promoter element. We are, however, still in the early stages of understanding the DPE. In this work we have investigated several fundamental questions regarding the role of the DPE in the transcription process. These experiments provide evidence for the function of TBP-associated factors (TAFs) in DPE-driven basal transcription and reveal that the DPE has many properties that are analogous to those of the TATA box.