Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase IItranscribed genes. The downstream core element (DCE) was discovered in the human ␤-globin promoter, and its sequence composition is distinct from that of the downstream promoter element (DPE). We show here that the DCE is a bona fide core promoter element present in a large number of promoters and with high incidence in promoters containing a TATA motif. Database analysis indicates that the DCE is found in diverse promoters, supporting its functional relevance in a variety of promoter contexts. The DCE consists of three subelements, and DCE function is recapitulated in a TFIID-dependent manner. Subelement 3 can function independently of the other two and shows a TFIID requirement as well. UV photo-cross-linking results demonstrate that TAF1/TAF II 250 interacts with the DCE subelement DNA in a sequence-dependent manner. These data show that downstream elements consist of at least two types, those of the DPE class and those of the DCE class; they function via different DNA sequences and interact with different transcription activation factors. Finally, these data argue that TFIID is, in fact, a core promoter recognition complex.Promoters transcribed by RNA polymerase II are complex and composed of different classes of elements, one of which consists of the core promoter elements represented by the TATA box, the TFIIB response elment (BRE), the initiator, the downstream promoter element (DPE), and other newly recognized elements (reviewed in reference 73). One view of core promoters is that they are fairly ubiquitous and that they play only a trivial role in transcriptional regulation. According to this view, the uniqueness and specificity inherent in a promoter derive from the various DNA binding activators and coactivators that recognize the regulatory elements usually located upstream of the TATA box and/or initiator. The small number of core promoter elements and their apparent lack of diversity compared to that of the staggering numbers of activators have supported such a view. Also contributing to this view is the fact that core promoters have been rather poorly studied in their natural context, and thus, regulatory phenomena may have been missed.Yet there are a few examples where the core promoter apparently plays a very specific role. Early examples include studies of the myoglobin and simian virus 40 TATA boxes (86) and the hsp70 TATA box (72) that indicated a requirement for TATA boxes of a particular sequence. The TdT promoter was also shown to become inactive upon the inclusion of a TATA box (20). Lastly, some activators display preferences for particular core promoter architectures (7,18,56).This perception of core promoters lacking diversity is being revised with the findings of other core promoter elements such as the BRE (41) and elements located downstream of the transcriptional start site such as the DPE (5, 6, 40, 89), the downstream core element (DCE) (43), and the motif 10 element (MTE) (48). The mo...

A selenocysteine insertion sequence (SECIS) element in the 3-untranslated region and an in-frame UGA codon are the requisite cis-acting elements for the incorporation of selenocysteine into selenoproteins. Equally important are the trans-acting factors SBP2, Sec-tRNA[Ser]Sec , and eEFSec. Multiple in-frame UGAs and two SECIS elements make the mRNA encoding selenoprotein P (Sel P) unique. To study the role of codon context in determining the efficiency of UGA readthrough at each of the 10 rat Sel P Sec codons, we individually cloned 27-nucleotide-long fragments representing each UGA codon context into a luciferase reporter construct harboring both Sel P SECIS elements. Significant differences, spanning an 8-fold range of UGA readthrough efficiency, were observed, but these differences were dramatically reduced in the presence of excess SBP2. Mutational analysis of the "fourth base" of contexts 1 and 5 revealed that only the latter followed the established rules for hierarchy of translation termination. In addition, mutations in either or both of the Sel P SECIS elements resulted in differential effects on UGA readthrough. Interestingly, even when both SECIS elements harbored a mutation of the core region required for Sec incorporation, context 5 retained a significantly higher level of readthrough than context 1. We also show that SBP2-dependent Sec incorporation is able to repress G418-induced UGA readthrough as well as eRF1-induced stimulation of termination. We conclude that a large codon context forms a cis-element that works together with Sec incorporation factors to determine readthrough efficiency. Selenocysteine (Sec),2 the 21st amino acid, is incorporated into proteins via a recoding of the UGA stop codon (1). Selenoproteins are primarily involved in protecting the cell from oxidative stress, and the concerted effort of several protein factors and RNA elements is required for the production of these proteins (2). Two cis-elements in the mRNA are required for the incorporation of selenocysteine into a nascent polypeptide.These are an in-frame UGA codon and a structure called the SECIS (Sec insertion sequence) element (3). The SECIS element is a stem loop structure consisting of a core stem and a terminal bulge or loop. The SECIS core is comprised of an AUGA motif positioned opposite a GA dinucleotide forming a non-Watson-Crick base-paired quartet, thus making this RNA a member of the kink-turn family of RNA motifs (3). The terminus of the SECIS stem consists of either a 9 -11-nucleotide loop (designated Form 1) or a 5Ј bulge followed by a smaller 6-nucleotide loop (designated Form 2). Both SECIS forms contain a conserved AAR motif within the loop or bulge, respectively (4). SECIS binding protein 2 (SBP2) (5), a Secspecific translation elongation factor eEFSec (6), and a SectRNA[Ser]Sec (7) are the three trans-acting factors that have been identified to be essential for Sec incorporation. Recently ribosomal protein L30 has been found to interact with the SECIS element but whether it is required for Sec inc...

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