Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

Abstract

Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase II-transcribed genes. The downstream core element (DCE) was discovered in the human β-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_II250 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.

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Functional Characterization of Core Promoter Elements: the Downstream Core Element Is Recognized by TAF1

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/.

ACKNOWLEDGMENTS

We thank Lynne Vales for critical reading of the manuscript, Edward Wagner for supplying the HSV U_L38 promoter constructs, Cheng-Ming Chiang and Robert Roeder for providing the FLAG-tagged TBP HeLa cell line, Laszlo Tora for the 3G3 TBP monoclonal antibody, and Thomas E. Shenk for providing adenovirus genomic DNA plasmids. B.A.L. thanks Stuart Orkin for his continued support and interest.

B.A.L. was supported by NIH/NIDDK grant K01 DK60001, and D.R. was supported by NIH grant GM 64844. D.R. is an investigator of the Howard Hughes Medical Institute.