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Molecular and Cellular Biology, July 2000, p. 4754-4764, Vol. 20, No. 13
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

The Downstream Promoter Element DPE Appears To Be as Widely Used as the TATA Box in Drosophila Core Promoters

Alan K. Kutach and James T. Kadonaga*

Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0347

Received 28 February 2000/Returned for modification 28 March 2000/Accepted 31 March 2000

The downstream promoter element (DPE) functions cooperatively with the initiator (Inr) for the binding of TFIID in the transcription of core promoters in the absence of a TATA box. We examined the properties of sequences that can function as a DPE as well as the range of promoters that use the DPE as a core promoter element. By using an in vitro transcription assay, we identified 17 new DPE-dependent promoters and found that all possessed identical spacing between the Inr and DPE. Moreover, mutational analysis indicated that the insertion or deletion of a single nucleotide between the Inr and DPE causes a reduction in transcriptional activity and TFIID binding. To explore the range of sequences that can function as a DPE, we constructed and analyzed randomized promoter libraries. These experiments yielded the DPE functional range set, which represents sequences that contribute to or are compatible with DPE function. We then analyzed the DPE functional range set in conjunction with a Drosophila core promoter database that we compiled from 205 promoters with accurately mapped start sites. Somewhat surprisingly, the DPE sequence motif is as common as the TATA box in Drosophila promoters. There is, in addition, a striking adherence of Inr sequences to the Inr consensus in DPE-containing promoters relative to DPE-less promoters. Furthermore, statistical and biochemical analyses indicated that a G nucleotide between the Inr and DPE contributes to transcription from DPE-containing promoters. Thus, these data reveal that the DPE exhibits a strict spacing requirement yet some sequence flexibility and appears to be as widely used as the TATA box in Drosophila.

* Corresponding author. Mailing address: Department of Biology, 0347, Pacific Hall, Room 2212B, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0347. Phone: (858) 534-4608. Fax: (858) 534-0555. E-mail: jkadonaga{at}ucsd.edu.

Molecular and Cellular Biology, July 2000, p. 4754-4764, Vol. 20, No. 13
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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  • Kobayashi, A., Miyake, T., Ohyama, Y., Kawaichi, M., Kokubo, T. (2001). Mutations in the TATA-binding Protein, Affecting Transcriptional Activation, Show Synthetic Lethality with the TAF145 Gene Lacking the TAF N-terminal Domain in Saccharomyces cerevisiae. J. Biol. Chem. 276: 395-405 [Abstract] [Full Text]  
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  • Thomas, C. P., Loftus, R. W., Liu, K. Z., Itani, O. A. (2002). Genomic organization of the 5' end of human beta -ENaC and preliminary characterization of its promoter. Am. J. Physiol. Renal Physiol. 282: F898-F909 [Abstract] [Full Text]  


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