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Molecular and Cellular Biology, November 2005, p. 9674-9686, Vol. 25, No. 21
0270-7306/05/$08.00+0     doi:10.1128/MCB.25.21.9674-9686.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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

Dong-Hoon Lee,1 Naum Gershenzon,3 Malavika Gupta,1 Ilya P. Ioshikhes,3 Danny Reinberg,1,2 and Brian A. Lewis1*

Department of Biochemistry,1 Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 683 Hoes Lane, Piscataway, New Jersey 08854,2 Department of Biomedical Informatics, The Ohio State University, 3184 Graves Hall, 333 W. 10th Ave., Columbus, Ohio 432103

Received 22 November 2004/ Returned for modification 10 December 2004/ Accepted 5 August 2005

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 ß-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/TAFII250 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.

* Corresponding author. Mailing address: Department of Biochemistry, Robert Woods Johnson Medical School, 683 Hoes Lane, Piscataway, NJ 08854. Phone: (732) 235-4194. Fax: (732) 235-5294. E-mail: lewisba{at}umdnj.edu.

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

Molecular and Cellular Biology, November 2005, p. 9674-9686, Vol. 25, No. 21
0022-538X/05/$08.00+0     doi:10.1128/MCB.25.21.9674-9686.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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