MCB Accepts, published online ahead of print on 8 January 2007

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Mol. Cell. Biol. doi:10.1128/MCB.01363-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

A new core promoter element XCPE1 (X core promoter element 1) directs activator-, mediator-, and TBP-dependent but TFIID-independent RNA polymerase II transcription from TATA-less promoters

Yumiko Tokusumi, Ying Ma, Xianzhou Song, Raymond H. Jacobson, and Shinako Takada^*

Department of Biochemistry and Molecular Biology, Gene and Development Program of Graduate School of Biomedical Science, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston TX77030

^* To whom correspondence should be addressed. Email: stakada{at}mdanderson.org.

The core promoter is a critical DNA element required for accurate transcription and the regulation of transcription. Several core promoter elements have been previously identified in eukaryotes, but those cannot account for transcription from most RNA polymerase II-transcribed genes. Additional, as yet unidentified core promoter elements must be present in eukaryotic genomes. From extensive analyses of the hepatitits B virus X gene promoter, here we identify a new core promoter element XCPE1 (the X gene core promoter element 1) that drives RNA polymerase II transcription. XCPE1 is located between nucleotides -8 to +2 relative to the transcriptional start site (+1) and has a consensus sequence of G/A/T-G/C-G-T/C-G-G-G/A-A-G/C₊₁-A/C. XCPE1 shows fairly weak transcriptional activity alone, but exerts significant, specific promoter activity when accompanied by activator-binding sites. XCPE1 is also found in the core promoter regions of about 1% human genes, particularly in poorly characterized TATA-less genes. Our in vitro transcription studies suggest that the XCPE1-driven transcription can be highly active in the absence of TFIID because it can utilize either free TBP or the complete TFIID complex. Our findings suggest the existence of a TAF1 (TFIID)-independent transcriptional initiation mechanism that may be used by a category of TATA-less promoters in higher eukaryotes.

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