The New Core Promoter Element XCPE1 (X Core Promoter Element 1) Directs Activator-, Mediator-, and TATA-Binding Protein-Dependent but TFIID-Independent RNA Polymerase II Transcription from TATA-Less Promoters

Abstract

The core promoter is a critical DNA element required for accurate transcription and 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 hepatitis 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 and +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% of 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 possibility of the existence of a TAF1 (TFIID)-independent transcriptional initiation mechanism that may be used by a category of TATA-less promoters in higher eukaryotes.

SUPPLEMENTAL MATERIAL

We thank Robert Tjian and James Goodrich for providing the anti-hTAF4 monoclonal antibody; Naoko Tanese for the nontagged human TBP expression vector; Joan Conaway, Shigeo Sato, and Chieri Sato for the MED26 cell line; Katsuro Koike for many HBV DNA constructs; David Graham (Texas Gulf Coast Digestive Disease Center, Study Design and Clinical Specimen Core Facility) for liver tissue samples; and Edith Wang for c-fos and cyclin A reporter plasmids and ts13 cells. We also thank Yutaka Suzuki for helping us search the DBTSS database.

This study was supported by an institutional research grant from the M. D. Anderson Cancer Center, by an American Gastroenterological Association/Elsevier Research Initiative Award, and by a grant (AI057504) from the NIH to S.T. DNA sequencing was supported by the DNA core facility at the M. D. Anderson Cancer Center.