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 TX 77030

* To whom correspondence should be addressed. Email:  stakada@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.

Additional References:

1. Giresi PG, Kim J, McDaniell RM, Iyer VR, and Lieb JD, "FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin".

2. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, and Rubin EM, "In vivo enhancer analysis of human conserved non-coding sequences".

3. Wu Q, Chen X, Zhang J, Loh Y-H, Low T-Y, Zhang W, Zhang W, Sze S-K, Lim B, and Ng H-H,
"Sall4 Interacts with Nanog and Co-occupies Nanog Genomic Sites in Embryonic Stem Cells",

4. Mollica LR, Crawley JTB, Liu K, Rance JB, Cockerill PN, Follows GA, Landry J-R, Wells DJ, and Lane DA, "Role of a 5'-enhancer in the transcriptional regulation of the human endothelial cell protein C receptor gene".

5. Hovsepian JA, and Frenster JH, "Sense and Antisense during RNA Initiation of the DNA Transcription Bubble".

A Brief History of  Activator RNA:

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".