This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Jiang, Y. Articles by Gralla, J. D. Search for Related Content PubMed PubMed Citation Articles by Jiang, Y. Articles by Gralla, J. D.

 Previous Article  |  Next Article 

Mol. Cell. Biol., Apr 1996, 1614-1621, Vol 16, No. 4
Copyright © 1996, American Society for Microbiology

A three-step pathway of transcription initiation leading to promoter clearance at an activation RNA polymerase II promoter

Y Jiang, M Yan and JD Gralla
Department of Chemistry and Biochemistry, University of California at Los Angeles, 90095-1569, USA.

The progress of transcription bubbles during inhibition in vitro was followed in order to learn how RNA polymerase II begins transcription at the activated adenovirus E4 promoter. The issues addressed include the multiple roles of ATP, the potential effect of polymerase C- terminal domain phosphorylation, and the ability of polymerase to clear the promoter for reinitiation. The results lead to a three-step model for the transition from closed complex to elongation complex, two steps of which use ATP independently. In the first step, studied previously, ATP is hydrolyzed to open the DNA strands over the start site. In a second step, apparently independent of ATP, transcription bubbles move into the initial transcribed region where RNA synthesis can stall. In the third step, transcripts can be made as polymerase is released from these stalled positions with the assistance of an ATP-dependent process, likely phosphorylation of the polymerase C-terminal domain. After this third step, the promoter becomes cleared, allowing for the reinitiation of transcription.

This article has been cited by other articles:

• Max, T., Sogaard, M., Svejstrup, J. Q. (2007). Hyperphosphorylation of the C-terminal Repeat Domain of RNA Polymerase II Facilitates Dissociation of Its Complex with Mediator. J. Biol. Chem. 282: 14113-14120 [Abstract] [Full Text]  
• Kanin, E. I., Kipp, R. T., Kung, C., Slattery, M., Viale, A., Hahn, S., Shokat, K. M., Ansari, A. Z. (2007). Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does not impair global mRNA synthesis. Proc. Natl. Acad. Sci. USA 104: 5812-5817 [Abstract] [Full Text]  
• Liu, Y., Kung, C., Fishburn, J., Ansari, A. Z., Shokat, K. M., Hahn, S. (2004). Two Cyclin-Dependent Kinases Promote RNA Polymerase II Transcription and Formation of the Scaffold Complex. Mol. Cell. Biol. 24: 1721-1735 [Abstract] [Full Text]  
• Fiedler, U., Timmers, H. Th. M. (2001). Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. Nucleic Acids Res 29: 2706-2714 [Abstract] [Full Text]  
• Wolner, B. S., Gralla, J. D. (2000). Roles for Non-TATA Core Promoter Sequences in Transcription and Factor Binding. Mol. Cell. Biol. 20: 3608-3615 [Abstract] [Full Text]  
• Yan, M., Gralla, J. D. (1999). The Use of ATP and Initiating Nucleotides during Postrecruitment Steps at the Activated Adenovirus E4 Promoter. J. Biol. Chem. 274: 34819-34824 [Abstract] [Full Text]  
• Guzman, E., Lis, J. T. (1999). Transcription Factor TFIIH Is Required for Promoter Melting In Vivo. Mol. Cell. Biol. 19: 5652-5658 [Abstract] [Full Text]  
• de Laat, W. L., Jaspers, N. G.J., Hoeijmakers, J. H.J. (1999). Molecular mechanism of nucleotide excision repair. Genes Dev. 13: 768-785 [Full Text]  
• Kuhlman, T. C., Cho, H., Reinberg, D., Hernandez, N. (1999). The General Transcription Factors IIA, IIB, IIF, and IIE Are Required for RNA Polymerase II Transcription from the Human U1 Small Nuclear RNA Promoter. Mol. Cell. Biol. 19: 2130-2141 [Abstract] [Full Text]  
• Kumar, K. P., Akoulitchev, S., Reinberg, D. (1998). Promoter-proximal stalling results from the inability to recruit transcription factor IIH to the transcription complex and is a regulated event. Proc. Natl. Acad. Sci. USA 95: 9767-9772 [Abstract] [Full Text]  
• Kugel, J. F., Goodrich, J. A. (1998). Promoter escape limits the rate of RNA polymerase II transcription and is enhanced by TFIIE, TFIIH, and ATP on negatively supercoiled DNA. Proc. Natl. Acad. Sci. USA 95: 9232-9237 [Abstract] [Full Text]  
• Tijerina, P., Sayre, M. H. (1998). A Debilitating Mutation in Transcription Factor IIE with Differential Effects on Gene Expression in Yeast. J. Biol. Chem. 273: 1107-1113 [Abstract] [Full Text]  
• Sandaltzopoulos, R., Becker, P. B. (1998). Heat Shock Factor Increases the Reinitiation Rate from Potentiated Chromatin Templates. Mol. Cell. Biol. 18: 361-367 [Abstract] [Full Text]  
• Wolner, B. S., Gralla, J. D. (1997). Promoter Activation via a Cyclic AMP Response Element in Vitro. J. Biol. Chem. 272: 32301-32307 [Abstract] [Full Text]  
• Sakurai, H., Fukasawa, T. (1997). Yeast Gal11 and Transcription Factor IIE Function through a Common Pathway in Transcriptional Regulation. J. Biol. Chem. 272: 32663-32669 [Abstract] [Full Text]  
• Brown, S. A., Kingston, R. E. (1997). Disruption of downstream chromatin directed by a transcriptional activator. Genes Dev. 11: 3116-3121 [Abstract] [Full Text]  
• Inamoto, S., Segil, N., Pan, Z.-Q., Kimura, M., Roeder, R. G. (1997). The Cyclin-dependent Kinase-activating Kinase (CAK) Assembly Factor, MAT1, Targets and Enhances CAK Activity on the POU Domains of Octamer Transcription Factors. J. Biol. Chem. 272: 29852-29858 [Abstract] [Full Text]  
• Tijsterman, M., Verhage, R. A., van de Putte, P., Jong, J. G. T.-d., Brouwer, J. (1997). Transitions in the coupling of transcription and nucleotide excision repair within RNA polymerase II-transcribed genes of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 94: 8027-8032 [Abstract] [Full Text]  
• Gerber, A N, Klesert, T R, Bergstrom, D A, Tapscott, S J (1997). Two domains of MyoD mediate transcriptional activation of genes in repressive chromatin: a mechanism for lineage determination in myogenesis.. Genes Dev. 11: 436-450 [Abstract]  
• Kugel, J. F., Goodrich, J. A. (2000). A Kinetic Model for the Early Steps of RNA Synthesis by Human RNA Polymerase II. J. Biol. Chem. 275: 40483-40491 [Abstract] [Full Text]