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

 Previous Article  |  Next Article 

Molecular and Cellular Biology, March 2003, p. 1623-1632, Vol. 23, No. 5
0270-7306/03/$08.00+0     DOI: 10.1128/MCB.23.5.1623-1632.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

Collaborative Competition Mechanism for Gene Activation In Vivo

Joanna A. Miller and Jonathan Widom*

Department of Biochemistry, Molecular Biology and Cellular Biology, Northwestern University, Evanston, Illinois 60208-3500,

Received 15 November 2002/ Accepted 21 November 2002

The mechanism by which gene regulatory proteins gain access to their DNA target sites is not known. In vitro, binding is inherently cooperative between arbitrary DNA binding proteins whose target sites are located within the same nucleosome. We refer to such competition-based cooperativity as collaborative competition. Here we show that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae. Coactivation requires that the cooperating target sites be within a nucleosome-length distance; it leads to increased occupancy by Gcn4 at its binding site; and it requires both Gcn5 and Swi/Snf which, at an endogenous Gcn4-dependent promoter, act subsequent to Gcn4 binding. These results imply that collaborative competition contributes to gene regulation in vivo. They further imply that, even in the presence of the cell's full wild-type complement of chromatin remodeling factors, competition of regulatory proteins with histone octamer for access to regulatory target sites remains a quantitative determinant of gene expression levels. We speculate that initial target site recognition and binding may occur via spontaneous nucleosomal site exposure, with remodeling factor action required downstream to lock in higher levels of regulatory protein occupancy.

* Corresponding author. Mailing address: Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2220 Campus Dr., Evanston, IL 60208-3500. Phone: (847) 467-1887. Fax: (847) 467-6489. E-mail: j-widom{at}northwestern.edu.

Molecular and Cellular Biology, March 2003, p. 1623-1632, Vol. 23, No. 5
0022-538X/03/$08.00+0     DOI: 10.1128/MCB.23.5.1623-1632.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Wasson, T., Hartemink, A. J. (2009). An ensemble model of competitive multi-factor binding of the genome. Genome Res 19: 2101-2112 [Abstract] [Full Text]  
  • Teif, V. B., Rippe, K. (2009). Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res 37: 5641-5655 [Abstract] [Full Text]  
  • Raveh-Sadka, T., Levo, M., Segal, E. (2009). Incorporating nucleosomes into thermodynamic models of transcription regulation. Genome Res 19: 1480-1496 [Abstract] [Full Text]  
  • Tirosh, I., Barkai, N. (2008). Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091 [Abstract] [Full Text]  
  • Shivaswamy, S., Iyer, V. R. (2008). Stress-Dependent Dynamics of Global Chromatin Remodeling in Yeast: Dual Role for SWI/SNF in the Heat Shock Stress Response. Mol. Cell. Biol. 28: 2221-2234 [Abstract] [Full Text]  
  • Teif, V. B. (2007). General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage {lambda}. Nucleic Acids Res 35: e80-e80 [Abstract] [Full Text]  
  • Hebbar, P. B., Archer, T. K. (2007). Chromatin-dependent Cooperativity between Site-specific Transcription Factors in Vivo. J. Biol. Chem. 282: 8284-8291 [Abstract] [Full Text]  
  • Ligr, M., Siddharthan, R., Cross, F. R., Siggia, E. D. (2006). Gene Expression From Random Libraries of Yeast Promoters. Genetics 172: 2113-2122 [Abstract] [Full Text]  
  • Mersfelder, E. L., Parthun, M. R. (2006). The tale beyond the tail: histone core domain modifications and the regulation of chromatin structure.. Nucleic Acids Res 34: 2653-2662 [Abstract] [Full Text]  
  • Yarragudi, A., Miyake, T., Li, R., Morse, R. H. (2004). Comparison of ABF1 and RAP1 in Chromatin Opening and Transactivator Potentiation in the Budding Yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 24: 9152-9164 [Abstract] [Full Text]  
  • Angelov, D., Lenouvel, F., Hans, F., Muller, C. W., Bouvet, P., Bednar, J., Moudrianakis, E. N., Cadet, J., Dimitrov, S. (2004). The Histone Octamer Is Invisible When NF-{kappa}B Binds to the Nucleosome. J. Biol. Chem. 279: 42374-42382 [Abstract] [Full Text]  
  • Bi, X., Yu, Q., Sandmeier, J. J., Zou, Y. (2004). Formation of Boundaries of Transcriptionally Silent Chromatin by Nucleosome-Excluding Structures. Mol. Cell. Biol. 24: 2118-2131 [Abstract] [Full Text]  
  • Ishii, H., Sen, R., Pazin, M. J. (2004). Combinatorial Control of DNase I-hypersensitive Site Formation and Erasure by Immunoglobulin Heavy Chain Enhancer-binding Proteins. J. Biol. Chem. 279: 7331-7338 [Abstract] [Full Text]  
  • Vitolo, J. M., Yang, Z., Basavappa, R., Hayes, J. J. (2004). Structural Features of Transcription Factor IIIA Bound to a Nucleosome in Solution. Mol. Cell. Biol. 24: 697-707 [Abstract] [Full Text]  
  • Ragab, A., Travers, A. (2003). HMG-D and histone H1 alter the local accessibility of nucleosomal DNA. Nucleic Acids Res 31: 7083-7089 [Abstract] [Full Text]  
  • Banerjee, N., Zhang, M. Q. (2003). Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Res 31: 7024-7031 [Abstract] [Full Text]  
  • Buchler, N. E., Gerland, U., Hwa, T. (2003). On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. USA 100: 5136-5141 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»