A fundamental requirement for gene regulation in eukaryotes--and hence for human health and development--is that gene regulatory proteins must be provided access to their DNA target sequences. However, the mechanisms by which such access is guaranteed and accomplished are not known. Existing ideas have well-established counter examples, or appear to violate fundamental physical principles, or leave essential questions unanswered. Our long-term goal is to develop a quantitative understanding of gene regulation in vivo. Our preliminary studies and their continuation, proposed here, begin our work toward this larger goal by investigating simple model systems in vitro. We recently developed a """"""""site-exposure"""""""" model that would provide the needed access of regulatory proteins. In preliminary studies we established that nucleosomes do exhibit a dynamic property of site exposure. Moreover, we find that the site exposure model has a striking predictive capability: it quantitatively accounts for a wide range of published observations in vitro, and it provides physically plausible explantions for a wide range of phenomena in vivo. The goal of the studies proposed here is to further develop and explore the site exposure model: to characterize the site exposure process in vitro and to explore to what extent it can quantitatively or even quantitatively account for aspects of gene regulation in vivo. An important feature of our appoach is that we pose definte, testable, models for the phenomena under investigation, and we design and carry out experiments that specifically test those ideas.
Four specific aims will be addresssed: (i) We will investigate experimental systems that more closely resemble the state of chromatin in vivo, and will allow us to quantitatively relate histone variants and posttranslational modifications to gene regulation. (ii) We will evaluate a prediction of our model which is that unrelated proteins will in general act cooperatively (synergistically) to facilitate each other's binding. (iii) We will analyze the structural consequences of the binding of regulatory proteins to nucleosomal DNA target sites. And (iv) We will test whether the site exposure model can quantitatively account for the roles of poly (dA:dT) elements at eukaryotic promoters.
| Moyle-Heyrman, Georgette; Viswanathan, Ramya; Widom, Jonathan et al. (2012) Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA. J Biol Chem 287:9002-12 |
| Moyle-Heyrman, Georgette; Tims, Hannah S; Widom, Jonathan (2011) Structural constraints in collaborative competition of transcription factors against the nucleosome. J Mol Biol 412:634-46 |
| Tims, Hannah S; Gurunathan, Kaushik; Levitus, Marcia et al. (2011) Dynamics of nucleosome invasion by DNA binding proteins. J Mol Biol 411:430-48 |
| Poirier, Michael G; Oh, Eugene; Tims, Hannah S et al. (2009) Dynamics and function of compact nucleosome arrays. Nat Struct Mol Biol 16:938-44 |
| Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362-6 |
| Field, Yair; Fondufe-Mittendorf, Yvonne; Moore, Irene K et al. (2009) Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet 41:438-45 |
| Morozov, Alexandre V; Fortney, Karissa; Gaykalova, Daria A et al. (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37:4707-22 |
| Segal, Eran; Widom, Jonathan (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19:65-71 |
| Shen, Hong Ming; Poirier, Michael G; Allen, Michael J et al. (2009) The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription. J Exp Med 206:1057-71 |
| Segal, Eran; Widom, Jonathan (2009) From DNA sequence to transcriptional behaviour: a quantitative approach. Nat Rev Genet 10:443-56 |
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