A central concern of the present post-genomic era of biology is understanding the chemical and physical mechanisms by which gene expression is regulated. Appropriate activation and repression of particular genes is necessary for maintaining normal cell function and is required for executing the programs of cell differentiation that are essential to the development of multicellular organisms. Collectively, gene regulatory systems are the "brain" of the cell that allows it to respond appropriately to environmental stimuli. Many cancers and other diseases result from deranged gene regulation. In this research project, we have developed and begun applying an entirely new approach to studying the molecular mechanisms of transcription and transcription regulation in vitro. Instead of studying populations of molecules, we directly visualize the RNA polymerase and regulatory proteins on an isolated single DNA molecule, following the progression of the molecular machinery through its different states in real time while simultaneously observing the extent of transcriptional activation. Such direct visualization is made possible by a multi-wavelength single-molecule fluorescence approach we call CoSMoS (co localization single- molecule spectroscopy). In this application, we propose applying the CoSMoS approach to elucidating the dynamic mechanisms of selected processes involved in regulation of transcription initiation and elongation in vitro using purified Escherichia coli proteins in reconstituted transcription reactions. Our goals are: 1) Test the hypothesis that RNAP holoenzyme molecules reach promoters through a bind-and-slide mechanism;2) Define the dynamic mechanisms by which secondary channel factors act alone and together to regulate transcription initiation and elongation;and 3) Define the dynamic mechanism by which the presence of the 70 and NusA components of the transcription apparatus is remodeled in the transition between transcription initiation and elongation.

Public Health Relevance

The proposed research will elucidate basic mechanisms of transcription regulation, which in the long term will improve public health by improving our understanding of human biology. In addition, the proposed research will help define the molecular bases for regulatory mechanisms that affect virulence and environmental dissemination of human pathogens. This basic knowledge is expected to aid in the scientific research aimed at development of agents to combat infectious disease.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-S (02))
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Lewis, Catherine D
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Brandeis University
Schools of Arts and Sciences
United States
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Larson, Joshua; Kirk, Matt; Drier, Eric A et al. (2014) Design and construction of a multiwavelength, micromirror total internal reflectance fluorescence microscope. Nat Protoc 9:2317-28
Anderson, Eric G; Hoskins, Aaron A (2014) Single molecule approaches for studying spliceosome assembly and catalysis. Methods Mol Biol 1126:217-41
Paramanathan, Thayaparan; Reeves, Daniel; Friedman, Larry J et al. (2014) A general mechanism for competitor-induced dissociation of molecular complexes. Nat Commun 5:5207
Friedman, Larry J; Mumm, Jeffrey P; Gelles, Jeff (2013) RNA polymerase approaches its promoter without long-range sliding along DNA. Proc Natl Acad Sci U S A 110:9740-5
Shcherbakova, Inna; Hoskins, Aaron A; Friedman, Larry J et al. (2013) Alternative spliceosome assembly pathways revealed by single-molecule fluorescence microscopy. Cell Rep 5:151-65
Crawford, Daniel J; Hoskins, Aaron A; Friedman, Larry J et al. (2013) Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5' splice site and branch site. Proc Natl Acad Sci U S A 110:6783-8
Friedman, Larry J; Gelles, Jeff (2012) Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation. Cell 148:679-89
Sanchez, Alvaro; Garcia, Hernan G; Jones, Daniel et al. (2011) Effect of promoter architecture on the cell-to-cell variability in gene expression. PLoS Comput Biol 7:e1001100
Hoskins, Aaron A; Friedman, Larry J; Gallagher, Sarah S et al. (2011) Ordered and dynamic assembly of single spliceosomes. Science 331:1289-95
Hoskins, Aaron A; Gelles, Jeff; Moore, Melissa J (2011) New insights into the spliceosome by single molecule fluorescence microscopy. Curr Opin Chem Biol 15:864-70

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