QSB: The Design and Construction of Coupled Genetic Regulatory Modules

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An important theme in post-genomic research is the dissection and quantitative analysis of the complex dynamical interactions involved in gene regulation. The molecular interaction maps involved in many important cellular processes often resemble circuit diagrams, and this analogy highlights the motivation for a quantitative description of gene regulation. An electrical circuit is invariably accompanied by a set of equations which faithfully describe its functionality, and it is built from knowledge of the properties of the individual components (resistors, capacitors, inductors, etc.) to provide a framework for predicting the circuit behavior resulting from component modifications. An acceptable model describing a given molecular interaction map should be similarly built from knowledge of the basic regulatory themes in order to enable the prediction of the effects of genetic perturbations of the system. This project focuses on the construction and utilization of genetic "circuits" for dissecting, analyzing, and controlling the dynamical interactions involved in gene regulation. Previous investigations of engineered gene circuits have included the development of positive feedback and co-repressive switching networks, as well as an oscillating circuit. These previous studies have explored several of the building-block modules that constitute large-scale genomic wiring, and thus represent a first step towards an understanding of whole-genome regulatory complexity. The current project will build upon these previous studies by designing and constructing higher order networks consisting of coupled genetic regulatory modules. Specifically, the investigators will model and construct a regulatory network which couples a co-repressive module with an unregulated constitutive module, and explore how such coupling can induce oscillations in a toggle switch. As a second project, they plan to model and construct a synthetic network which couples the phase oscillator known as the "repressilator" with a relaxation oscillator module, and explore the synchronization properties of the coupled oscillator system. This approach could lead to an experimentally validated set of mathematical rules for understanding the complex circuitry of whole-genome regulatory processes. The top-down approaches, which are used by many investigators to analyze the expression states of thousands of genes, have contributed towards understanding the global patterns of gene expression and assessing gene lethality. The bottom-up approach to be used in this project, which reduces the complexity of these gene networks to their essential components, will lead to the modular dissection of network architectures and refined descriptions of gene expression dynamics. The combination of these two complementary approaches will eventually lead to the elucidation of the organization and functioning of gene regulatory networks. In addition, work stemming from this research should enhance the ability to utilize synthetic gene networks as new logical forms of cellular control, and could in turn lead to important applications in functional genomics, nanotechnology, and gene and cell therapies.