QSB: The Design and Construction of Coupled Genetic Regulatory Modules

后基因组研究的一个重要主题是对基因调控中复杂的动力学相互作用进行解剖和定量分析。许多重要的细胞过程所涉及的分子相互作用图通常类似于电路图，这种类比突出了定量描述基因调控的动机。 电路总是伴随着一组忠实地描述其功能的方程，并且它是根据各个组件（电阻器，电容器，电感器等）的属性知识构建的。以提供用于预测由组件修改引起的电路行为的框架。一个可接受的模型，描述一个给定的分子相互作用的地图，应类似地建立从基本的监管主题的知识，以便能够预测系统的遗传扰动的影响。该项目的重点是构建和利用遗传“电路”，以解剖，分析和控制基因调控中涉及的动态相互作用。以前的工程基因电路的研究包括正反馈和共抑制开关网络的发展，以及振荡电路。这些先前的研究已经探索了几个构成大规模基因组布线的积木模块，因此代表了理解全基因组调控复杂性的第一步。目前的项目将建立在这些以前的研究，设计和构建更高阶的网络组成的耦合遗传调控模块。具体来说，研究人员将建模和构建一个调控网络，该网络将一个共抑制模块与一个不受调控的组成模块耦合在一起，并探索这种耦合如何在拨动开关中诱导振荡。作为第二个项目，他们计划建模和构建一个合成网络，该网络将称为“repressilator”的相位振荡器与张弛振荡器模块耦合，并探索耦合振荡器系统的同步特性。这种方法可能会导致一组实验验证的数学规则，用于理解全基因组调控过程的复杂电路。自上而下的方法被许多研究人员用来分析数千个基因的表达状态，有助于理解基因表达的全球模式和评估基因致死性。在这个项目中使用的自下而上的方法，它减少了这些基因网络的复杂性，其基本组成部分，将导致网络架构的模块化解剖和基因表达动态的精细描述。这两种互补方法的结合将最终导致基因调控网络的组织和功能的阐明。此外，这项研究的工作应该能够提高利用合成基因网络作为细胞控制的新逻辑形式的能力，并可能反过来导致功能基因组学，纳米技术以及基因和细胞疗法的重要应用。

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.