Genomic Architecture and the Consequences for Prokaryotic Gene Regulation

描述（由申请人提供）：拟议工作的目标是系统地表征基因组组织对大肠杆菌通过蛋白质转录因子的转录调控有效调控其基因的能力的影响。细菌能够感知和适应环境的基本机制是通过转录因子对其基因的协调调节。理论上，这些调控分子控制表达的能力可能取决于调控因子和它们调控的靶点之间的相对染色体距离。由此产生的进化压力可以解释在E. coli染色体。所提出的方法将联合收割机的实验和理论方法，定量表征和模型的基因组组织的基因调控的有效性的影响。利用分子生物学方法结合细菌遗传学，对大肠杆菌表达调控网络的天然排列进行了研究。大肠杆菌染色体将被破坏和重组，并将使用最先进的单细胞和单分子技术测量对基因调节的效率、随机性和生物物理学的影响。然后，将所得数据直接与基因调控的理论模型进行比较，以区分转录因子靶点搜索的竞争理论，更全面地描述驱动染色体组织的基本潜在机制。 公共卫生相关性：各种人类疾病，包括出生缺陷，癌症和表观遗传疾病都是基因调控不当的结果。通过这些拟议的研究所获得的理解作为一个起点，以解决相应的问题，在真核生物中的基因调控，基因调控是远远不够了解，更复杂的空间组织的关注只会加剧基因调控的困难。通过对原核生物和高等生物基因调控机制的更全面了解，我们将能够更好地利用和操纵这些机制来治疗和预防遗传和微生物疾病，以及设计基因途径，以实现影响公共健康和福祉的目标。

DESCRIPTION (provided by applicant): The goal of the proposed work is to systematically characterize the effects of genomic organization on the ability of Escherichia coli to efficiently and effectively regulate its genes through transcriptional regulation by protein transcription factors. The fundamental mechanism through which bacteria are able to sense and adapt to their environment is through the coordinated regulation of their genes by transcription factors. In theory, the ability of these regulatory molecules to control expression may depend on the relative chromosomal distance between regulators and the targets they regulate. The resulting evolutionary pressures may explain the unusually high degree of transcription factor-target co-localization on the E. coli chromosome. The proposed approach will combine experimental and theoretical methods to quantitatively characterize and model the effects of genome organization on the effectiveness of gene regulation. By using molecular methods combined with bacterial genetics, the native arrangement of regulatory networks on the E. coli chromosome will be disrupted and reorganized and the resulting effects on the efficiency, stochasticity, and biophysics of gene regulation will be measured using state of the art single cell and single molecule techniques. The resulting data can then be directly compared to theoretical models of gene regulation to distinguish between competing theories of transcription factor target search, more fully describing the fundamental underlying mechanisms driving chromosomal organization. PUBLIC HEALTH RELEVANCE: A variety of human diseases, including birth defects, cancer, and epigenetic diseases are the result of improper gene regulation. The understanding gained through these proposed studies serve as a starting point for addressing the corresponding questions regarding gene regulation in eukaryotes, where gene regulation is far less well understood, and more complex spatial organization concerns only exacerbate the difficulties of gene regulation. By developing a more complete understanding of the mechanisms underlying gene regulation in both prokaryotes and higher organisms, we will be in a better position to exploit and manipulate these mechanisms in the treatment and prevention of genetic and microbial diseases, as well as to engineer gene pathways in order to accomplish goals that will influence public health and well-being.