Quantitative Characterization & Modeling of sRNA-Mediated Gene Regulation

定量表征

• 批准号: 7616190
• 负责人: TERENCE HWA
• 金额: $ 28.06万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7616190
• 关键词: Bacteria; Behavior; Binding; Bioinformatics; Biological Assay; Biological Models; Characteristics; Complex; DNA-Protein Interaction; Dependence; Development; Devices; Drug usage; Educational process of instructing; Escherichia coli; Eukaryota; Exhibits; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Homeostasis; Intervention; Iron; Joints; Kinetics; Knowledge; Laboratories; Lead; Light; Mediating; Messenger RNA; Modeling; Molecular; Molecular Biology; Molecular Chaperones; Monitor; Noise; Organism; Outcomes Research; Play; Post-Transcriptional Regulation; Prokaryotic Cells; Property; Proteins; RNA; Recombinants; Regulation; Regulator Genes; Regulon; Reporter; Repressor Proteins; Research; Resistance; Role; Series; Signal Transduction; Small RNA; Testing; Theoretical Studies; Time; Transcriptional Regulation; design; gene interaction; genome-wide; interest; molecular scale; mutant; novel; programs; promoter; research study; response; synthetic construct; tool

DESCRIPTION (provided by applicant): In recent years, there has been a growing appreciation for the complex roles that small regulatory RNA (sRNA) can play in coordinating gene activities in both prokaryotes and eukaryotes. There exists by now a basic understanding of the molecular components and mechanisms involved in sRNA-mediated gene regulation in bacteria. Theoretical analysis by our lab suggest a number of unique functional features for sRNA-mediated gene regulation, including a threshold-linear response and a resistance to noisy fluctuation, with interesting implications on properties of genetic circuits involving sRNA. Here we propose a joint experimental/computational research program to characterize the functions of sRNA in E. coli at multiple scales. At the molecular scale, we will elucidate the sequence determinant of sRNA-target interaction for the most common RyhB-class sRNA by characterizing the gene expression of selected mutants, and constructing biopysical/bioinformatic models of the interaction. At the "device" scale, we will characterize various novel properties predicted for sRNA-mediated regulation, including hierarchical cross talk between different targets of the same sRNA. At the circuit scale, we will construct synthetic circuits and study the properties of common circuit motifs such as the cascade and switches, and investigate their temporal characteristics. In addition we will develop models to design antisense sRNAthat target and silence specific host genes. We expect that the knowledge of the molecular interaction to lead to predictive tools to identify the potentially large number of sRNA targets and construct additional layers of the gene regulatory network involving sRNA in E. coli, while knowledge of the devices and common circuit motifs will shed light towards understanding the special roles that sRNA regulators may play in coordinating larger scale networks. Additionally, the silencing of endogenous target may lead to an effective tool to generate multiple gene knockdown strains which may be used for drug discover studies as well as gene- gene interaction studies at the genome-wide scale.

描述（由申请人提供）：近年来，人们对小调节RNA（SRNA）在原核和真核生物的协调基因活性中发挥的复杂作用越来越多。到目前为止，存在对细菌中SRNA介导的基因调节所涉及的分子成分和机制的基本理解。我们实验室的理论分析表明，SRNA介导的基因调节的许多独特功能特征，包括阈值线性响应和对嘈杂波动的抗性，对涉及SRNA的遗传回路的性质具有有趣的意义。在这里，我们提出了一个联合实验/计算研究计划，以表征SRNA在多个尺度上的大肠杆菌中的功能。在分子尺度上，我们将通过表征所选突变体的基因表达以及构建相互作用的生物物理/生物信息学模型来阐明最常见的RYHB级SRNA的SRNA靶标相互作用的序列决定因素。在“设备”量表上，我们将表征SRNA介导的调节所预测的各种新型特性，包括同一SRNA的不同靶标之间的分层交叉谈话。在电路尺度上，我们将构建合成电路，并研究诸如级联和开关等公路图案的特性，并研究其时间特征。此外，我们将开发模型来设计反义SRNATHAT靶标和静音特定宿主基因。我们期望分子相互作用的知识会导致预测工具，以识别涉及大肠杆菌中SRNA的基因调节网络的其他层层，而对设备和公共电路主题的知识将阐明SRNA调节器在SRNA调节器中可能在较大规模的网络中起着特殊作用。此外，内源性靶标的沉默可能会导致有效的工具，以产生多种基因敲低菌株，该菌株可用于药物发现研究以及基因相互作用研究，并在全基因组范围内使用。