Massively parallel mapping of all molecular interactions in a single tube

单管中所有分子相互作用的大规模并行映射

• 批准号: 9145743
• 负责人: Saeed F Tavazoie
• 金额: $ 65.03万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-21 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9145743
• 关键词: Affect; Architecture; Binding; Biological Assay; Biological Process; Biology; Cell physiology; Cells; Chemicals; Communities; Computing Methodologies; DNA; Data; Development; Disease; Engineering; Environment; Enzymes; Event; Evolution; Genomics; Health; High-Throughput Nucleotide Sequencing; Human; Hybrids; Knowledge; Laboratories; Lead; Libraries; Life; Ligation; Maps; Measurement; Measures; Mediating; Messenger RNA; Methods; Modeling; Molecular; Monitor; Nature; Nucleic Acids; Organism; Pathway interactions; Patient Self-Report; Pharmaceutical Preparations; Physiological; Population Heterogeneity; Process; Proteins; RNA; RNA-Protein Interaction; Reaction; Reading; Research; Research Personnel; Robotics; Scheme; Surveys; System; Systems Biology; Technology; Temperature; Textbooks; Time; Tube; Variant; Vision; Work; Yeasts; base; computerized tools; cost; design; high throughput technology; in vivo; innovation; insight; interest; molecular recognition; network architecture; new technology; novel; protein aminoacid sequence; rapid detection; research study; response; scaffold; transcriptomics; yeast two hybrid system

 DESCRIPTION (provided by applicant): Molecular interactions are at the core of all biological processes. Despite the existence of powerful methods such as the yeast two-hybrid and its variants, comprehensive quantitative surveys of molecular interactions remain low-throughput, costly, labor-intensive, and suffer from biases that limit coverage to only a few percent of all possible interactions. A major challenge in biology is to develop novel methods that allow rapid, near- comprehensive coverage of all bi-molecular interactions. If they were available, such ultra-deep interactome maps will revolutionize biology by providing a rich knowledge scaffold for a systems-level understanding of biological processes and their high-level organization. We propose to develop a revolutionary ultra-high- throughput technology to easily and comprehensively map protein-protein, protein-DNA, and protein-RNA interactions in any organism of interest. The technology will be: (1) ultra-high-throughput, allowing a single investigator to conduct a deep and comprehensive survey of all pair-wise interactions (e.g. ~109 for all human proteins) in a single tube; (2) It will have the sensitivity and dynamic-range to provide a quantitative readout of interaction-strengths; (3) It will be extremely fast, enabling a single investigator to conduct a global survey on the timescale of a few days; (4) It will enable the monitoring of interactome dynamics-as a function of cellular- state or other perturbations; (5) it will capture the native in vivo physiological state of proteins; and (6) It will be extremely lo-cost and not require the use of specialized robotics or large laboratory real estate. The comprehensive and quantitative nature of these maps will allow us to go beyond the current low-hanging-fruit limits, and for the first time, measure the entire distribution of interaction strengths. This capacity will reveal an unbiased view of connectivity and modularity, potentially revamping our fundamental understanding of molecular network evolution and function. The unprecedented scale of these observations will present unique opportunities for extracting novel insights that are not possible with the low coverage and sparsity of existing technologies. In the second major aim, with the development of computational tools, we aim to achieve a predictive understanding of the observed molecular interactions in terms of nucleic-acid and peptide sequence- motifs that mediate interactions. The astronomical scale of these observations may enable a new plateau in understanding and modeling molecular recognition rules, paving the way for ab initio engineering of molecular network architecture and dynamics.

 描述（由适用提供）：分子相互作用是所有生物过程的核心。尽管存在强大的方法，例如酵母双杂交及其变体，但分子相互作用的全面定量调查仍然是低通量，昂贵，劳动力密集的，并且偏见只能将覆盖范围限制在所有可能的相互作用的百分之几中。生物学的一个主要挑战是开发新的方法，以允许对所有双分子相互作用的快速，几乎整理覆盖。如果可用，这种超深的相互作用图将通过为生物学过程及其高级组织提供丰富的知识支架来彻底改变生物学。我们建议开发一种革命性的超高通量技术，以轻松，全面地绘制任何感兴趣的组织中的蛋白质 - 蛋白质蛋白质，蛋白-DNA和蛋白-RNA相互作用。将是：（1）超高通量，使单个研究者能够对单个管中的所有配对相互作用进行深入，全面的调查（例如，对于所有人类蛋白质）； （2）它将具有灵敏度和动态范围，以提供相互作用强度的定量读数； （3）这将是非常快的，使一个调查员能够对几天的时间表进行全球调查； （4）它将能够监视相互作用的动力学 - 作为细胞状态或其他扰动的函数； （5） 它将捕获原生体内蛋白质的生理状态； （6）这将是极其fo ost的，并且不需要使用专门的机器人技术或大型实验室房地产。这些地图的全面和定量性质将使我们能够超越当前的低悬挂限制，并且首次衡量相互作用强度的整个分布。这种能力将揭示出对连通性和模块化的无偏见，可能会改变我们对分子网络演化和功能的基本理解。这些观察结果的前所未有的规模将提供独特的机会，以提取新的见解，而现有技术的覆盖范围低和稀疏性是不可能的。在第二个主要目的中，随着计算工具的开发，我们旨在通过核酸和肽序列（介导相互作用的核基序列）来实现对观察到的分子相互作用的预测理解。这些观察结果的天文规模可能使理解和建模分子识别规则的新高原，从而掩盖了分子网络架构和动力学的初始工程的道路。