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（由申请人提供）：分子相互作用是所有生物过程的核心，尽管存在诸如酵母二杂交及其变体等强大的方法，但分子相互作用的定量综合调查仍然是低通量、昂贵的、劳力的。生物学中的一个主要挑战是开发能够快速、近乎全面地覆盖所有双分子相互作用的新方法（如果有的话）。超深相互作用组图谱将为生物过程及其高级组织的系统级理解提供丰富的知识支架，从而彻底改变生物学。我们建议开发一种革命性的超高通量技术，以轻松、全面地绘制蛋白质-蛋白质、蛋白质-蛋白质图谱。任何感兴趣的生物体中的 DNA 和蛋白质-RNA 相互作用将是：(1) 超高通量，允许单个研究人员对所有成对相互作用进行深入和全面的调查（例如，所有配对的相互作用约为 109）。人类蛋白质）在一个管中； (2) 它将具有提供相互作用强度的定量读数的灵敏度和动态范围；(3) 速度极快，使单个研究者能够在几天的时间内进行全球调查 (4) ）它将能够监测相互作用组动态——作为细胞状态或其他扰动的函数（5）； 它将捕获蛋白质的天然体内生理状态；（6）成本极低，不需要使用专门的机器人或大型实验室空间，这些图谱的全面性和定量性将使我们能够进行下去。超越当前容易实现的限制，并首次测量相互作用强度的整个分布，这种能力将揭示对连接性和模块化的公正看法，有可能改变我们对分子网络进化和功能的基本理解。这些观察的规模将带来独特的机会提取现有技术的低覆盖率和稀疏性不可能获得的新见解在第二个主要目标中，随着计算工具的发展，我们的目标是对观察到的核酸和分子相互作用进行预测性理解。介导相互作用的肽序列基序的天文规模可能使分子识别规则的理解和建模达到新的水平，为分子网络结构和动力学的从头开始工程铺平道路。