Massively parallel mapping of all molecular interactions in a single tube

 描述（由申请人提供）：分子相互作用是所有生物过程的核心。尽管存在强大的方法，如酵母双杂交及其变体，分子相互作用的全面定量调查仍然是低通量，昂贵，劳动密集型，并受到偏见的限制，覆盖范围仅为所有可能的相互作用的百分之几。生物学中的一个主要挑战是开发允许快速、近乎全面地覆盖所有双分子相互作用的新方法。如果它们是可用的，这种超深的相互作用组图谱将通过为系统水平的生物过程及其高级组织的理解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生物体中的蛋白质-蛋白质，蛋白质-DNA和蛋白质-RNA相互作用。该技术将：（1）超高通量，允许单个研究者对所有成对相互作用进行深入和全面的调查（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，使一名调查员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; 它将捕获蛋白质的天然体内生理状态;和（6）它将是非常低成本的，并且不需要使用专门的机器人或大型实验室真实的资产。这些地图的全面性和定量性将使我们能够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。这种能力将揭示连接性和模块性的公正观点，可能会改变我们对分子网络进化和功能的基本理解。这些观测的空前规模将为提取新的见解提供独特的机会，而这些见解在现有技术的低覆盖率和稀疏性下是不可能的。在第二个主要目标中，随着计算工具的发展，我们的目标是实现对所观察到的分子相互作用的预测性理解，这些分子相互作用是根据核酸和肽序列-介导相互作用的基序。这些观测的天文尺度可能使理解和建模分子识别规则成为一个新的平台，为分子网络结构和动力学的从头算工程铺平了道路。

 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.