Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells.
Noise genetics: inferring protein function by correlating phenotype with protein levels and localization in individual human cells.
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DOI：
10.1371/journal.pgen.1004176
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发表时间：
2014-03
期刊：
影响因子：
4.5
通讯作者：
Alon U
中科院分区：
文献类型：
--
作者：
Farkash-Amar S;Zimmer A;Eden E;Cohen A;Geva-Zatorsky N;Cohen L;Milo R;Sigal A;Danon T;Alon U
为了了解基因功能，遗传分析使用较大的扰动，例如基因删除、敲低或过度表达。大的扰动有缺点：它们使细胞远离其正常工作点，因此可能被脱靶效应或其他基因的补偿所掩盖。在这里，我们提供了一种补充方法，称为噪声遗传学。我们利用蛋白质水平和定位方面的自然细胞间变异，并将它们与相同细胞表型的自然变异相关联。动态蛋白质组学的最新进展使观察这些变化成为可能，动态蛋白质组学允许测量单个活细胞中随时间变化的蛋白质。使用人类癌细胞的运动性作为模型系统，并对 566 个荧光标记蛋白进行延时显微镜检查，我们发现了 74 个候选运动性基因，其水平或定位与单个细胞的运动性密切相关。我们恢复了 30 个已知的运动基因，并通过温和的敲除实验验证了几个新的基因。噪声遗传学可以补充各种表型的标准遗传学。推断蛋白质的功能及其在细胞过程中发挥的作用对于我们理解细胞生物学、遗传学和生物学至关重要。标准的遗传方法对细胞使用较大的扰动，例如基因敲除、基因敲除或过度表达。这种方法很强大，但缺点是使电池远离其正常工作点。在这里，我们提供了一种新的、更温和的方法，它使用蛋白质水平和表达模式的自然细胞间变异作为温和扰动的来源。我们在显微镜下监测单个活癌细胞，并将它们的蛋白质水平和定位与同一细胞中的表型相关联。我们使用人类癌细胞的运动性作为模型系统，这对于理解癌症的转移非常重要。我们发现我们的方法揭示了大多数已知的运动蛋白，以及我们使用敲低实验验证的新蛋白。我们的新方法广泛适用于任何可以在单个细胞中可视化的表型，以及任何可以测量单个细胞中蛋白质的生物体。
To understand gene function, genetic analysis uses large perturbations such as gene deletion, knockdown or over-expression. Large perturbations have drawbacks: they move the cell far from its normal working point, and can thus be masked by off-target effects or compensation by other genes. Here, we offer a complementary approach, called noise genetics. We use natural cell-cell variations in protein level and localization, and correlate them to the natural variations of the phenotype of the same cells. Observing these variations is made possible by recent advances in dynamic proteomics that allow measuring proteins over time in individual living cells. Using motility of human cancer cells as a model system, and time-lapse microscopy on 566 fluorescently tagged proteins, we found 74 candidate motility genes whose level or localization strongly correlate with motility in individual cells. We recovered 30 known motility genes, and validated several novel ones by mild knockdown experiments. Noise genetics can complement standard genetics for a variety of phenotypes. Inferring the function of proteins and the role they play in cellular processes is essential for our understanding of cell biology, genetics and biology in general. Standard genetic approaches use large perturbations to cells such as gene knockout, knockdown or over expression of genes. Such methods are powerful, but have the drawback of taking the cell far from its normal working point. Here, we provide a new and much milder approach, which uses the natural cell-cell variation in protein level and expression pattern as a source of mild perturbation. We monitor individual live cancer cells under the microscope and correlate their protein levels and localization with phenotype in the same cells. We use the motility of human cancer cells as a model system that is highly important for understanding metastasis in cancer. We find that our approach uncovers most of the known motility proteins, as well as new ones which we validate using knockdown experiments. Our novel approach is widely applicable to any phenotype that can be visualized in individual cells, and for any organism for which one can measure proteins in individual cells.
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影响因子：
3
作者：
Chebira A;Barbotin Y;Jackson C;Merryman T;Srinivasa G;Murphy RF;Kovacević J
通讯作者：
Kovacević J
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