Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
Protein-RNA specificity by high-throughput principal component analysis of NMR spectra.
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DOI：
10.1093/nar/gku1372
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发表时间：
2015-03-31
影响因子：
14.9
通讯作者：
Ramos A
中科院分区：
文献类型：
--
作者：
Collins KM;Oregioni A;Robertson LE;Kelly G;Ramos A
定义调节 mRNA 代谢的蛋白质的 RNA 靶标选择性是 RNA 生物学的一个关键问题。在这里，我们提出了一种主成分分析 (PCA) 的新用途，用于提取 RNA 结合蛋白的 RNA 序列偏好。我们证明，PCA 可用于比较蛋白质在结合一组准简并 RNA 后核磁共振 (NMR) 谱的变化，并定义核碱基特异性。我们将 PCA 的这种应用与自动 NMR 谱记录和处理协议结合起来，并获得一种无偏且高通量的 NMR 方法，用于分析蛋白质-RNA 相互作用中的核碱基偏好。我们在 RNA 代谢的三个重要调节因子的 RNA 结合域上测试了该方法。
Defining the RNA target selectivity of the proteins regulating mRNA metabolism is a key issue in RNA biology. Here we present a novel use of principal component analysis (PCA) to extract the RNA sequence preference of RNA binding proteins. We show that PCA can be used to compare the changes in the nuclear magnetic resonance (NMR) spectrum of a protein upon binding a set of quasi-degenerate RNAs and define the nucleobase specificity. We couple this application of PCA to an automated NMR spectra recording and processing protocol and obtain an unbiased and high-throughput NMR method for the analysis of nucleobase preference in protein–RNA interactions. We test the method on the RNA binding domains of three important regulators of RNA metabolism.