Cirillo Davide, Marchese Domenica, Agostini Federico, Livi Carmen Maria, Botta-Orfila Teresa, Tartaglia Gian Gaetano
Genome Biol. 2014 Jan 2;15(1):R13. doi: 10.1186/gb-2014-15-1-r13.
RNA-binding proteins regulate a number of cellular processes, including synthesis, folding, translocation, assembly and clearance of RNAs. Recent studies have reported that an unexpectedly large number of proteins are able to interact with RNA, but the partners of many RNA-binding proteins are still uncharacterized.
We combined prediction of ribonucleoprotein interactions, based on catRAPID calculations, with analysis of protein and RNA expression profiles from human tissues. We found strong interaction propensities for both positively and negatively correlated expression patterns. Our integration of in silico and ex vivo data unraveled two major types of protein-RNA interactions, with positively correlated patterns related to cell cycle control and negatively correlated patterns related to survival, growth and differentiation. To facilitate the investigation of protein-RNA interactions and expression networks, we developed the catRAPID express web server.
Our analysis sheds light on the role of RNA-binding proteins in regulating proliferation and differentiation processes, and we provide a data exploration tool to aid future experimental studies.
RNA结合蛋白调控许多细胞过程，包括RNA的合成、折叠、转运、组装和清除。最近的研究报道，数量出乎意料多的蛋白质能够与RNA相互作用，但许多RNA结合蛋白的相互作用伙伴仍未得到表征。
我们将基于catRAPID计算的核糖核蛋白相互作用预测与来自人类组织的蛋白质和RNA表达谱分析相结合。我们发现正相关和负相关表达模式均具有很强的相互作用倾向。我们对计算机模拟数据和体外数据的整合揭示了两种主要的蛋白质-RNA相互作用类型，正相关模式与细胞周期调控有关，负相关模式与存活、生长和分化有关。为便于研究蛋白质-RNA相互作用和表达网络，我们开发了catRAPID express网络服务器。
我们的分析揭示了RNA结合蛋白在调控增殖和分化过程中的作用，并且我们提供了一个数据探索工具以辅助未来的实验研究。
