鉴于他们在翻译中的核心作用,拼接,转录本的定位和稳定性,RNA结合蛋白(RBP)是几种细胞过程的关键调节因子。虽然已经进行了实验努力来研究RBPs如何与转录本结合,关于RNA对相互作用的贡献知之甚少。这里,我们回顾了最常见的以RNA为中心的方法来揭示与RBPs的相互作用:两者都是在体外(SELEX,SEQR,RNA竞争和RBNS)和计算机模拟(MEME,Seamot,GLAM2,iDeep,MEMERIS,RNA上下文,RCK,RNApromo和GraphProt)。我们强调了每种技术的主要优点和缺点,并强调了有助于鉴定RBP识别中涉及的RNA基序的关键物理化学特征。我们讨论了影响蛋白质-RNA结合的外在决定因素,例如转录后和翻译后修饰以及转录本的表达和位置。
Given their central role in translation, splicing, localization and stability of transcripts, RNA binding proteins (RBPs) are key regulators of several cellular processes. While experimental efforts have been put to
study how RBPs bind to transcripts, very little is known about the RNA contributions to the interaction. Here, we review the most common RNA-centric methods to reveal interactions with RBPs: both in vitro (SELEX, SEQR, RNA-compete and RBNS) and in silico (MEME, SeAMotE, GLAM2, iDeep, MEMERIS, RNA context, RCK, RNApromo and GraphProt). We emphasize the main advantages and disadvantages of each technique and highlight the key physico-chemical features contributing to the identification of RNA motifs involved in RBP recognition. We discuss extrinsic determinants influencing protein-RNA binding, such as post-transcriptional and post-translational modifications as well as expression and location of transcripts.