Cottrell Kyle A, Chaudhari Hemangi G, Cohen Barak A, Djuranovic Sergej
Department of Cell Biology and Physiology, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
Department of Genetics, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
Nat Commun. 2018 Jan 19;9(1):301. doi: 10.1038/s41467-017-02745-0.
RNA binding proteins (RBP) and microRNAs (miRNAs) often bind sequences in 3' untranslated regions (UTRs) of mRNAs, and regulate stability and translation efficiency. With the identification of numerous RBPs and miRNAs, there is an urgent need for new technologies to dissect the function of the cis-acting elements of RBPs and miRNAs. We describe post-transcriptional regulatory element sequencing (PTRE-seq), a massively parallel method for assaying the target sequences of miRNAs and RBPs. We use PTRE-seq to dissect sequence preferences and interactions between miRNAs and RBPs. The binding sites for these effector molecules influenced different aspects of the RNA lifecycle: RNA stability, translation efficiency, and translation initiation. In some cases, post-transcriptional control is modular, with different factors acting independently of each other, while in other cases factors show specific epistatic interactions. The throughput, flexibility, and reproducibility of PTRE-seq make it a valuable tool to study post-transcriptional regulation by 3'UTR elements.
RNA结合蛋白（RBP）和微小RNA（miRNA）常常与信使核糖核酸（mRNA）3'非翻译区（UTR）中的序列结合，并调节其稳定性和翻译效率。随着众多RBP和miRNA的鉴定，迫切需要新技术来剖析RBP和miRNA顺式作用元件的功能。我们描述了转录后调控元件测序（PTRE-seq），这是一种用于检测miRNA和RBP靶序列的大规模平行方法。我们使用PTRE-seq来剖析miRNA和RBP的序列偏好及相互作用。这些效应分子的结合位点影响了RNA生命周期的不同方面：RNA稳定性、翻译效率和翻译起始。在某些情况下，转录后调控是模块化的，不同因素相互独立起作用，而在其他情况下，各因素表现出特定的上位相互作用。PTRE-seq的通量、灵活性和可重复性使其成为研究3'UTR元件转录后调控的宝贵工具。
