Gan Hin Hark, Gunsalus Kristin C
Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA.
Center for Genomics and Systems Biology, NYU Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates.
Methods Mol Biol. 2019;1970:43-64. doi: 10.1007/978-1-4939-9207-2_4.
Translational repression and degradation of transcripts by microRNAs (miRNAs) is mediated by a ribonucleoprotein complex called the miRNA-induced silencing complex (miRISC, or RISC). Advances in experimental determination of RISC structures have enabled detailed analysis and modeling of known miRNA targets, yet a full appreciation of the structural factors influencing target recognition remains a challenge, primarily because target recognition involves a combination of RNA-RNA and RNA-protein interactions that can vary greatly among different miRNA-target pairs. In this chapter, we review progress toward understanding the role of tertiary structure in miRNA target recognition using computational approaches to assemble RISC complexes at known targets and physics-based methods for computing target interactions. Using this framework to examine RISC structures and dynamics, we describe how the conformational flexibility of Argonautes plays an important role in accommodating the diversity of miRNA-target duplexes formed at canonical and noncanonical target sites. We then discuss applications of tertiary structure-based approaches to emerging topics, including the structural effects of SNPs in miRNA targets and cooperative interactions involving Argonaute-Argonaute complexes. We conclude by assessing the prospects for genome-scale modeling of RISC structures and modeling of higher-order Argonaute complexes associated with miRNA biogenesis, mRNA regulation, and other functions.
微小RNA（miRNA）对转录本的翻译抑制和降解是由一种名为微小RNA诱导沉默复合体（miRISC，或RISC）的核糖核蛋白复合体介导的。RISC结构实验测定方面的进展使得对已知miRNA靶标的详细分析和建模成为可能，然而，全面理解影响靶标识别的结构因素仍然是一项挑战，主要是因为靶标识别涉及RNA-RNA和RNA-蛋白质相互作用的组合，不同的miRNA-靶标对之间差异很大。在本章中，我们回顾了在利用计算方法在已知靶标处组装RISC复合体以及基于物理的方法计算靶标相互作用来理解三级结构在miRNA靶标识别中的作用方面取得的进展。利用这个框架来研究RISC结构和动力学，我们描述了AGO蛋白的构象灵活性如何在适应在经典和非经典靶标位点形成的miRNA-靶标双链体的多样性方面发挥重要作用。然后，我们讨论基于三级结构的方法在新兴主题中的应用，包括miRNA靶标中SNP的结构效应以及涉及AGO-AGO复合体的协同相互作用。我们通过评估RISC结构的全基因组规模建模以及与miRNA生物合成、mRNA调控和其他功能相关的高阶AGO复合体建模的前景来结束本章。
