Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale

作     者：Jing Gongt Yanyan Jut Di Shao Qiangfeng Cliff Zhang 

作者机构：MOE Key Laboratory of BioinformaticsBeijing Advanced Innovation Center for Structural BiologyCenter for Synthetic and Systems BiologyTsinghua-Peking Joint Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China 

出 版 物：《Frontiers of Electrical and Electronic Engineering in China》 (中国电气与电子工程前沿（英文版）)

年 卷 期：2018年第6卷第3期

页      面：239-252页

核心收录：

学科分类：0711[理学-系统科学] 07[理学] 081104[工学-模式识别与智能系统] 08[工学] 09[农学] 0901[农学-作物学] 0836[工学-生物工程] 090102[农学-作物遗传育种] 0811[工学-控制科学与工程] 071102[理学-系统分析与集成] 081103[工学-系统工程] 

基　　金：国家自然科学基金 the National Thousand Young Talents Program of China to Qiangfeng Cliff Zhang 

主　　题：RNA-RNA interactions PARIS SPLASH LIGR-seq next generation sequencing 

摘      要：RNA molecules play crucial roles in various biological processes. Their regulation and function are mediated by interacting with other molecules. Among them RNA-RNA interactions （RRIs） are important in many basic cellular activities including transcription, RNA processing, localization, and translation. However, we just start to unveil the complexity of the knowledge and underlying mechanisms of RRIs. Results： In this review, we will summarize approaches for RRI identifications, including both conventional, focused biophysical and biochemical methods and recently developed large scale sequencing-based techniques. We will also discuss discoveries per RRI type revealed by using these technologies, as well as challenges towards a systematic and functional understanding of RRIs. Conclusions： The development of sequencing-based techniques has revolutionized the study of RRIs. Applying these techniques in multiple organisms has identified thousands of RRls, many of which could potentially regulate multiple aspects of gene expression. However, despite the great breakthrough, the RNA-RNA interactome of any species remains far from complete due to intrinsic complex nature of RRI and limitations in current techniques. More efficient experimental methods and computational framework are needed to obtain the full image of RRI networks, and their possible regulatory roles in biology and medicine.