Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs
Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs作者机构:Center for RNA Science and TherapeuticsCase Western Reserve UniversityClevelandOH 44106USA
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:228-238页
核心收录:
学科分类:0710[理学-生物学] 0810[工学-信息与通信工程] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 081001[工学-通信与信息系统]
基 金:supported by funds from the National Institutes of Health to LLZ
主 题:RNA binding proteins CLIP post-transcriptional regulation RNA networks
摘 要:Background: Our understanding of post-transcriptional gene regulation has increased exponentially with the development of robust methods to define protein-RNA interactions across the transcriptome. In this review, we highlight the evolution and successful applications of crosslinking and immunoprecipitation (CLIP) methods to interrogate protein-RNA interactions in a transcriptome-wide manner. Results: Here, we survey the vast array of in vitro and in vivo approaches used to identify protein-RNA interactions, including but not limited to electrophoretic mobility shift assays, systematic evolution of ligands by exponential enrichment (SELEX), and RIP-seq. We particularly emphasize the advancement of CLIP technologies, and detail protocol improvements and computational tools used to analyze the output data. Importantly, we discuss how profiling protein-RNA interactions can delineate biological functions including splicing regulation, alternative polyadenylation, cytoplasmic decay substrates, and miRNA targets. Conclusions: In summary, this review summarizes the benefits of characterizing RNA-protcin networks to further understand the regulation of gene expression and disease pathogenesis. Our review comments on how future CLIP technologies can be adapted to address outstanding questions related to many aspects of RNA metabolism and further advance our understanding of RNA biology.