title: CLIP: viewing the RNA world from an RNA-protein interactome perspective.
abstract: The pervasive transcription of the genome creates many types of non-coding RNAs (ncRNAs). However, we know very little regarding the functions and the regulatory mechanisms of these ncRNAs. Exploring the interactions of RNA and RNA binding proteins (RBPs) is vital because it can allow us to truly understand how these ncRNAs behave in vivo. High-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP or CLIP-seq) and its variants have been successfully used as systemic techniques to study RBP binding sites. In this review, we will explain the major differences between the CLIP techniques, summarize successful applications of these techniques, discuss limitations of CLIP, present some suggested solutions and project their promising future roles in studying the RNA world.
authors.affiliation: Key Laboratory of Gene Engineering of Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-Sen University, Guangzhou, 510275, China.
authors.forename: Yin
authors.initials: Y
authors.lastname: Zhang
authors.forename: ShuJuan
authors.initials: S
authors.lastname: Xie
authors.forename: Hui
authors.initials: H
authors.lastname: Xu
authors.forename: LiangHu
authors.initials: L
authors.lastname: Qu
mesh_terms: D004591:Electrophoresis, Polyacrylamide Gel; D047468:Immunoprecipitation; D011485:Protein Binding; D012313:RNA / Q000737:chemistry*; D012326:RNA Splicing; D016601:RNA-Binding Proteins / Q000737:chemistry*
chemical_list: D016601:RNA-Binding Proteins; D012313:RNA