title: CLIPing Staufen to secondary RNA structures: size and location matter!
abstract: hiCLIP (RNA hybrid and individual-nucleotide resolution ultraviolet cross-linking and immunoprecipitation), is a novel technique developed by Sugimoto et al. (2015). Here, the use of different adaptors permits a controlled ligation of the two strands of a RNA duplex allowing the identification of each arm in the duplex upon sequencing. The authors chose a notoriously difficult to study double-stranded RNA-binding protein (dsRBP) termed Staufen1, a mammalian homolog of Drosophila Staufen involved in mRNA localization and translational control. Using hiCLIP, they discovered a dominance of intramolecular RNA duplexes compared to the total RNA duplexes identified. Importantly, the authors discovered two different types of intramolecular duplexes in the cell: highly translated mRNAs with long-range duplexes in their 3'-UTRs and poorly translated mRNAs with duplexes in their coding region. In conclusion, the authors establish hiCLIP as an important novel technique for the identification of RNA secondary structures that serve as in vivo binding sites for dsRBPs.
authors.affiliation: BioMedical Center, Department for Anatomy and Cell Biology, Ludwig-Maximilians-University, Munich, Germany.
authors.forename: Sandra M
authors.initials: SM
authors.lastname: Fernández Moya
authors.affiliation: BioMedical Center, Department for Anatomy and Cell Biology, Ludwig-Maximilians-University, Munich, Germany.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Kiebler
mesh_terms: D000818:Animals; D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry; D006801:Humans; D047468:Immunoprecipitation / Q000379:methods; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D003432:Cross-Linking Reagents; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012313:RNA
keywords: RNA binding protein; RNA localization; RNA secondary structure; Staufen; hiCLIP; learning and memory; local protein synthesis; synapse