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Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein

Item Type:Article
Title:Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein
Creators Name:Sugimoto, Y. and Chakrabarti, A.M. and Luscombe, N.M. and Ule, J.
Abstract:The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing. Mapping of the sequenced arms to a reference transcriptome identifies the exact locations of duplexes. hiCLIP data can directly identify all types of RNA duplexes bound by RBPs, including those that are challenging to predict computationally, such as intermolecular and long-range intramolecular duplexes. Moreover, the use of an adaptor that links the two arms of the RNA duplex permits hiCLIP to unambiguously identify the duplexes. Here we describe in detail the procedure for a hiCLIP experiment and the subsequent streamlined data analysis with an R package, 'hiclipr' (https://github.com/luslab/hiclipr/). Preparation of the library for high-throughput DNA sequencing takes ∼7 d and the basic bioinformatic pipeline takes 1 d.
Keywords:Artificial Membranes, Cell Line, Collodion, Computational Biology, Immunoprecipitation, Polyacrylamide Gel Electrophoresis, Protein Binding, RNA, RNA-Binding Proteins, Substrate Specificity
Source:Nature Protocols
Publisher:Nature Publishing Group
Page Range:611-637
Date:March 2017
Official Publication:https://doi.org/10.1038/nprot.2016.188
PubMed:View item in PubMed

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