hiCLIP – transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins

The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans-acting factors. However, little is known about the in vivo structure of full-length mRNAs. Now researchers from the MRC Laboratory of Molecular Biology have developed hiCLIP, a biochemical technique for transcriptome-wide identification of RNA secondary structures interacting with RNA-binding proteins (RBPs). Using this technique to investigate RNA structures bound by Staufen 1 (STAU1) in human cells, they uncover a dominance of intra-molecular RNA duplexes, a depletion of duplexes from coding regions of highly translated mRNAs, an unexpected prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of single nucleotide polymorphisms in duplex-forming regions. The researchers also discover a duplex spanning 858 nucleotides in the 3′ UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. This study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes.

rna-seq

Availability – a computational pipeline for data analysis, which is freely accessible from (https://github.com/jernejule/STAU1_hiCLIP). The pipeline is implemented as a package of codes that enables the user to reproduce most plots and results using the sequencing data as input. All sequencing data are available from ArrayExpress (iCLIP and hiCLIP: E-MTAB-2937, mRNA-seq: E-MTAB-2940, ribosome profiling: E-MTAB-2941).

Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D’Ambrogio A, Luscombe NM, Ule J. (2015) hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature 519(7544):491-4. [abstract]

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