hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

• Published in: Nature (London) 2015-03, Vol.519 (7544), p.491-494
• Main Authors: Sugimoto, Yoichiro, Vigilante, Alessandra, Darbo, Elodie, Zirra, Alexandra, Militti, Cristina, D’Ambrogio, Andrea, Luscombe, Nicholas M., Ule, Jernej
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions - genetics; 631/1647/2258/1267; 631/337/1645/2020; 631/45/500; 631/553/2711; Analysis; Base Sequence; Cell cycle; Cytoplasm - genetics; Cytoplasm - metabolism; Cytoskeletal Proteins - metabolism; DNA-Binding Proteins - genetics; Endoplasmic reticulum; Genetic regulation; Humanities and Social Sciences; Humans; letter; Messenger RNA; Molecular structure; multidisciplinary; Mutation; Nucleic Acid Conformation; Polymorphism, Single Nucleotide - genetics; Protein binding; Proteins; Regulatory Factor X Transcription Factors; Ribonucleic acid; RNA; RNA Splicing; RNA Stability; RNA, Messenger - chemistry; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA-Binding Proteins - metabolism; Science; Transcription Factors - genetics; X-Box Binding Protein 1
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature14280

A method, termed hiCLIP, has been developed to determine the RNA duplexes bound by RNA-binding proteins, revealing an unforeseen prevalence of long-range duplexes in 3′ untranslated regions (UTRs), and a decreased incidence of SNPs in duplex-forming regions; the results also show that RNA structure is able to regulate gene expression. Probing native RNA structure The single-stranded nature of cellular RNAs allows them flexibility to adopt different secondary structures that can affect their function. However, current methods of measuring RNA structure in vivo are limited. Two papers published in this week's issue of Nature present new techniques to address this gap. Howard Chang and colleagues have exploited a click methodology that enables the first global view of RNA secondary structures in living cells for all four bases. While some structures are stable and seem to be programmed by sequence, others are dynamic, reflecting the binding of proteins or modification of the bases. This method may allow RNA to be analysed in vivo from a structural genomics perspective. In the second study, Jernej Ule and colleagues have developed a method, hiCLIP, to specifically measure RNA structures bound by proteins. Various features are observed, such as a preference for intramolecular interactions and an under-representation of structures in coding regions. The results confirm that RNA structure is able to regulate gene expression. While the functional significance is not known, it is notable that SNPs are not present at the expected frequency in coding regions. The structure of messenger RNA is important for post-transcriptional regulation, mainly because it affects binding of trans -acting factors 1 . However, little is known about the in vivo structure of full-length mRNAs. Here we present 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, we 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. We 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