TY - JOUR
T1 - HiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
AU - Sugimoto, Yoichiro
AU - Vigilante, Alessandra
AU - Darbo, Elodie
AU - Zirra, Alexandra
AU - Militti, Cristina
AU - D'Ambrogio, Andrea
AU - Luscombe, Nicholas M.
AU - Ule, Jernej
N1 - Funding Information:
Acknowledgements We wish to thank S. Granneman and C. Sibley for discussions on the development of hiCLIP protocol; K. Zarnack, N. Haberman, C. Ravarani and B. Lang for assistance with bioinformatic analyses; D. Daujotyte andP. Lukavskyfor sharing the STAU1 plasmid and helping in setting up the project; L. Maquat for sharing the ARF1 SBS plasmid; the genomic team at the Cancer Research UK Cambridge Institute for Illumina HiSeq sequencing, and M. Babu Mohan and Ule group members for support and comments on the manuscript. This work was supported by funding from Human Frontier Science Program (RGP0024/2008-C), European Research Council (206726-CLIP and 617837-Translate) and Medical Research Council (U105185858) to J.U., Cancer Research UK and UCL to N.M.L., a Wellcome Trust Joint Investigator Award to N.M.L. and J.U. (103760/Z/14/Z), the Nakajima Foundation fellowship and MRC Centenary Early Career Award to Y.S.
Publisher Copyright:
© 2015 Macmillan Publishers Limited. All rights reserved.
PY - 2015/3/26
Y1 - 2015/3/26
N2 - 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. 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 3'2 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 3'2 UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our 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.
AB - 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. 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 3'2 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 3'2 UTR of the X-box binding protein 1 (XBP1) mRNA that regulates its cytoplasmic splicing and stability. Our 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.
UR - http://www.scopus.com/inward/record.url?scp=84925799191&partnerID=8YFLogxK
U2 - 10.1038/nature14280
DO - 10.1038/nature14280
M3 - Article
C2 - 25799984
AN - SCOPUS:84925799191
SN - 0028-0836
VL - 519
SP - 491
EP - 494
JO - Nature
JF - Nature
IS - 7544
ER -