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

Yoichiro Sugimoto; Alessandra Vigilante; Elodie Darbo; Alexandra Zirra; Cristina Militti; Andrea D'Ambrogio; Nicholas M. Luscombe; Jernej Ule

doi:10.1038/nature14280

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

Yoichiro Sugimoto, Alessandra Vigilante, Elodie Darbo, Alexandra Zirra, Cristina Militti, Andrea D'Ambrogio, Nicholas M. Luscombe, Jernej Ule^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

216 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	491-494
Number of pages	4
Journal	Nature
Volume	519
Issue number	7544
DOIs	https://doi.org/10.1038/nature14280
Publication status	Published - 26 Mar 2015

Access to Document

10.1038/nature14280

Cite this

@article{ef05022b9a2e431f92272df4502fb9db,

title = "HiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1",

abstract = "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.",

author = "Yoichiro Sugimoto and Alessandra Vigilante and Elodie Darbo and Alexandra Zirra and Cristina Militti and Andrea D'Ambrogio and Luscombe, {Nicholas M.} and Jernej Ule",

note = "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: {\textcopyright} 2015 Macmillan Publishers Limited. All rights reserved.",

year = "2015",

month = mar,

day = "26",

doi = "10.1038/nature14280",

language = "English",

volume = "519",

pages = "491--494",

journal = "Nature",

issn = "0028-0836",

publisher = "Springer Nature",

number = "7544",

}

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 -

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

Abstract

Access to Document

Other files and links

Fingerprint

Cite this