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PMID: 25799984 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nature ·Vol. 519 ·No. 7544 ·2015-03-26 ·Pages 491-4

Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J

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' 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 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.

MeSH Terms
3' Untranslated Regions/genetics Base Sequence Cytoplasm/genetics,metabolism Cytoskeletal Proteins/metabolism DNA-Binding Proteins/genetics Humans Nucleic Acid Conformation Polymorphism, Single Nucleotide/genetics RNA Splicing RNA Stability RNA, Messenger/chemistry,genetics,metabolism RNA-Binding Proteins/metabolism Regulatory Factor X Transcription Factors Transcription Factors/genetics X-Box Binding Protein 1
Chemicals
3' Untranslated Regions Cytoskeletal Proteins DNA-Binding Proteins RNA, Messenger RNA-Binding Proteins Regulatory Factor X Transcription Factors STAU1 protein, human Transcription Factors X-Box Binding Protein 1 XBP1 protein, human
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Sugimoto Yoichiro
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
Vigilante Alessandra
1] Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK [2] UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
Darbo Elodie
Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
Zirra Alexandra
Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
Militti Cristina
Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
D'Ambrogio Andrea
1] MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK [2] Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
Luscombe Nicholas M
1] Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK [2] UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK [3] Okinawa Institute of Science &Technology, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan.
Ule Jernej
1] MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK [2] Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK.
References (62)
62 references, click to expand
  1. Landscape and variation of RNA secondary structure across the human transcriptome.
    Nature. 2014 Jan 30;505(7485):706-9 PMID: 24476892
  2. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding.
    Cell. 2013 Apr 25;153(3):654-65 PMID: 23622248
  3. Mammalian microRNAs predominantly act to decrease target mRNA levels.
    Nature. 2010 Aug 12;466(7308):835-40 PMID: 20703300
  4. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
    Science. 2009 Apr 10;324(5924):218-23 PMID: 19213877
  5. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.
    Nature. 2014 Jan 30;505(7485):701-5 PMID: 24336214
  6. A human sequence homologue of Staufen is an RNA-binding protein that is associated with polysomes and localizes to the rough endoplasmic reticulum.
    Mol Cell Biol. 1999 Mar;19(3):2212-9 PMID: 10022908
  7. Understanding the transcriptome through RNA structure.
    Nat Rev Genet. 2011 Sep;12(9):641-55 PMID: 21850044
  8. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
    Bioinformatics. 2009 Oct 1;25(19):2607-8 PMID: 19654119
  9. The multifunctional Staufen proteins: conserved roles from neurogenesis to synaptic plasticity.
    Trends Neurosci. 2014 Sep;37(9):470-9 PMID: 25012293
  10. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
    Nat Struct Mol Biol. 2010 Jul;17(7):909-15 PMID: 20601959
  11. Ubiquitination of the peroxisomal targeting signal type 1 receptor, Pex5p, suggests the presence of a quality control mechanism during peroxisomal matrix protein import.
    J Biol Chem. 2005 Jan 21;280(3):1921-30 PMID: 15536088
  12. iCLIP: protein-RNA interactions at nucleotide resolution.
    Methods. 2014 Feb;65(3):274-87 PMID: 24184352
  13. Molecular mapping of the determinants involved in human Staufen-ribosome association.
    Biochem J. 2002 Aug 1;365(Pt 3):817-24 PMID: 12133005
  14. Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.
    Nature. 2014 Sep 11;513(7517):256-60 PMID: 25043050
  15. Estimating enrichment of repetitive elements from high-throughput sequence data.
    Genome Biol. 2010;11(6):R69 PMID: 20584328
  16. Circos: an information aesthetic for comparative genomics.
    Genome Res. 2009 Sep;19(9):1639-45 PMID: 19541911
  17. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements.
    Nature. 2011 Feb 10;470(7333):284-8 PMID: 21307942
  18. Differential expression analysis for sequence count data.
    Genome Biol. 2010;11(10):R106 PMID: 20979621
  19. ViennaRNA Package 2.0.
    Algorithms Mol Biol. 2011 Nov 24;6:26 PMID: 22115189
  20. T4 RNA ligase: substrate chain length requirements.
    FEBS Lett. 1974 Sep 15;46(1):271-5 PMID: 4609429
  21. Cell cycle-dependent regulation of the RNA-binding protein Staufen1.
    Nucleic Acids Res. 2014 Jul;42(12):7867-83 PMID: 24906885
  22. Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.
    Mol Cell. 2014 Jun 19;54(6):1042-54 PMID: 24857550
  23. LIN28A is a suppressor of ER-associated translation in embryonic stem cells.
    Cell. 2012 Nov 9;151(4):765-77 PMID: 23102813
  24. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.
    Brief Bioinform. 2013 Mar;14(2):178-92 PMID: 22517427
  25. DMS footprinting of structured RNAs and RNA-protein complexes.
    Nat Protoc. 2007;2(10):2608-23 PMID: 17948004
  26. Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast.
    Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):10010-5 PMID: 21610164
  27. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges.
    Nat Struct Mol Biol. 2013 Dec;20(12):1434-42 PMID: 24213538
  28. Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships.
    J Virol. 2009 Jul;83(13):6326-34 PMID: 19369331
  29. STAU1 binding 3' UTR IRAlus complements nuclear retention to protect cells from PKR-mediated translational shutdown.
    Genes Dev. 2013 Jul 1;27(13):1495-510 PMID: 23824540
  30. RNA targets and specificity of Staufen, a double-stranded RNA-binding protein in Caenorhabditis elegans.
    J Biol Chem. 2013 Jan 25;288(4):2532-45 PMID: 23195953
  31. The intimate relationships of mRNA decay and translation.
    Trends Genet. 2013 Dec;29(12):691-9 PMID: 24091060
  32. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).
    Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8 PMID: 21642531
  33. Fast and effective prediction of microRNA/target duplexes.
    RNA. 2004 Oct;10(10):1507-17 PMID: 15383676
  34. Mammalian Staufen1 recruits Upf1 to specific mRNA 3'UTRs so as to elicit mRNA decay.
    Cell. 2005 Jan 28;120(2):195-208 PMID: 15680326
  35. SylArray: a web server for automated detection of miRNA effects from expression data.
    Bioinformatics. 2010 Nov 15;26(22):2900-1 PMID: 20871108
  36. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
    Nat Methods. 2010 Dec;7(12):995-1001 PMID: 21057495
  37. BEDTools: a flexible suite of utilities for comparing genomic features.
    Bioinformatics. 2010 Mar 15;26(6):841-2 PMID: 20110278
  38. Integrative genomics viewer.
    Nat Biotechnol. 2011 Jan;29(1):24-6 PMID: 21221095
  39. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.
    Cell. 2011 Nov 11;147(4):789-802 PMID: 22056041
  40. Reversible cross-linking combined with immunoprecipitation to study RNA-protein interactions in vivo.
    Methods. 2002 Feb;26(2):182-90 PMID: 12054895
  41. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
    Genome Biol. 2009;10(3):R25 PMID: 19261174
  42. Mammalian endoplasmic reticulum stress sensor IRE1 signals by dynamic clustering.
    Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16113-8 PMID: 20798350
  43. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.
    Nat Protoc. 2012 Aug;7(8):1534-50 PMID: 22836135
  44. Global analysis of RNA secondary structure in two metazoans.
    Cell Rep. 2012 Jan 26;1(1):69-82 PMID: 22832108
  45. Mammalian staufen is a double-stranded-RNA- and tubulin-binding protein which localizes to the rough endoplasmic reticulum.
    Mol Cell Biol. 1999 Mar;19(3):2220-30 PMID: 10022909
  46. Staufen1 regulates diverse classes of mammalian transcripts.
    EMBO J. 2007 Jun 6;26(11):2670-81 PMID: 17510634
  47. Regulatory sequence analysis tools.
    Nucleic Acids Res. 2003 Jul 1;31(13):3593-6 PMID: 12824373
  48. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
    Nat Protoc. 2009;4(1):44-57 PMID: 19131956
  49. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.
    Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92 PMID: 15123812
  50. The unfolded protein response: from stress pathway to homeostatic regulation.
    Science. 2011 Nov 25;334(6059):1081-6 PMID: 22116877
  51. Staufen1 senses overall transcript secondary structure to regulate translation.
    Nat Struct Mol Biol. 2014 Jan;21(1):26-35 PMID: 24336223
  52. Control of somatic tissue differentiation by the long non-coding RNA TINCR.
    Nature. 2013 Jan 10;493(7431):231-5 PMID: 23201690
  53. Genome-wide measurement of RNA secondary structure in yeast.
    Nature. 2010 Sep 2;467(7311):103-7 PMID: 20811459
  54. Functional signature for the recognition of specific target mRNAs by human Staufen1 protein.
    Nucleic Acids Res. 2014 Apr;42(7):4516-26 PMID: 24470147
  55. Staufen2 regulates neuronal target RNAs.
    Cell Rep. 2013 Dec 26;5(6):1511-8 PMID: 24360961
  56. REVIGO summarizes and visualizes long lists of gene ontology terms.
    PLoS One. 2011;6(7):e21800 PMID: 21789182
  57. Determination of in vivo RNA structure in low-abundance transcripts.
    Nat Commun. 2013;4:2971 PMID: 24336128
  58. Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity.
    Nucleic Acids Res. 2013 Nov;41(20):9438-60 PMID: 23945942
  59. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.
    Nature. 2014 Jan 30;505(7485):696-700 PMID: 24270811
  60. The ribosome uses two active mechanisms to unwind messenger RNA during translation.
    Nature. 2011 Jul 7;475(7354):118-21 PMID: 21734708
  61. Structures of the human and Drosophila 80S ribosome.
    Nature. 2013 May 2;497(7447):80-5 PMID: 23636399
  62. Localization of the binding site for protein S4 on 16 S ribosomal RNA by chemical and enzymatic probing and primer extension.
    J Mol Biol. 1986 Nov 5;192(1):101-10 PMID: 3820298
Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature14280
Published
2015-03-26
Epub
2015-00-18
Pages
491-4
Language
English
Region
England
NLM ID
0410462
PMCID
PMC4376666
Subset
IM
Grants
European Research Council · 617837 · International
Medical Research Council · U105185858 · United Kingdom
Medical Research Council · MC_U105185858 · United Kingdom
Wellcome Trust · 103760 · United Kingdom
Wellcome Trust · 103760/Z/14/Z · United Kingdom
Cancer Research UK · A16358 · United Kingdom
European Research Council · 206726 · International
Corrections
CommentIn
PMID: 25854184
External Links
PubMed source DOI: 10.1038/nature14280 PMC Full Text View journal details
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