Cited by 309RNA Research and SplicingRNA and protein synthesis mechanismsRNA modifications and cancer

Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast

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Kudla, Grzegorz, Granneman, Sander, Hahn, Daniela, Beggs, Jean D., Tollervey, David·2011·Proceedings of the National Academy of Sciences

Abstract

Many protein-protein and protein-nucleic acid interactions have been experimentally characterized, whereas RNA-RNA interactions have generally only been predicted computationally. Here, we describe a high-throughput method to identify intramolecular and intermolecular RNA-RNA interactions experimentally by cross-linking, ligation, and sequencing of hybrids (CLASH). As validation, we identified 39 known target sites for box C/D modification-guide small nucleolar RNAs (snoRNAs) on the yeast pre-rRNA. Novel snoRNA-rRNA hybrids were recovered between snR4-5S and U14-25S. These are supported by native electrophoresis and consistent with previously unexplained data. The U3 snoRNA was found to be associated with sequences close to the 3' side of the central pseudoknot in 18S rRNA, supporting a role in formation of this structure. Applying CLASH to the yeast U2 spliceosomal snRNA led to a revised predicted secondary structure, featuring alternative folding of the 3' domain and long-range contacts between the 3' and 5' domains. CLASH should allow transcriptome-wide analyses of RNA-RNA interactions in many organisms.

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  • Early CLASH publications showed the utility of chimeric analysis in mapping snoRNA interactions in yeast, and more recently it was utilized to generate an extensive catalog of putative snoRNA interactions and reveal novel targets of orphan snoRNAs.

    “early CLASH publications showed the utility of the chimeric analysis approach in mapping snoRNA interactions in yeast (Kudla et al., 2011) and more recently was utilized to generate an extensive catalog of putative snoRNA interactions and reveal novel targets of orphan snoRNAs (Gumienny et al., 2017).”

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Authors
Kudla, G., Granneman, S., Hahn, D., Beggs, J. D., & Tollervey, D.
Affiliations
Wellcome Centre for Cell Biology (GB)
Venue
Proceedings of the National Academy of Sciences
Published
2011-05-24
Volume
108
Issue
24
Pages
10010-10015
ISSN
  • 0027-8424 (ISSN-L)
  • 1091-6490
OpenAlex
W2117165052
Cited by
308
References
39
Citations by year
2026: 12 · 2025: 16 · 2024: 17 · 2023: 23 · 2022: 22 · 2021: 22 · 2020: 25 · 2019: 16 · 2018: 37 · 2017: 25 · 2016: 32 · 2015: 22 · 2014: 12 · 2013: 16 · 2012: 9
FWCI
5.07
Type
journal article
Language
en
Open access
Locations
  • Proceedings of the National Academy of Sciences (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
Funders
Wellcome Trust
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
RNA-RNA interactions, CLASH, box C/D snoRNA, small nucleolar RNA, pre-rRNA, U3 snoRNA, U2 snRNA, spliceosome, RNA secondary structure, Saccharomyces cerevisiae
MeSH terms
Base Sequence, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Fungal, RNA, Ribosomal, RNA, Ribosomal, 18S, RNA, Small Nuclear, Saccharomyces cerevisiae, Blotting, Northern, Spliceosomes, Sequence Analysis, DNA, DNA, Complementary, RNA, Small Nucleolar

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