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

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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

DOI 10.1073/pnas.1017386108PMC PMC3116431

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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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Authors: Kudla, G., Granneman, S., Hahn, D., Beggs, J. D., & Tollervey, D.
Affiliations: Wellcome Centre for Cell Biology (GB)
ORCID: Kudla, Grzegorz
Granneman, Sander
Beggs, Jean D.
Tollervey, David
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 2011-05-24
Volume: 108
Issue: 24
Pages: 10010-10015
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.1017386108
PMC: PMC3116431
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: green
www.ncbi.nlm.nih.gov
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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Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast

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