The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast
Open accessAbstract
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 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).”
From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Kudla et al., 2011
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Cites
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652
DINAMelt web server for nucleic acid melting prediction
Markham, N. R., & Zuker, M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki591 · Cited by 947
Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs
Kiss-László, Z., Henry, Y. A. L., Bachellerie, J., Caizergues‐Ferrer, M., & Kiss, T. (1996) · Cell · doi:10.1016/s0092-8674(00)81308-2 · Cited by 855
Kiss (2002) · doi:10.1016/s0092-8674(02)00718-3 · Cited by 816
Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M. (2005) · Journal of the American Chemical Society · doi:10.1021/ja043822v · Cited by 791
RNA processing and its regulation: global insights into biological networks
Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 777
Genome-wide measurement of RNA secondary structure in yeast
Kertesz, M., Wan, Y., Mazor, E., Rinn, J. L., Nutter, R. C., Chang, H. Y., & Segal, E. (2010) · Nature · doi:10.1038/nature09322 · Cited by 769
Parker, R., Siliciano, P. G., & Guthrie, C. (1987) · Cell · doi:10.1016/0092-8674(87)90564-2 · Cited by 513
Guthrie, C., & Patterson, B. (1988) · Annual Review of Genetics · doi:10.1146/annurev.ge.22.120188.002131 · Cited by 476
Function and synthesis of small nucleolar RNAs
Tollervey, D. W., & Kiss, T. (1997) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(97)80005-1 · Cited by 467
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Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 2,041
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Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.043 · Cited by 1,269
Self-citationHsu, S., Tseng, Y., Shrestha, S., Lin, Y., Khaleel, A., Chou, C., Chu, C.-F., Huang, H., Lin, C.-M., Ho, S.-Y., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1266 · Cited by 1,044
Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae
Woolford, J. L., & Baserga, S. J. (2013) · Genetics · doi:10.1534/genetics.113.153197 · Cited by 780
Sloan, K. E., Warda, A. S., Sharma, S., Entian, K.-D., Lafontaine, D. L. J., & Bohnsack, M. T. (2017) · RNA Biology · doi:10.1080/15476286.2016.1259781 · Cited by 707
Metadata
- 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
- Publisher
- National Academy of Sciences
- Published
- 2011-05-24
- Volume
- 108
- Issue
- 24
- Pages
- 10010-10015
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- 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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