Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (24), p.10010-10015
2011
Details
- Autor(en) / Beteiligte
- Titel
- Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast
- Ist Teil von
- Proceedings of the National Academy of Sciences - PNAS, 2011-06, Vol.108 (24), p.10010-10015
- Ort / Verlag
- United States: National Academy of Sciences
- Erscheinungsjahr
- 2011
- Link zum Volltext
- Quelle
- EZB Electronic Journals Library
- Beschreibungen/Notizen
- 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.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 0027-8424eISSN: 1091-6490DOI: 10.1073/pnas.1017386108Titel-ID: cdi_proquest_journals_872187345
- Format
- –
- Schlagworte
- Base Sequence, Biochemistry, Biological Sciences, Blotting, Northern, Chimeras, crosslinking, Data processing, Datasets, DNA, Complementary - chemistry, DNA, Complementary - genetics, Electrophoresis, Genetic mutation, hybrids, Ligation, Models, Molecular, Molecular chemistry, Molecular Sequence Data, Nucleic Acid Conformation, Nucleoli, Nucleotides, Protein structure, Proteins, Ribonucleic acid, ribosomal RNA, RNA, RNA, Fungal - chemistry, RNA, Fungal - genetics, RNA, Fungal - metabolism, RNA, Ribosomal - chemistry, RNA, Ribosomal - genetics, RNA, Ribosomal - metabolism, RNA, Ribosomal, 18S - chemistry, RNA, Ribosomal, 18S - genetics, RNA, Ribosomal, 18S - metabolism, RNA, Small Nuclear - chemistry, RNA, Small Nuclear - genetics, RNA, Small Nuclear - metabolism, RNA, Small Nucleolar - chemistry, RNA, Small Nucleolar - genetics, RNA, Small Nucleolar - metabolism, rRNA 18S, Saccharomyces cerevisiae - genetics, Secondary structure, Sequence Analysis, DNA, Small nuclear RNA, Small nucleolar RNA, snoRNA, snoRNA U3, snRNA, spliceosomes, Spliceosomes - genetics, Spliceosomes - metabolism, Splicing, Yeast, Yeasts