Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE Chemical Probing
| Autor: | H. U. Göringer, Leeder Wm |
|---|---|
| Rok vydání: | 2019 |
| Předmět: |
chemistry.chemical_classification
0303 health sciences RNA 010402 general chemistry G-quadruplex 01 natural sciences Primer extension 0104 chemical sciences Acylation 03 medical and health sciences chemistry.chemical_compound chemistry RNA editing Complementary DNA Ribose Biophysics Nucleotide 030304 developmental biology |
| Zdroj: | Methods in Molecular Biology ISBN: 9781071602300 |
| DOI: | 10.1007/978-1-0716-0231-7_10 |
| Popis: | Mitochondrial pre-mRNAs in African trypanosomes adopt intricately folded, highly stable 2D and 3D structures. The RNA molecules are substrates of a U-nucleotide-specific insertion/deletion-type RNA editing reaction, which is catalyzed by a 0.8 MDa protein complex known as the editosome. RNA binding to the editosome is followed by a chaperone-mediated RNA remodeling reaction. The reaction increases the dynamic of specifically U-nucleotides to lower their base-pairing probability and as a consequence generates a simplified RNA folding landscape that is critical for the progression of the editing reaction cycle. Here we describe a chemical mapping method to quantitatively monitor the chaperone-driven structural changes of pre-edited mRNAs upon editosome binding. The method is known as selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). SHAPE is based on the differential electrophilic modification of ribose 2'-hydroxyl groups in structurally constraint (double-stranded) versus structurally unconstrained (single-stranded) nucleotides. Electrophilic anhydrides such as 1-methyl-7-nitroisatoic anhydride are used as probing reagents, and the ribose 2'-modified nucleotides are mapped as abortive cDNA synthesis products. As a result, SHAPE allows the identification of all single-stranded and base-paired regions in a given RNA, and the data are used to compute experimentally derived RNA 2D structures. A side-by-side comparison of the RNA 2D folds in the pre- and post-chaperone states finally maps the chaperone-induced dynamic of the different pre-mRNAs with single-nucleotide resolution. |
| Databáze: | OpenAIRE |
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