Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
| Autor: | Audrey Jacq, Denis Becquet, Maria-Montserrat Bello-Goutierrez, Bénédicte Boyer, Anne-Marie François-Bellan, Jean-Louis Franc, Séverine Guillen |
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| Přispěvatelé: | Institut de neurophysiopathologie (INP), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS) |
| Rok vydání: | 2021 |
| Předmět: |
General Immunology and Microbiology
Base pair Oligonucleotide [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology General Chemical Engineering General Neuroscience Computational Biology High-Throughput Nucleotide Sequencing Proteins RNA Computational biology Biology Interactome General Biochemistry Genetics and Molecular Biology Long non-coding RNA MicroRNAs chemistry.chemical_compound chemistry RNA Long Noncoding Identification (biology) Protein secondary structure DNA |
| Zdroj: | Journal of visualized experiments : JoVE Journal of visualized experiments : JoVE, JoVE, 2021, ⟨10.3791/62475⟩ Journal of visualized experiments : JoVE, 2021, 173, ⟨10.3791/62475⟩ |
| ISSN: | 1940-087X |
| Popis: | International audience; The growing role attributed nowadays to long non-coding RNAs (lncRNA) in physiology and pathophysiology makes it crucial to characterize their interactome by identifying their molecular partners, DNA, proteins and/or RNAs. The latter can interact with lncRNA through networks involving proteins, but they can also be engaged in direct RNA/RNA interactions. We, therefore, developed an easy-to-use RNA pull-down procedure that allowed identification of RNAs engaged in direct RNA/RNA interaction with a lncRNA using psoralen, a molecule that cross-links only RNA/RNA interactions. Bioinformatics modeling of the lncRNA secondary structure allowed the selection of several specific antisense DNA oligonucleotide probes with a strong affinity for regions displaying a low probability of internal base pairing. Since the specific probes that were designed targeted accessible regions throughout the length of the lncRNA, the RNA-interaction zones could be delineated in the sequence of the lncRNA. When coupled with a high throughput RNA sequencing, this protocol can be used for the whole direct RNA interactome studies of a lncRNA of interest. |
| Databáze: | OpenAIRE |
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