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RNA–protein interaction methods to study viral IRES elements
- Francisco-Velilla, Rosario, Fernandez-Chamorro, Javier, Lozano, Gloria, Diaz-Toledano, Rosa, Martínez-Salas, Encarnación
- Methods 2015 v.91 pp. 3-12
- RNA viruses, RNA-binding proteins, messenger RNA, nucleotide sequences, protein synthesis, ribosomes, transactivators, translation (genetics)
- Translation control often takes place through the mRNA untranslated regions, involving direct interactions with RNA-binding proteins (RBPs). Internal ribosome entry site elements (IRESs) are cis-acting RNA regions that promote translation initiation using a cap-independent mechanism. A subset of positive-strand RNA viruses harbor IRESs as a strategy to ensure efficient viral protein synthesis. IRESs are organized in modular structural domains with a division of functions. However, viral IRESs vary in nucleotide sequence, secondary RNA structure, and transacting factor requirements. Therefore, in-depth studies are needed to understand how distinct types of viral IRESs perform their function. In this review we describe methods to isolate and identify RNA-binding proteins important for IRES activity, and to study the impact of RNA structure and RNA–protein interactions on IRES activity.