title: RNA-protein interaction methods to study viral IRES elements.
abstract: 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.
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Rosario
authors.initials: R
authors.lastname: Francisco-Velilla
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Fernandez-Chamorro
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Gloria
authors.initials: G
authors.lastname: Lozano
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
authors.forename: Rosa
authors.initials: R
authors.lastname: Diaz-Toledano
authors.affiliation: Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain. Electronic address: emartinez@cbm.csic.es.
authors.forename: Encarnación
authors.initials: E
authors.lastname: Martínez-Salas
mesh_terms: D002846:Chromatography, Affinity / Q000379:methods; D019075:Electrophoresis, Capillary; D000067556:Internal Ribosome Entry Sites; D013058:Mass Spectrometry; D009690:Nucleic Acid Conformation; D012328:RNA Viruses / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012367:RNA, Viral / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000302:isolation & purification / Q000378:metabolism*
chemical_list: D000067556:Internal Ribosome Entry Sites; D012333:RNA, Messenger; D012367:RNA, Viral; D016601:RNA-Binding Proteins
keywords: IRES elements; RNA structure; RNA virus; RNA-binding proteins; Translation control