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Identification of RNA-Binding Proteins Associated to RNA Structural Elements

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Part of the Methods in Molecular Biology book series (MIMB,volume 2323)


RNA motifs guide the interaction with specific proteins leading to the assembly of ribonucleoprotein complexes that perform key functions in cellular processes. Internal ribosome entry site (IRES) elements are organized in structural domains that determine internal initiation of translation. In this chapter we describe a pull-down assay using streptavidin-aptamer tagged RNAs that combines RNA structure-dependent protein isolation with proteomic analysis to identify novel interactors recognizing RNA structural domains. This approach takes advantage of tRNA-scaffold guided expression, allowing the identification of factors belonging to networks involved in RNA and protein metabolism.

Key words

  • RNA structure
  • RNA-binding proteins
  • Pull-down
  • Streptavidin aptamer
  • tRNA scaffold
  • IRES elements
  • Translation control

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  • DOI: 10.1007/978-1-0716-1499-0_9
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We thank L. Ponchon for reagents, J. Ramajo for technical assistance, and A. Escos for comments on the protocol. This work was supported by MINECO (grant BFU2017-84492-R), Comunidad de Madrid (B2017/BMD-3770) and an Institutional grant from Fundación Ramón Areces.

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Correspondence to Encarnacion Martinez-Salas .

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Fernandez-Chamorro, J., Francisco-Velilla, R., Embarc-Buh, A., Martinez-Salas, E. (2021). Identification of RNA-Binding Proteins Associated to RNA Structural Elements. In: Ponchon, L. (eds) RNA Scaffolds. Methods in Molecular Biology, vol 2323. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1498-3

  • Online ISBN: 978-1-0716-1499-0

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