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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Medina-Munoz, Hugo C; Kofman, Eric; Jagannatha, Pratibha; Boyle, Evan A; Yu, Tao; Jones, Krysten L; Mueller, Jasmine R; Lykins, Grace D; Doudna, Andrew T; Park, Samuel S; Blue, Steven M; Ranzau, Brodie L; Kohli, Rahul M; Komor, Alexis C; Yeo, Gene W.
Afiliación
  • Medina-Munoz HC; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
  • Kofman E; Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
  • Jagannatha P; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
  • Boyle EA; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
  • Yu T; Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
  • Jones KL; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
  • Mueller JR; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
  • Lykins GD; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
  • Doudna AT; Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
  • Park SS; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
  • Blue SM; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
  • Ranzau BL; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
  • Kohli RM; Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
  • Komor AC; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
  • Yeo GW; Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
bioRxiv ; 2023 Sep 25.
Article en En | MEDLINE | ID: mdl-37808757
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos