Native Circular RNA Pulldown Method to Simultaneously Profile RNA and Protein Interactions

Marta M. Gabryelska, Stuart T. Webb, He Lin, Laura Gantley, Kirsty Kirk, Ryan Liu, Brett W. Stringer, Vanessa M. Conn, Simon J. Conn

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical splicing of pre-mRNA, a process called back-splicing. Back-splicing results in circRNAs which are distinguishable from their cognate mRNA as they possess a unique sequence of nucleic acids called the backsplice junction (BSJ). CircRNAs have been shown to play key functional roles in various cellular contexts and achieve this through their interaction with other macromolecules, particularly other RNA molecules and proteins. To elucidate the molecular mechanisms underlying circRNA function, it is necessary to identify these interacting partners. Herein, we present an optimized strategy for the simultaneous purification of the circRNA interactome within eukaryotic cells, allowing the identification of both circRNA-RNA and circRNA-protein interactions.

Original languageEnglish
Title of host publicationCircular RNAs
EditorsChristoph Dieterich, Marie-Laure Baudet
Place of PublicationNew York
PublisherSpinger
Chapter16
Pages299-309
Number of pages11
Volume2765
ISBN (Electronic)978-1-0716-3678-7
ISBN (Print)978-1-0716-3677-0
DOIs
Publication statusPublished - 2024

Publication series

NameMethods in molecular biology (Clifton, N.J.)
PublisherSpringer
Volume2765
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • circRNA
  • circRNA–protein
  • circRNA–RNA
  • circular RNA
  • Interactome
  • Pulldown
  • RNA-binding proteins
  • RNA–RNA interactions

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