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Related Experiment Video

Updated: Nov 17, 2025

Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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CBRPP: a new RNA-centric method to study RNA-protein interactions.

Yunfei Li1, Shengde Liu1, Lili Cao1

  • 1Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, China.

RNA Biology
|February 18, 2021
PubMed
Summary

Researchers developed CRISPR-based RNA proximity proteomics (CBRPP), a novel RNA-centric method to identify proteins interacting with specific RNA molecules in cells. This technique aids in understanding cellular processes and diseases linked to RNA-protein interactions.

Keywords:
RNA-protein interactionsapex2basubioid2dPspCas13bdRfxCas13dturboid

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genomics

Background:

  • RNA and protein interactions are vital for cellular functions.
  • Dysfunctional RNA-protein interactions are implicated in various human diseases.
  • Existing protein-centric methods lack robust RNA-centric approaches for studying these interactions.

Purpose of the Study:

  • To develop a novel RNA-centric method for identifying proteins associated with endogenous RNA.
  • To provide a tool for mapping RNA-protein interaction networks in their native cellular context.
  • To overcome limitations of existing RNA-protein interaction study methods.

Main Methods:

  • Development of CRISPR-based RNA proximity proteomics (CBRPP).
  • Fusion of dCas13 (a CRISPR-associated enzyme) with a proximity-based labeling (PBL) enzyme.
  • Utilizing dCas13 to target and deliver the PBL enzyme to specific endogenous RNA molecules.
  • Identification of labeled proteins via mass spectrometry.

Main Results:

  • CBRPP enables specific targeting of endogenous RNA without prior manipulation.
  • The method allows for the identification of proteins in close proximity to the target RNA within the native cellular environment.
  • Successful application of CBRPP to map RNA-protein interactions.

Conclusions:

  • CBRPP is a robust and specific RNA-centric method for studying RNA-protein interactions.
  • This technique advances the understanding of cellular mechanisms and disease pathogenesis.
  • CBRPP offers a valuable tool for RNA biology research.