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Updated: Nov 1, 2025

An Assay for Quantifying Protein-RNA Binding in Bacteria

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

A New Method for Studying RNA-binding Proteins on Specific RNAs.

Weiping Sun^1,2,3, Ziheng Zhang^1,2,3, Ji-Long Liu¹

¹School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

|June 21, 2021

Summary

We developed CRISPR-based RNA-United Interacting System (CRUIS) to map RNA-protein interactions in cells. This method uses deactivated Cas13a and proximity labeling to identify proteins binding specific RNAs.

Keywords:

CRISPR CRUIS PUP-IT Proximity-based protein labeling RNA-binding protein

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Last Updated: Nov 1, 2025

An Assay for Quantifying Protein-RNA Binding in Bacteria

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Published on: June 12, 2019

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

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Published on: December 2, 2009

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Identifying RNA-protein interactions is crucial for understanding gene regulation.
Existing methods often have limitations in capturing transient or low-abundance interactions in vivo.

Purpose of the Study:

To introduce a novel proximity-based method, CRISPR-based RNA-United Interacting System (CRUIS), for capturing RNA-protein interactions in living cells.
To provide a general procedure for utilizing CRUIS for interaction mapping.

Main Methods:

CRUIS combines the RNA-binding specificity of CRISPR/Cas13 with the proximity-tagging system PUP-IT.
Enzymatically deactivated Cas13a (dCas13a) is fused to the proximity labeling enzyme PafA.
Guide RNA directs dCas13a to target RNA, enabling PafA to label proximal proteins with biotinylated Pup.

Main Results:

Proximal proteins are labeled with biotin-tagged Pup upon target RNA binding by dCas13a.
Labeled proteins can be enriched using streptavidin pull-down.
Enriched proteins are identified via mass spectrometry.

Conclusions:

CRUIS offers a powerful tool for unbiased identification of RNA-binding proteins in their native cellular context.
This method facilitates the study of RNA-protein interactions, advancing our understanding of cellular processes.