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Updated: Oct 26, 2025

Monitoring Protein-RNA Interaction Dynamics In Vivo at High Temporal Resolution Using χCRAC
Published on: May 9, 2020
Visualization and characterization of RNA-protein interactions in living cells
Ningjun Duan1,2, Maria Arroyo3, Wen Deng1,4
1Department of Biology II, Ludwig Maximilians University Munich, Munich 81377, Germany.
Abstract:
RNA-protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA-protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA-protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA-protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA-protein interactions in living cells.
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