Studying RNA-Protein Interaction Using Riboproteomics.
Sonali Chaturvedi1, A L N Rao2
1Gladstone Institute of Virology and Immunology, Gladstone Institutes, San Francisco, CA, USA.
Methods in Molecular Biology (Clifton, N.J.)
|August 16, 2020
Summary
Researchers developed a riboproteomics protocol to identify host proteins interacting with RNA. This method uses a satellite RNA from Cucumber mosaic virus and is applicable to various organisms.
Area of Science:
- Molecular Biology
- Proteomics
- Bioinformatics
Background:
- Protein-protein interactions (PPI) regulate cellular functions.
- RNA-protein interactions are crucial for gene expression.
- Current methods for RNA-protein interaction characterization are limited.
Purpose of the Study:
- To develop a stepwise protocol for identifying host proteomes interacting with RNA.
- To characterize RNA-protein interactions using riboproteomics.
- To investigate the role of long noncoding RNAs (lnc-RNAs) in plant biology.
Main Methods:
- In vitro transcription of RNA.
- Preparation of RNA affinity column.
- Co-immunoprecipitation (Co-IP) and Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS).
Main Results:
- A detailed protocol for identifying RNA-interacting proteins was established.
- The protocol was validated using a plant pathogenic satellite RNA (Sat-RNA) from Cucumber mosaic virus (CMV).
- The method successfully identified host proteomes interacting with the Sat-RNA.
Conclusions:
- The described riboproteomics approach is a valuable tool for studying RNA-protein interactions.
- This protocol is applicable to a wide range of RNAs in eukaryotic and prokaryotic organisms.
- It facilitates the characterization of host proteomes interacting with specific RNAs, including lnc-RNAs.
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