Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in IArabidopsis thaliana/I: A Telomerase RNA Case Study

The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, wit...

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Bibliographic Details
Published in:Plants (Basel) 2024-03, Vol.13 (6)
Main Authors: Bozděchová, Lucie, Rudolfová, Anna, Hanáková, Kateřina, Fojtová, Miloslava, Fajkus, Jiří
Format: Article
Language:English
Subjects:
Arabidopsis thaliana
Binding proteins
Botanical research
Genetic aspects
Identification and classification
Mass spectrometry
Protein-protein interactions
RNA
Telomerase
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Summary:The current repertoire of methods available for studying RNA-protein interactions in plants is somewhat limited. Employing an RNA-centric approach, particularly with less abundant RNAs, presents various challenges. Many of the existing methods were initially designed for different model systems, with their application in plants receiving limited attention thus far. The Comprehensive Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) technique, initially developed for mammalian cells, has been adapted in this study for application in Arabidopsis thaliana. The procedures have been meticulously modified and optimized for telomerase RNA, a notable example of a low-abundance RNA recently identified. Following these optimization steps, ChIRP-MS can serve as an effective screening method for identifying candidate proteins interacting with any target RNA of interest.
ISSN:2223-7747
2223-7747
DOI:10.3390/plants13060850