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

BOZDĚCHOVÁ, Lucie, Anna RUDOLFOVÁ, Kateřina HANÁKOVÁ, Miloslava FOJTOVÁ and Jiří FAJKUS. Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study. Plants. MDPI, 2024, vol. 13, No 6, p. 1-12. ISSN 2223-7747. Available from: https://dx.doi.org/10.3390/plants13060850.

Basic information

• Original name: Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in Arabidopsis thaliana: A Telomerase RNA Case Study
• Authors: BOZDĚCHOVÁ, Lucie (203 Czech Republic, belonging to the institution), Anna RUDOLFOVÁ (203 Czech Republic, belonging to the institution), Kateřina HANÁKOVÁ (203 Czech Republic, belonging to the institution), Miloslava FOJTOVÁ (203 Czech Republic, belonging to the institution) and Jiří FAJKUS (203 Czech Republic, guarantor, belonging to the institution).
• Edition: Plants, MDPI, 2024, 2223-7747.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: Switzerland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 4.500 in 2022
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.3390/plants13060850
• UT WoS: 001193531900001
• Keywords in English: Arabidopsis thaliana; ChIRP-MS; RNA; RNA-centric methods; RNA-protein interactions; telomerase; telomerase RNA
• Tags: International impact, Reviewed

Abstract

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.

Links

• EF18_046/0015974, research and development project: Name: Modernizace České infrastruktury pro integrativní strukturní biologii
• EH22_008/0004581, research and development project: Name: Nové poznatky pro plodiny nové generace
• GX20-01331X, research and development project: Name: Biogeneze a evoluce telomerázy u rostlin

Investor: Czech Science Foundation

• LM2023042, research and development project: Name: Česká infrastruktura pro integrativní strukturní biologii

Investor: Ministry of Education, Youth and Sports of the CR, CIISB - Czech Infrastructure for Integrative Structural Biology

• MUNI/C/0039/2022, interní kód MU: Name: Studium komponent rostlinné telomerázy (Acronym: sense)

Investor: Masaryk University, Excellent diploma thesis

• 90254, large research infrastructures: Name: e-INFRA CZ II