Proteomics

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Optimization of an RNA-centric approach searching for RNA-interacting proteins in Arabidopsis thaliana

ABSTRACT: The number of methods used to study RNA-protein interactions in plants is currently relatively limited. The RNA-centric approach, starting with RNA of interest, brings several difficulties, especially when the RNA belongs to the less abundant RNAs. These methods for identification of RNA-interacting proteins used to be developed for different model systems, however, their application in plants is delayed. The Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) method was originally developed for mammalian cells. This work describes the modified ChIRP-MS procedure applicable in Arabidopsis thaliana. All steps were optimized for the telomerase RNA which was recently described as a low-abundant RNA. Following this optimization procedure, it is possible to use ChIRP-MS as a screening method for the identification of candidate proteins interacting with the target RNA.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Whole Body

SUBMITTER: Katerina Hanakova  

LAB HEAD: Zbynek Zdrahal

PROVIDER: PXD046839 | Pride | 2024-05-22

REPOSITORIES: Pride

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Dataset's files

Source:
Action DRS
221215_main_search_5269.log.txt Txt
221215_main_search_5269.tsv Tabular
400_850_20W_overlap.txt Txt
5080_Lumos1_DIA_74min-400_850_20W_FASP_WT1_antisense_01.raw Raw
5080_Lumos1_DIA_74min-400_850_20W_FASP_attr_antisense_01.raw Raw
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Publications

Optimizing ChIRP-MS for Comprehensive Profiling of RNA-Protein Interactions in <i>Arabidopsis thaliana</i>: A Telomerase RNA Case Study.

Bozděchová Lucie L   Rudolfová Anna A   Hanáková Kateřina K   Fojtová Miloslava M   Fajkus Jiří J  

Plants (Basel, Switzerland) 20240315 6

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 mammalia  ...[more]