PXD046839

PXD046839 is an original dataset announced via ProteomeXchange.

Title	Optimization of an RNA-centric approach searching for RNA-interacting proteins in Arabidopsis thaliana
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-05-22
AnnouncementXML	Submission_2024-05-22_02:04:56.374.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Katerina Hanakova
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-10 02:04:54	ID requested
⏵ 1	2024-05-22 02:04:57	announced

Bozd, ě, chov, á L, Rudolfov, á A, Han, á, kov, á K, Fojtov, á M, Fajkus J, : A Telomerase RNA Case Study. Plants (Basel), 13(6):(2024) [pubmed]

10.3390/plants13060850;

submitter keyword: Arabidopsis thaliana, telomerase, RNA, RNA-centric methods, RNA-protein interactions, ChIRP-MS, telomerase RNA, LC-MS/MS

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
Katerina Hanakova
contact affiliation	CEITEC MU
contact email	katerina.hanak@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD046839

PRIDE project URI

• PRIDE
  1. PXD046839
     1. Label: PRIDE project
     2. Name: Optimization of an RNA-centric approach searching for RNA-interacting proteins in Arabidopsis thaliana