PXD026752

PXD026752 is an original dataset announced via ProteomeXchange.

Title	MS analysis of GAR1 methylation immunopurified from HEK-293 Cells
Description	The conserved box H/ACA RNPs consist of one box H/ACA RNA and 4 core proteins: Dyskerin, NHP2, NOP10 and GAR1. The assembly of the H/ACA RNPs is a stepwise process which requires several assembly factors: SHQ1, NAF1, the Survival of Motor Neuron complex SMN, and the R2TP complex. It implicates the co-transcriptional assembly of a pre-particle containing the nascent RNAs, Dyskerin, NOP10, NHP2 and NAF1. The latest keeps the H/ACA RNP inactive, and needs to be replaced by GAR1 to produce mature and functional H/ACA RNPs in the Cajal bodies. In this study, we explore in details the molecular mechanism leading to the assembly of mature box H/ACA RNPs. We performed extensive analysis of GAR1, NHP21 and NAF interactomes by quantitative stable isotope labeling by amino acids in cell culture proteomic analyses (SILAC), and revealed new assembly intermediates: 1) an early protein-only pre-H/ACA RNP complex containing the core proteins DKC1, NOP10 and NHP2, and the assembly factors SHQ1 and NAF1, and 2) a late assembly intermediates containing the RNA, the core proteins and NAF1. We showed that the SMN complex is associated with late forming H/ACA pre-RNP complexes containing GAR1. Moreover, our study identifies new proteins highly and specifically associated with GAR1, NHP2 and NAF1, reflecting their importance in box H/ACA assembly or function, such as the PRMT1 and PRMT5 arginine methylases. MS analysis of purified GAR1 revealed new sites of arginine methylations in the two GAR domains of GAR1, and showed that most of these methylated arginines exist both in mono-methylated and di-methylated forms in cells. By different methods, we showed that unmethylated GAR1 is correctly incorporated in H/ACA RNPs. Therefore, GAR1 methylation should be important for its function.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:46:16.539.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Franck Vandermoere
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; dimethylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-06-16 09:36:22	ID requested
1	2023-05-10 13:11:26	announced
⏵ 2	2023-11-14 08:46:17	announced	2023-11-14: Updated project metadata.

Schlotter F, M, é, rouani S, Flayac J, Kogey V, Issa A, Dodr, é M, Huttin A, Branlant C, Bertrand E, Labialle S, Vandermoere F, Verheggen C, Massenet S, Proteomic analyses reveal new features of the box H/ACA RNP biogenesis. Nucleic Acids Res, 51(7):3357-3374(2023) [pubmed]

submitter keyword: methylation,APMS

Severine Massenet
contact affiliation	UMR 7367 CNRS-UL IMoPA Biopôle de l'Université de Lorraine Campus Brabois-Santé 9 avenue de la forêt de Haye 54505 Vandoeuvre-les-Nancy FRANCE
contact email	severine.massenet@univ-lorraine.fr
lab head
Franck Vandermoere
contact affiliation	IGF, CNRS, INSERM, University of Montpellier, Montpellier, France
contact email	franck.vandermoere@igf.cnrs.fr
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/2023/05/PXD026752

PRIDE project URI

• PRIDE
  1. PXD026752
     1. Label: PRIDE project
     2. Name: MS analysis of GAR1 methylation immunopurified from HEK-293 Cells