PXD063805-1

PXD063805 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	mouse spermatogonial stem cells LC-MS
Description	Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood. In this study, we employed RIC-seq (RNA in situ conformation sequencing) and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RNA-binding protein (RBP) that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation. Our findings provide novel mechanistic insights into the lncRNA-mRNA regulatory axis in SSC differentiation and establish a foundation for understanding the molecular etiology of male germ cell developmental disorders and spermatogenic dysfunction.
HostingRepository	PRIDE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-07_16:08:21.037.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Weijun Gao
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro 2

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-09 07:47:43	ID requested
⏵ 1	2026-06-07 16:08:21	announced

Publication List

10.1186/s13578-026-01599-8;
Gao W, Xu B, Ma W, He X, Wu J, lncRNA-operated stem cell fate control: RPS3 mediates the in situ Gm16751-Zhx3 interactome to program spermatogonial stem cell differentiation. Cell Biosci, 16(1):(2026) [pubmed]

10.1186/s13578-026-01599-8;

Gao W, Xu B, Ma W, He X, Wu J, lncRNA-operated stem cell fate control: RPS3 mediates the in situ Gm16751-Zhx3 interactome to program spermatogonial stem cell differentiation. Cell Biosci, 16(1):(2026) [pubmed]

Keyword List

submitter keyword: mouse,SSC,LC-MS

submitter keyword: mouse,SSC,LC-MS

Contact List

Ji Wu
contact affiliation	Ningxia Medical University
contact email	gwj20190228@163.com
lab head
Weijun Gao
contact affiliation	Ningxia Medical University
contact email	gwj20190228@163.com
dataset submitter

Full Dataset Link List

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/2026/06/PXD063805
PRIDE project URI

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/2026/06/PXD063805

PRIDE project URI

Repository Record List

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