PXD039249

PXD039249 is an original dataset announced via ProteomeXchange.

Title	Temporal Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins during Osteogenic Differentiation of Human Embryonic Stem Cells
Description	Osteogenesis is the process of bone formation and is modulated by multiple regulatory networks. With the rapid development of the epitranscriptomics field, RNA modifications and their reader, writer, and eraser (RWE) proteins are shown to be involved in the regulation of various biological processes. Few studies, however, were conducted to investigate the functions of RNA modifications and their RWE proteins in osteogenesis. By using a parallel-reaction monitoring (PRM)-based targeted proteomics method, we performed a comprehensive quantitative assessment of 154 epitranscriptomic RWE proteins during the time course of osteogenic differentiation of H9 human embryonic stem cells (ESCs). We found that approximately half of the 126 detected RWE proteins were downregulated during osteogenic differentiation, and they included mainly those proteins involved in RNA methylation and pseudouridine synthesis. Protein-protein interaction (PPI) network analysis revealed a high connectivity between the downregulated epitranscriptomic RWE proteins and osteogenesis-related proteins. Gene set enrichment analysis of previously published RNA-seq data from osteogenesis imperfecta patients suggested a potential role of METTL1, the top-ranked hub protein of downregulated RWE proteins, in osteogenesis through the cytokine network. Together, this is the first targeted profiling of epitranscriptomic RWE proteins during osteogenic differentiation of human ESCs and our work unveiled potential regulatory roles of these proteins in osteogenesis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:45:51.911.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jiekai Yin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-01-04 04:05:18	ID requested
1	2023-05-23 11:54:01	announced
⏵ 2	2024-10-22 05:45:52	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Epitranscriptomic Reader, Writer and Eraser, Osteogenesis

Yinsheng Wang
contact affiliation	Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, United States
contact email	Yinsheng.Wang@ucr.edu
lab head
Jiekai Yin
contact affiliation	University of California, Riverside
contact email	jyin026@ucr.edu
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/PXD039249

PRIDE project URI

• PRIDE
  1. PXD039249
     1. Label: PRIDE project
     2. Name: Temporal Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins during Osteogenic Differentiation of Human Embryonic Stem Cells