PXD039249 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Epitranscriptomic Reader, Writer and Eraser, Osteogenesis |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD039249
- Label: PRIDE project
- Name: Temporal Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins during Osteogenic Differentiation of Human Embryonic Stem Cells