PXD055082-1
PXD055082 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | mRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation |
| Description | Pseudouridine (psi) is one of the most abundant human mRNA modifications generated via psi synthases, including TRUB1 and PUS7. Nanopore direct RNA sequencing combined with our recent tool, Mod-p ID, enables psi mapping, transcriptome-wide, without chemical derivatization of the input RNA and/or conversion to cDNA. This method is sensitive for detecting changes in positional psi occupancies across cell types, which can inform our understanding of the impact on gene expression. We sequenced, mapped, and compared the positional psi occupancy across six immortalized human cell lines derived from diverse tissue types. We found that lung-derived cells have the highest proportion of psi, while liver-derived cells have the lowest. Further, we find that conserved psi positions correspond to higher levels of protein expression than expected, suggesting translation regulation. Interestingly, we identify cell type-specific sites of psi modification in ubiquitously expressed genes. Finally, we characterize sites with multiple psi modifications on the same transcript and found that these can be conserved or cell type specific, including examples of multiple psi modifications within the same k-mer. Our data support the hypothesis that psi modifications contribute to regulating translation and that cell type-specific trans-acting factors play a major role in driving pseudouridylation. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-08-22 |
| AnnouncementXML | Submission_2024-08-22_09:27:28.028.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Sara Rouhanifard |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-08-22 09:22:54 | ID requested | |
| ⏵ 1 | 2024-08-22 09:27:28 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Proteomics , RNA Modifications, Pseudouridine |
Contact List
| Sara Rouhanifard | |
|---|---|
| contact affiliation | Northeastern University |
| contact email | s.rouhanifard@northeastern.edu |
| lab head | |
| Sara Rouhanifard | |
| contact affiliation | Northeastern University |
| contact email | s.rouhanidard@northeastern.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset 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://massive.ucsd.edu/v08/MSV000095673/ |
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