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PXD055082

PXD055082 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitlemRNA psi profiling using nanopore DRS reveals cell type-specific pseudouridylation
DescriptionPseudouridine (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.
HostingRepositoryMassIVE
AnnounceDate2024-08-22
AnnouncementXMLSubmission_2024-08-22_09:27:28.028.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSara Rouhanifard
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-08-22 09:22:54ID requested
12024-08-22 09:27:28announced
Publication List
no publication
Keyword List
submitter keyword: Proteomics , RNA Modifications, Pseudouridine
Contact List
Sara Rouhanifard
contact affiliationNortheastern University
contact emails.rouhanifard@northeastern.edu
lab head
Sara Rouhanifard
contact affiliationNortheastern University
contact emails.rouhanidard@northeastern.edu
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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