MassIVE MSV000095673

Partial Public PXD055082

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. [doi:10.25345/C50G3H92P] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Proteomics ; RNA Modifications ; Pseudouridine

Contact

Principal Investigators:
(in alphabetical order)
Sara Rouhanifard, Northeastern University, United States of America
Submitting User: RouhanifardLab
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