PXD060209 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Ribosome biogenesis mediates the translational increase of non-optimal codon transcripts during IFN stimulation |
| Description | The interferon response is a signaling pathway unique to vertebrates that links the innate and adaptive immune responses. Interferons signal through a cascade of factors including the JAK-STAT pathway to induce the transcription of hundreds of interferon stimulated genes (ISGs). Although the main interferon signal transduction pathways and ISGs have been elucidated, translational regulation of ISG transcripts has not been fully investigated. Prior work demonstrated that ribosomal protein RPL28 negatively regulates a subset of ISGs; however, we find that this effect may be due to a reduction in overall ribosome availability. Multi-omics analysis of RNA-seq and LC-MS/MS data reveal proteins that are translationally up-regulated in IFN-β-stimulated cells depleted of ribosome biogeneis factor BOP1, including an enrichment of ISGs. Analysis of codon usage demonstrates a significant reduction in codon optimality for proteins that are translationally up-regulated during BOP1 knockdown and IFN-β stimulation. Using reporter constructs, we demonstrate that codon non-optimal reporters are translated more that codon-optimized reporters in BOP1-depleted IFN-β cells. We propose that ribosome biogenesis regulates translational fine-tuning of integral protein production to ensure optimal interferon responses. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-05-01 |
| AnnouncementXML | Submission_2026-04-30_23:55:25.239.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Brenna Hay |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Bruker Daltonics timsTOF series; impact II |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-01-25 18:11:38 | ID requested | |
| ⏵ 1 | 2026-04-30 23:55:25 | announced | |
Publication List
| Dataset with its publication pending |
Keyword List
Contact List
| Leonard J |
|---|
| contact affiliation | Department of Biochemistry and Molecular Biology; Michael Smith Laboratories; University of British Columbia |
| contact email | foster@msl.ubc.ca |
| lab head | |
| Brenna Hay |
|---|
| contact affiliation | UBC |
| contact email | b_hay@live.ca |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD060209
- Label: PRIDE project
- Name: Ribosome biogenesis mediates the translational increase of non-optimal codon transcripts during IFN stimulation
