PXD060209

PXD060209 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-25 18:11:38	ID requested
⏵ 1	2026-04-30 23:55:25	announced

Dataset with its publication pending

submitter keyword: None

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

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://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD060209

PRIDE project URI

• PRIDE
  1. PXD060209
     1. Label: PRIDE project
     2. Name: Ribosome biogenesis mediates the translational increase of non-optimal codon transcripts during IFN stimulation