PXD053175 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | In vivo RNA Affinity Purification of wildtype and nonstop mutant VHL tumor suppressor mRNA |
Description | Nonstop extension or stop-loss mutations in the von Hippel Lindau (VHL) tumor suppressor gene are recurrently found in kidney cancer patients as observed from the NonStopDB database. We observed that presence of this nonstop extension mutation caused loss of the protein via the ubiquitin-proteasome pathway. Stabilization of the nonstop extended VHL with proteasome inhibitor Bortezomib revealed that the mutant protein was preferentially translated from an upstream alternative start site compared to the wild-type. The objective of this study was to identify proteins bound to the VHL mRNA that could be responsible for the differential start site selection. For this, we employed the in vivo RNA-affinity purification method to pull down wild-type and nonstop mutant VHL mRNAs along with their bound proteins after cross-linking using UV irradiation and pull-down with raPOOLs, which are a pool of biotinylated DNA oligonucleotides reverse complementary to the VHL mRNA. The RNA-protein complexes were then pulled down by streptavidin beads, the bound proteins were isolated and subjected to mass-spectrometry based identification. |
HostingRepository | PRIDE |
AnnounceDate | 2025-05-07 |
AnnouncementXML | Submission_2025-05-06_19:43:37.761.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Sven Diederichs |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | iodoacetamide derivatized residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-06-17 08:48:43 | ID requested | |
⏵ 1 | 2025-05-06 19:43:38 | announced | |
Publication List
Pal J, Riester M, Ganner A, Ghosh A, Dhamija S, Mookherjee D, Voss C, Frew IJ, Kotsis F, Neumann-Haefelin E, Spang A, Diederichs S, and affect multiple stages of protein translation. Sci Adv, 11(7):eadr6375(2025) [pubmed] |
10.1126/sciadv.adr6375; |
Keyword List
submitter keyword: RNA affinity purification, nonstop extension mutation, von Hippel Lindau, VHL,Nonstop mutation, protein isoform, start codon, translation initiation, stop-loss, RAP |
Contact List
Sven Diederichs |
contact affiliation | Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, Germany |
contact email | s.diederichs@dkfz.de |
lab head | |
Sven Diederichs |
contact affiliation | Division of Cancer Research, Dept. of Thoracic Surgery, University Medical Center Freiburg |
contact email | s.diederichs@dkfz.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD053175
- Label: PRIDE project
- Name: In vivo RNA Affinity Purification of wildtype and nonstop mutant VHL tumor suppressor mRNA