PXD044722 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in transcriptomes of virus and host |
Description | RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists to identify the proteins bound to specific regions in endogenous RNAs in an unbiased fashion. Here, we develop SHIFTR (Selective RNase-H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected RNA regions in live cells. Compared to state-of-the-art RNA antisense purification techniques, SHIFTR is superior in accuracy, captures close to zero background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA biotypes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with multiplexed RNA interactome release in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5ʹ and 3ʹ-terminal regions of the authentic SARS-CoV-2 RNA genome in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type, which has the potential to revolutionize our understanding of the transcriptomes of pathogens and their hosts. |
HostingRepository | PRIDE |
AnnounceDate | 2024-01-18 |
AnnouncementXML | Submission_2024-01-18_03:20:03.146.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Frank Stein |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-08-22 01:45:00 | ID requested | |
⏵ 1 | 2024-01-18 03:20:03 | announced | |
Publication List
Keyword List
submitter keyword: interactomes,RNA-protein interactions, virus-host interactions, SARS-CoV-2, RNA-binding proteins |
Contact List
Mathias Munschauer |
contact affiliation | Helmholtz Center for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI) Uiniversity of Würzburg |
contact email | mathias.munschauer@helmholtz-hiri.de |
lab head | |
Frank Stein |
contact affiliation | EMBL |
contact email | frank.stein@embl.de |
dataset submitter | |
Full Dataset Link List
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/2024/01/PXD044722 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD044722
- Label: PRIDE project
- Name: SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in transcriptomes of virus and host