PXD044722

PXD044722 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-22 01:45:00	ID requested
⏵ 1	2024-01-18 03:20:03	announced

10.1093/NAR/GKAE038;

submitter keyword: interactomes,RNA-protein interactions, virus-host interactions, SARS-CoV-2, RNA-binding proteins

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

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

• PRIDE
  1. PXD044722
     1. Label: PRIDE project
     2. Name: SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in transcriptomes of virus and host