PXD003593

PXD003593 is an original dataset announced via ProteomeXchange.

Title	Identification of Host factors that Interact with Dengue virus RNA in cell culture
Description	Host factors are essential for efficient amplification of Dengue virus (DENV), yet the current knowledge of these cellular proteins remains limited. Here, we used quantitative thiouridine cross-linking mass spectrometry (qTUX-MS) to cross-link proteins to viral RNA during a live DENV infection in cell culture. We identified 79 novel host proteins that have not been previously implicated in DENV infection, and demonstrated the reliability of qTUX-MS by validating a subset of these factors. Analysis of proteome changes revealed critical pathways up- and down-regulated during DENV infection, while the levels of qTUX-MS identified factors remained largely unchanged. Knockdown of HMCES, RBMX and hnRNP F reduced the levels of both intracellular viral RNA and DENV titers, suggesting roles in viral amplification prior to packaging and release. In contrast, knockdown of hnRNP M or NONO caused a dramatic drop in viral titers without impacting viral RNA accumulation, indicating a role downstream of DENV replication. Importantly, none of these five host factors were essential for cell viability or amplification of an unrelated virus, adenovirus, demonstrating that knockdown of these host factors did not reduce cell fitness for viral amplification. Thus, qTUX-MS can be used to identify host factor interactions for any RNA virus.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_01:16:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	T Greco
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-09 01:54:21	ID requested
1	2016-09-26 05:30:33	announced
⏵ 2	2017-10-24 01:16:05	announced	Updated project metadata.

Viktorovskaya OV, Greco TM, Cristea IM, Thompson SR, Identification of RNA Binding Proteins Associated with Dengue Virus RNA in Infected Cells Reveals Temporally Distinct Host Factor Requirements. PLoS Negl Trop Dis, 10(8):e0004921(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: DENV, RNA-protein interactions, UV crosslinking, human, SILAC

Ileana M Cristea
contact affiliation	Department of Molecular Biology, Princeton University, Princeton, NJ USA
contact email	icristea@princeton.edu
lab head
T Greco
contact affiliation	Molecular Biology
contact email	tgreco@princeton.edu
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/2016/09/PXD003593

PRIDE project URI

• PRIDE
  1. PXD003593
     1. Label: PRIDE project
     2. Name: Identification of Host factors that Interact with Dengue virus RNA in cell culture