PXD037523-1

PXD037523 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution
Description	The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.
HostingRepository	MassIVE
AnnounceDate	2022-10-18
AnnouncementXML	Submission_2022-10-18_10:07:14.250.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Gogce Ceren Crynen
SpeciesList	scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562;
ModificationList	Oxidation; Deamidated
Instrument	Orbitrap Fusion Lumos

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-18 06:31:05	ID requested
⏵ 1	2022-10-18 10:07:14	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: RNA-protein interactions, TMT, CLIP, Hfq, RNA-Seq

submitter keyword: RNA-protein interactions, TMT, CLIP, Hfq, RNA-Seq

Contact List

Chaitanya Jain
contact affiliation	University of Miami
contact email	CJain@med.miami.edu
lab head
Gogce Ceren Crynen
contact affiliation	UF Scripps Biomedical Research
contact email	gogce@ufl.edu
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

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://massive.ucsd.edu/MSV000090547/