PXD037523
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 |
Keyword List
| 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 |
| 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/ |
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