PXD013720

PXD013720 is an original dataset announced via ProteomeXchange.

Title	Identification of proteins and miRNAs that specifically bind an mRNA in vivo
Description	Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were so far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to a selected mRNA in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a novel and specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR provides a platform for investigating RNA in vivo regulation in diverse biological systems.
HostingRepository	PRIDE
AnnounceDate	2019-08-12
AnnouncementXML	Submission_2019-08-12_01:48:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kathrin Theil
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-05-06 07:27:32	ID requested
⏵ 1	2019-08-12 01:48:42	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Caenorhabditis elegans, RNA pulldown, Q Exactive plus, Q Exactive HF-X

Nikolaus Rajewsky
contact affiliation	Systems Biology of Gene Regulatory Elements Berlin Institute for Medical Systems Biology (BIMSB) Max Delbrück Center for Molecular Medicine in the Helmholtz Association Hannoversche Str. 28, 10115 Berlin, Germany
contact email	rajewsky@mdc-berlin.de
lab head
Kathrin Theil
contact affiliation	BIMSB/MDC
contact email	kathrin.theil@mdc-berlin.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/2019/08/PXD013720

PRIDE project URI

• PRIDE
  1. PXD013720
     1. Label: PRIDE project
     2. Name: Identification of proteins and miRNAs that specifically bind an mRNA in vivo