PXD008914-1

PXD008914 is an original dataset announced via ProteomeXchange.

Title	RNA-binding protein repertoire of embryonic stem cells
Description	RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.
HostingRepository	PRIDE
AnnounceDate	2018-08-29
AnnouncementXML	Submission_2018-08-29_06:55:15.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sophia Foehr
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-09 05:46:58	ID requested
⏵ 1	2018-08-29 06:55:16	announced
2	2024-10-22 04:42:57	announced	2024-10-22: Updated project metadata.

Kwon SC, Yi H, Eichelbaum K, F, ö, hr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, Kim VN, The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol, 20(9):1122-30(2013) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: mouse, mECS, LC-MS, RNA-binding

Prof. Dr. Krijgsveld
contact affiliation	German Cancer Research Center
contact email	j.krijgsveld@dkfz.de
lab head
Sophia Foehr
contact affiliation	DKFZ
contact email	sophia.foehr@dkfz.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/2018/08/PXD008914

PRIDE project URI

• PRIDE
  1. PXD008914
     1. Label: PRIDE project
     2. Name: RNA-binding protein repertoire of embryonic stem cells