Proteomics

Dataset Information

0

RNA-binding protein repertoire of embryonic stem cells


ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Embryonic Stem Cell

SUBMITTER: Sophia Foehr  

LAB HEAD: Prof. Dr. Krijgsveld

PROVIDER: PXD008914 | Pride | 2018-08-29

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
111201_KS_A8_5_5_1.raw Raw
111201_KS_A8_5_5_5.raw Raw
111201_KS_A8_7_5_1.raw Raw
111201_KS_A8_7_5_5.raw Raw
111229_KS_A8_5_8_1.raw Raw
Items per page:
1 - 5 of 43
altmetric image

Publications

The RNA-binding protein repertoire of embryonic stem cells.

Kwon S Chul SC   Yi Hyerim H   Eichelbaum Katrin K   Föhr Sophia S   Fischer Bernd B   You Kwon Tae KT   Castello Alfredo A   Krijgsveld Jeroen J   Hentze Matthias W MW   Kim V Narry VN  

Nature structural & molecular biology 20130804 9


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 annotat  ...[more]

Similar Datasets

2015-09-24 | E-GEOD-73369 | biostudies-arrayexpress
2021-09-01 | E-MTAB-9612 | biostudies-arrayexpress
2015-03-01 | E-GEOD-65089 | biostudies-arrayexpress
2008-06-15 | E-GEOD-7506 | biostudies-arrayexpress
2012-11-17 | E-GEOD-33781 | biostudies-arrayexpress
2010-02-22 | E-GEOD-16364 | biostudies-arrayexpress
2013-11-06 | E-GEOD-49309 | biostudies-arrayexpress
2010-02-05 | E-GEOD-16526 | biostudies-arrayexpress
2013-04-17 | E-GEOD-37338 | biostudies-arrayexpress
2023-01-10 | PXD030497 | Pride