Proteomics

Dataset Information

40

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  

TISSUE(S): Cell Culture

DISEASE(S): Not Available

SUBMITTER: Sophia Foehr  

LAB HEAD: Prof. Dr. Krijgsveld

PROVIDER: PXD008914 | Pride | 2018-08-29

REPOSITORIES: Pride

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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]

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