IBS Publications Repository: The RNA-binding protein repertoire of embryonic stem cells

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The RNA-binding protein repertoire of embryonic stem cells

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Author(s): S. Chul Kwon; Hyerim Yi; Eichelbaum, Katrin; Foehr, Sophia; Fischer, Bernd; Kwon Tae You; Castello, Alfredo; Krijgsveld, Jeroen; Hentze, Matthias W.; V. Narry Kim

Subject: esc protein, ; heterogeneous nuclear ribonucleoprotein, ; heterogeneous nuclear ribonucleoprotein A, ; heterogeneous nuclear ribonucleoprotein C, ; messenger RNA, ; Myc protein, ; oligonucleotide protein, ; RNA binding protein, ; trim25 protein, ; trim71 protein, ; ubiquitin protein ligase E3, ; unclassified drug, ; animal cell, ; article, ; binding affinity, ; cell differentiation, ; cell function, ; controlled study, ; embryonic stem cell, ; gene interaction, ; human, ; human cell, ; in vitro study, ; mass spectrometry, ; mouse, ; mRNA interactome, ; nonhuman, ; priority journal, ; protein cross linking, ; protein expression, ; protein isolation, ; protein modification, ; RNA binding, ; ultraviolet radiation, ; Animals, ; Cells, Cultured, ; DNA-Binding Proteins, ; Embryonic Stem Cells, ; Gene Regulatory Networks, ; Humans, ; Induced Pluripotent Stem Cells, ; Mice, ; Proto-Oncogene Proteins c-myc, ; RNA, Messenger, ; RNA-Binding Proteins, ; Species Specificity, ; Transcription Factors, ; Ubiquitination

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. © 2013 Nature America, Inc. All rights reserved.