title: The 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.
authors.affiliation: 1] Center for RNA Research, Institute for Basic Science (IBS), Seoul, Korea. [2] School of Biological Sciences, Seoul National University, Seoul, Korea.
authors.forename: S Chul
authors.initials: SC
authors.lastname: Kwon
authors.forename: Hyerim
authors.initials: H
authors.lastname: Yi
authors.forename: Katrin
authors.initials: K
authors.lastname: Eichelbaum
authors.forename: Sophia
authors.initials: S
authors.lastname: Föhr
authors.forename: Bernd
authors.initials: B
authors.lastname: Fischer
authors.forename: Kwon Tae
authors.initials: KT
authors.lastname: You
authors.forename: Alfredo
authors.initials: A
authors.lastname: Castello
authors.forename: Jeroen
authors.initials: J
authors.lastname: Krijgsveld
authors.forename: Matthias W
authors.initials: MW
authors.lastname: Hentze
authors.forename: V Narry
authors.initials: VN
authors.lastname: Kim
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D053263:Gene Regulatory Networks; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D051379:Mice; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D004268:DNA-Binding Proteins; C511366:LIN-41 protein, mouse; C489428:Myc protein, mouse; D016271:Proto-Oncogene Proteins c-myc; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C490034:Trim25 protein, mouse
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