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.

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Figure 1: Identification of RBPs in mESCs.
Figure 2: Characteristics of the mESC mRNA interactome in comparison to known RBPs.
Figure 3: Validation of RNA-binding activity of novel RBP candidates.
Figure 4: Regulation of RBPs in stem cells.
Figure 5: Trim25 and Trim71 are RNA-binding E3 ubiquitin ligases.

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Acknowledgements

We thank H. Chang for teaching and sharing Python codes, A. Cho, Y.C. Chang and H. Kim for technical help, and all members of our laboratories for helpful discussion. We gratefully acknowledge the EMBL Proteomics Core Facility for technical support. We are grateful to G. Dreyfuss (University of Pennsylvania), F.G. Wulczyn (Charité–Universitätsmedizin Berlin), S.H. Baek (Seoul National University), H.-Y. Kao (Case Western Reserve University), D.-E. Zhang (The Scripps Research Institute), D. Rimm (Yale School of Medicine), K. Helin (Københavns Universitet) and Y. Kawakami (University of Minnesota) for valuable plasmids and antibodies. This work was supported by the Research Center Program (EM1202) of the Institute for Basic Science (S.C.K., H.Y., K.T.Y. and V.N.K.) and the BK21 Research Fellowships (S.C.K. and H.Y.) from the Ministry of Education, Science and Technology of Korea. Work in the group of M.W.H. was funded by an ERC Advanced grant (ERC-2011-ADG_20110310) to M.W.H.

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S.C.K., A.C., M.W.H. and V.N.K. designed the project; S.C.K., H.Y. and K.T.Y. performed biochemical experiments and analyzed ESC-related data; K.E., S.F. and J.K. performed and analyzed MS experiments; B.F., A.C. and M.W.H. analyzed the mRNA interactome; S.C.K. and V.N.K. wrote the manuscript.

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Correspondence to V Narry Kim.

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Kwon, S., Yi, H., Eichelbaum, K. et al. The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol 20, 1122–1130 (2013). https://doi.org/10.1038/nsmb.2638

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