Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network |
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| Authors: | Paul A Cassar Richard L Carpenedo Payman Samavarchi‐Tehrani Jonathan B Olsen Chang Jun Park Wing Y Chang Zhaoyi Chen Chandarong Choey Sean Delaney Huishan Guo Hongbo Guo R Matthew Tanner Theodore J Perkins Scott A Tenenbaum Andrew Emili Jeffrey L Wrana Derrick Gibbings William L Stanford |
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| Institution: | 1. Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada;2. Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada;3. Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada;4. Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada;5. Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada;6. Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada;7. Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada;8. Colleges of Nanoscale Science & Engineering, SUNY Polytechnic Institute, Albany, NY, USA;9. Center for Systems Biology, Lunenfeld‐Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada;10. Institute of Medical Science, University of Toronto, Toronto, ON, Canada;11. Ottawa Institute of Systems Biology, Ottawa, ON, Canada |
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| Abstract: | In embryonic stem cells (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors regulating the ESC state is not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 ubiquitin ligase protein Makorin‐1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems‐level analyses, we compiled a MKRN1‐centered interactome in undifferentiated ESCs at the proteomic and ribonomic level. Proteomic analyses in undifferentiated ESCs revealed that MKRN1 associates with RNA‐binding proteins, and ensuing RIP‐chip analysis determined that MKRN1 associates with mRNAs encoding functionally related proteins including proteins that function during cellular stress. Subsequent biological validation identified MKRN1 as a novel stress granule‐resident protein, although MKRN1 is not required for stress granule formation, or survival of unstressed ESCs. Thus, our unbiased systems‐level analyses support a role for the E3 ligase MKRN1 as a ribonucleoprotein within the ESC GRN. |
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| Keywords: | embryonic stem cells makorin‐ 1 RNA metabolism stress granules |
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