Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

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

doi:10.15252/embr.201540974

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

EMBO Rep. 2015 Oct;16(10):1334-57. doi: 10.15252/embr.201540974. Epub 2015 Aug 11.

Authors

Paul A Cassar¹, Richard L Carpenedo², Payman Samavarchi-Tehrani³, Jonathan B Olsen⁴, Chang Jun Park⁵, Wing Y Chang², Zhaoyi Chen⁶, Chandarong Choey², Sean Delaney⁶, Huishan Guo⁷, Hongbo Guo⁸, R Matthew Tanner⁶, Theodore J Perkins⁹, Scott A Tenenbaum¹⁰, Andrew Emili¹¹, Jeffrey L Wrana¹², Derrick Gibbings⁷, William L Stanford¹³

Affiliations

¹ Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada.
² Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
³ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁴ Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁵ Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
⁶ Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
⁷ Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
⁸ Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada.
⁹ Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
¹⁰ Colleges of Nanoscale Science & Engineering SUNY Polytechnic Institute, Albany, NY, USA.
¹¹ Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada.
¹² Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
¹³ Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada wstanford@ohri.ca.

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.

Keywords: RNA metabolism; embryonic stem cells; makorin‐1; stress granules.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cytoplasm / metabolism
Embryonic Stem Cells / physiology*
Gene Regulatory Networks / genetics*
Genomics
Mice
Nerve Tissue Proteins / chemistry
Nerve Tissue Proteins / genetics*
Proteomics
RNA / metabolism
RNA-Binding Proteins / metabolism
Ribonucleoproteins / chemistry
Ribonucleoproteins / genetics*
Ubiquitin-Protein Ligases / metabolism

Substances

Makorin ring finger protein 1
Nerve Tissue Proteins
RNA-Binding Proteins
Ribonucleoproteins
RNA
Ubiquitin-Protein Ligases

Associated data

GEO/GSE59394

Grants and funding

Canadian Institutes of Health Research/Canada