Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network.
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.
Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada.
Paul A
PA
Cassar
Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Richard L
RL
Carpenedo
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Payman
P
Samavarchi-Tehrani
Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Jonathan B
JB
Olsen
Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
Chang Jun
CJ
Park
Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Wing Y
WY
Chang
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.
Zhaoyi
Z
Chen
Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Chandarong
C
Choey
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.
Sean
S
Delaney
Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
Huishan
H
Guo
Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada.
Hongbo
H
Guo
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.
R Matthew
RM
Tanner
Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
Theodore J
TJ
Perkins
Colleges of Nanoscale Science & Engineering SUNY Polytechnic Institute, Albany, NY, USA.
Scott A
SA
Tenenbaum
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.
Andrew
A
Emili
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.
Jeffrey L
JL
Wrana
Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
Derrick
D
Gibbings
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.
William L
WL
Stanford
D000818:Animals; D003593:Cytoplasm / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000502:physiology*; D053263:Gene Regulatory Networks / Q000235:genetics*; D023281:Genomics; D051379:Mice; D009419:Nerve Tissue Proteins / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics; D012313:RNA / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D012261:Ribonucleoproteins / Q000737:chemistry / Q000235:genetics*; D044767:Ubiquitin-Protein Ligases / Q000378:metabolism
C410808:Makorin ring finger protein 1; D009419:Nerve Tissue Proteins; D016601:RNA-Binding Proteins; D012261:Ribonucleoproteins; D012313:RNA; D044767:Ubiquitin-Protein Ligases
RNA metabolism; embryonic stem cells; makorin‐1; stress granules