Integrative genomics positions MKRN 1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

• DOI: 10.15252/embr.201540974
• Publication Date: 2015-08-12T00:59:47Z
• Authors: Paul A Cassar; Richard L Carpenedo; Payman Samavarchi...; 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
• Keywords: Proteomics; 0301 basic medicine; Cytoplasm; Ubiquitin-Protein Ligases; RNA-Binding Proteins; Nerve Tissue Proteins; Articles; Genomics; Mice; 03 medical and health sciences; Ribonucleoproteins; Animals; RNA; Gene Regulatory Networks; Embryonic Stem Cells

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.