Evidence map›Paper›PMID 26265008›Full record

ArticleEMBO reports2015

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 and 8 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in EMBO reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
1.2field-weighted citation impact, top 21% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed, 32 citations in OpenAlex.

  1. Article
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  3. A ubiquitin language communicates ribosomal distress.Seminars in cell & developmental biology · 2024
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 5 institutions in 2 countries.

Paul A CassarInstitute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada.
Richard L CarpenedoSprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Payman Samavarchi-TehraniDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Jonathan B OlsenCollaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Chang Jun ParkInstitute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada.
Wing Y ChangSprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Zhaoyi ChenSprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
Chandarong ChoeySprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada.
Sean DelaneySprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
Huishan GuoDepartment of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
Hongbo GuoBanting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada.
R Matthew TannerSprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
Theodore J PerkinsSprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
Scott A TenenbaumColleges of Nanoscale Science & Engineering SUNY Polytechnic Institute, Albany, NY, USA.
Andrew EmiliCollaborative 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.
Jeffrey L WranaCollaborative 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.
Derrick GibbingsDepartment of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada.
William L StanfordInstitute 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.
University of Toronto · CAOttawa Hospital Research InstituteUniversity of Ottawa · CAOttawa Hospital · CASUNY Polytechnic Institute · US

Funding

Canadian Institutes of Health Research
6 · The paper itself

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.

Indexed as

AnimalsCytoplasmEmbryonic Stem CellsGene Regulatory NetworksGenomicsMiceNerve Tissue ProteinsProteomicsRibonucleoproteinsRNARNA-Binding ProteinsUbiquitin-Protein LigasesMakorin ring finger protein 1Nerve Tissue ProteinsRibonucleoproteinsRNARNA-Binding ProteinsUbiquitin-Protein Ligasesembryonic stem cellsmakorin‐1RNA metabolismstress granules

Identifiers

PMID26265008
PMCPMC4670460
OpenAlexW2132508093

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.