Network plasticity of pluripotency transcription factors in embryonic stem cells

Adam Filipczyk; Carsten Marr; Simon Hastreiter; Justin Feigelman; Michael Schwarzfischer; Philipp S Hoppe; Dirk Loeffler; Konstantinos D Kokkaliaris; Max Endele; Bernhard Schauberger; Oliver Hilsenbeck; Stavroula Skylaki; Jan Hasenauer; Konstantinos Anastassiadis; Fabian J Theis; Timm Schroeder

doi:10.1038/ncb3237

Network plasticity of pluripotency transcription factors in embryonic stem cells

Nat Cell Biol. 2015 Oct;17(10):1235-46. doi: 10.1038/ncb3237. Epub 2015 Sep 21.

Authors

Adam Filipczyk¹, Carsten Marr², Simon Hastreiter^{1

3}, Justin Feigelman², Michael Schwarzfischer², Philipp S Hoppe^{1

3}, Dirk Loeffler^{1

3}, Konstantinos D Kokkaliaris^{1

3}, Max Endele^{1

3}, Bernhard Schauberger^{1

2}, Oliver Hilsenbeck^{1

2

3}, Stavroula Skylaki^{1

3}, Jan Hasenauer^{2

4}, Konstantinos Anastassiadis⁵, Fabian J Theis^{2

4}, Timm Schroeder^{1

3}

Affiliations

¹ Research Unit Stem Cell Dynamics, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
² Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
³ Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
⁴ Technische Universität München, Center for Mathematics, Chair of Mathematical Modelling of Biological Systems, Boltzmannstraße 3, 85748 Garching, Germany.
⁵ Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.

PMID: 26389663
DOI: 10.1038/ncb3237

Abstract

Transcription factor (TF) networks are thought to regulate embryonic stem cell (ESC) pluripotency. However, TF expression dynamics and regulatory mechanisms are poorly understood. We use reporter mouse ESC lines allowing non-invasive quantification of Nanog or Oct4 protein levels and continuous long-term single-cell tracking and quantification over many generations to reveal diverse TF protein expression dynamics. For cells with low Nanog expression, we identified two distinct colony types: one re-expressed Nanog in a mosaic pattern, and the other did not re-express Nanog over many generations. Although both expressed pluripotency markers, they exhibited differences in their TF protein correlation networks and differentiation propensities. Sister cell analysis revealed that differences in Nanog levels are not necessarily accompanied by differences in the expression of other pluripotency factors. Thus, regulatory interactions of pluripotency TFs are less stringently implemented in individual self-renewing ESCs than assumed at present.

MeSH terms

Animals
Bacterial Proteins / genetics
Bacterial Proteins / metabolism
Cell Differentiation / genetics
Cell Tracking / methods
Cells, Cultured
Embryonic Stem Cells / cytology
Embryonic Stem Cells / metabolism*
Gene Expression
Gene Regulatory Networks*
Green Fluorescent Proteins / genetics
Green Fluorescent Proteins / metabolism
Homeodomain Proteins / genetics
Homeodomain Proteins / metabolism
Luminescent Proteins / genetics
Luminescent Proteins / metabolism
Mice
Microscopy, Fluorescence
Nanog Homeobox Protein
Octamer Transcription Factor-3 / genetics
Octamer Transcription Factor-3 / metabolism
Pluripotent Stem Cells / cytology
Pluripotent Stem Cells / metabolism*
Recombinant Fusion Proteins / genetics
Recombinant Fusion Proteins / metabolism
Red Fluorescent Protein
Single-Cell Analysis / methods
Time-Lapse Imaging / methods
Transcription Factors / genetics*
Transcription Factors / metabolism
Transduction, Genetic

Substances

Bacterial Proteins
Homeodomain Proteins
Luminescent Proteins
Nanog Homeobox Protein
Nanog protein, mouse
Octamer Transcription Factor-3
Recombinant Fusion Proteins
Transcription Factors
yellow fluorescent protein, Bacteria
Green Fluorescent Proteins