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Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

Nature Cell Biology volume 15, pages 363–372 (2013)Cite this article

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An Erratum to this article was published on 02 May 2013

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Abstract

Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterized by distinctive transcription factor expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated transcription factor pairings, including previously unrecognized relationships between Gata2, Gfi1 and Gfi1b. Validation using transcriptional and transgenic assays confirmed direct regulatory interactions consistent with a regulatory triad in immature blood stem cells, where Gata2 may function to modulate cross-inhibition between Gfi1 and Gfi1b. Single-cell expression profiling therefore identifies network states and allows reconstruction of network hierarchies involved in controlling stem cell fate choices, and provides a blueprint for studying both normal development and human disease.

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Figure 1: Single-cell gene expression analysis of a core haematopoietic transcriptional regulatory network.
Figure 2: Haematopoietic transcription factors show heterogeneous expression in haematopoietic stem and progenitor cells.
Figure 3: Single-cell gene expression analysis reveals cell-type-specific regulatory states.
Figure 4: Single-cell expression analysis of haematopoietic transcription factors identifies previously unrecognized putative regulatory interactions between key transcription factors.
Figure 5: Direct repression of Gata2 by GFI1 through a distal enhancer element provides a mechanism for negatively correlated expression.
Figure 6: Direct activation of Gfi1b by GATA2 through distal enhancer elements.

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  • 02 April 2013

    In the version of this Article originally published, Fig. 6d was incorrect; the red label should have read GFI1. This has now been corrected in the HTML and PDF versions.

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Acknowledgements

We thank S. A. Clark for help with FACS sorting. Research in the authors’ laboratory is supported by the Medical Research Council, Leukaemia and Lymphoma Research, The Leukaemia and Lymphoma Society, Cancer Research UK, and core support grants by the Wellcome Trust to the Cambridge Institute for Medical Research and Wellcome Trust–MRC Cambridge Stem Cell Institute.

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Authors and Affiliations

  1. Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK

    Victoria Moignard, Judith Schütte, Fernando J. Calero-Nieto, Sarah Kinston, Anagha Joshi, Rebecca Hannah & Berthold Göttgens

  2. Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK

    Iain C. Macaulay & Sten Eirik Jacobsen

  3. MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK

    Gemma Swiers & Marella F. de Bruijn

  4. Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Ingolstadter Landstraße 1, 85764 Neuherberg, Germany

    Florian Buettner & Fabian J. Theis

  5. Department of Mathematics, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany

    Fabian J. Theis

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  1. Victoria Moignard
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Contributions

V.M. designed and performed single-cell experiments, performed analysis and wrote the paper. B.G. conceived the study, designed experiments and wrote the paper. I.C.M. and S.E.J. designed and performed FACS and wrote the paper. F.B. and F.T. analysed GPLVM data and wrote the paper. S.K. and J.S. performed transgenic and luciferase analysis. A.J. and R.H. performed bioinformatic analysis. F.J.C-N. performed ChIP-seq experiments. G.S. and M.F.d.B. designed experiments and performed preliminary studies.

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Correspondence to Berthold Göttgens.

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Moignard, V., Macaulay, I., Swiers, G. et al. Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nat Cell Biol 15, 363–372 (2013). https://doi.org/10.1038/ncb2709

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