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Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Nature Neuroscience volume 16, pages 12191227 (2013) | Download Citation

Abstract

Efficient transcriptional programming promises to open new frontiers in regenerative medicine. However, mechanisms by which programming factors transform cell fate are unknown, preventing more rational selection of factors to generate desirable cell types. Three transcription factors, Ngn2, Isl1 and Lhx3, were sufficient to program rapidly and efficiently spinal motor neuron identity when expressed in differentiating mouse embryonic stem cells. Replacement of Lhx3 by Phox2a led to specification of cranial, rather than spinal, motor neurons. Chromatin immunoprecipitation–sequencing analysis of Isl1, Lhx3 and Phox2a binding sites revealed that the two cell fates were programmed by the recruitment of Isl1-Lhx3 and Isl1-Phox2a complexes to distinct genomic locations characterized by a unique grammar of homeodomain binding motifs. Our findings suggest that synergistic interactions among transcription factors determine the specificity of their recruitment to cell type–specific binding sites and illustrate how a single transcription factor can be repurposed to program different cell types.

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Acknowledgements

We would like to thank I. Lieberam (King's College) for assistance introducing the Hb9-GFP transgene, members of the Wichterle laboratory for helpful comments, S. Brenner-Morton and T. Jessell (Columbia University) for sharing clones of Isl monoclonal antibodies, J.-F. Brunet for Phox2a and Phox2b antibodies, and I. Schieren for technical assistance with flow cytometry. E.O.M. receives funding from the Damon Runyon Cancer Research Foundation (DRG-1937-07). Personnel and work were supported by the Project ALS foundation and US National Institutes of Health grants P01 NS055923 (D.K.G. and H.W.) and R01 NS078097 (H.W.).

Author information

Author notes

    • Esteban O Mazzoni
    •  & Shaun Mahony

    These authors contributed equally to this work.

Affiliations

  1. Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University Medical Center, New York, New York, USA.

    • Esteban O Mazzoni
    • , Michael Closser
    • , Carolyn A Morrison
    • , Stephane Nedelec
    •  & Hynek Wichterle
  2. Department of Biology, New York University, New York, New York, USA.

    • Esteban O Mazzoni
    •  & Disi An
  3. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Shaun Mahony
    •  & David K Gifford
  4. Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, Pennsylvania State University, University Park, Pennsylvania, USA.

    • Shaun Mahony
  5. Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, New York, USA.

    • Damian J Williams

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Contributions

E.O.M., S.M., D.K.G. and H.W. conceived the experiments, analyzed the data and wrote the manuscript. E.O.M. generated and validated inducible cell lines and performed the majority of experiments. S.M. performed all of the computational and statistical analyses of genomic, expression and sequencing data. M.C. performed motor neuron quantifications, synapse analysis and co-immunoprecipitation experiments. C.A.M. assisted with ChIP-seq experiments. S.N. performed axon pathfinding analysis. D.J.W. performed electrophysiological recordings. D.A. assisted with the analysis of single gene inducible lines and motor neuron induction.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Esteban O Mazzoni or David K Gifford or Hynek Wichterle.

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DOI

https://doi.org/10.1038/nn.3467

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