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Cis-regulatory architecture of a brain signaling center predates the origin of chordates

Nature Genetics volume 48, pages 575580 (2016) | Download Citation

  • An Erratum to this article was published on 27 July 2016

This article has been updated

Abstract

Genomic approaches have predicted hundreds of thousands of tissue-specific cis-regulatory sequences, but the determinants critical to their function and evolutionary history are mostly unknown1,2,3,4. Here we systematically decode a set of brain enhancers active in the zona limitans intrathalamica (zli), a signaling center essential for vertebrate forebrain development via the secreted morphogen Sonic hedgehog (Shh)5,6. We apply a de novo motif analysis tool to identify six position-independent sequence motifs together with their cognate transcription factors that are essential for zli enhancer activity and Shh expression in the mouse embryo. Using knowledge of this regulatory lexicon, we discover new Shh zli enhancers in mice and a functionally equivalent element in hemichordates, indicating an ancient origin of the Shh zli regulatory network that predates the chordate phylum. These findings support a strategy for delineating functionally conserved enhancers in the absence of overt sequence homologies and over extensive evolutionary distances.

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Change history

  • 16 May 2016

    In the version of this article initially published, the received date for the manuscript was incorrectly listed as 28 January 2015. The correct date is 28 January 2016. The error has been corrected in the HTML and PDF versions of the article.

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Acknowledgements

We thank J. Richa and his staff at the Transgenic and Chimeric Mouse Facility (Perelman School of Medicine, University of Pennsylvania) for assistance with transgenic mouse generation. We also thank S. Liebhaber, K. Kaestner, C. Brown, K. Zaret and members of the Epstein laboratory for helpful discussions and comments on the manuscript. This work was funded by grants from the National Institutes of Health, R01 NS039421 (D.J.E.) and R21 EY023104 (L.G.), and the National Science Foundation, 1258169 (C.J.L.), and by a predoctoral fellowship from the Louis-Jeantet Foundation (O.S.).

Author information

Author notes

    • Paul J Minor
    •  & Ying-Tao Zhao

    These authors contributed equally to this work.

Affiliations

  1. Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Yao Yao
    • , Ying-Tao Zhao
    • , Anna N King
    •  & Douglas J Epstein
  2. Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, USA.

    • Paul J Minor
    • , Ariel M Pani
    •  & Christopher J Lowe
  3. Department of Genetic Engineering, College of Life Sciences and Graduate School of Biotechnology, Kyung Hee University, Yongin-si, Republic of Korea.

    • Yongsu Jeong
  4. Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

    • Orsolya Symmons
    •  & François Spitz
  5. Department of Ophthalmology, University of Rochester Medical Center, Rochester, New York, USA.

    • Lin Gan
  6. Columbia Center for Human Development, Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Medical Center, New York, New York, USA.

    • Wellington V Cardoso

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Contributions

Y.Y. and D.J.E. conceived the project, designed the experiments and wrote the manuscript. Y.Y. performed the cotransfection, transgenic mouse, gene expression and ChIP assays. P.J.M. performed the transgenic hemichordate reporter assays. Y.J. performed the transgenic mouse reporter assays with core region constructs. Y.-T.Z. performed the statistical analysis. Y.Y. and A.N.K. performed the motif analysis. A.M.P. and C.J.L. provided reagents and advice on the hemichordate experiments. Y.Y., L.G., O.S., W.V.C. and F.S. generated mutant mouse lines and provided embryos.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Douglas J Epstein.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–10

Excel files

  1. 1.

    Supplementary Table 1

    This table lists the genomic positions of SBE1 and the 52 SBE1-like enhancers in the human (hg19) and mouse (mm9) genome.

  2. 2.

    Supplementary Table 2

    This table contains a list of the primers used in this study.

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DOI

https://doi.org/10.1038/ng.3542

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