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Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona

Author

Listed:
  • Lenny J. Negrón-Piñeiro

    (New York University College of Dentistry)

  • Yushi Wu

    (New York University College of Dentistry)

  • Sydney Popsuj

    (Georgia Institute of Technology)

  • Diana S. José-Edwards

    (Washington University)

  • Alberto Stolfi

    (Georgia Institute of Technology)

  • Anna Di Gregorio

    (New York University College of Dentistry)

Abstract

Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.

Suggested Citation

  • Lenny J. Negrón-Piñeiro & Yushi Wu & Sydney Popsuj & Diana S. José-Edwards & Alberto Stolfi & Anna Di Gregorio, 2024. "Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46850-3
    DOI: 10.1038/s41467-024-46850-3
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    References listed on IDEAS

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    2. Alexander M. Tsankov & Hongcang Gu & Veronika Akopian & Michael J. Ziller & Julie Donaghey & Ido Amit & Andreas Gnirke & Alexander Meissner, 2015. "Transcription factor binding dynamics during human ES cell differentiation," Nature, Nature, vol. 518(7539), pages 344-349, February.
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