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Dynamic enhancer landscapes in human craniofacial development

Author

Listed:
  • Sudha Sunil Rajderkar

    (Lawrence Berkeley National Laboratory)

  • Kitt Paraiso

    (Lawrence Berkeley National Laboratory)

  • Maria Luisa Amaral

    (University of California San Diego)

  • Michael Kosicki

    (Lawrence Berkeley National Laboratory)

  • Laura E. Cook

    (Lawrence Berkeley National Laboratory)

  • Fabrice Darbellay

    (Lawrence Berkeley National Laboratory
    University of Geneva)

  • Cailyn H. Spurrell

    (Lawrence Berkeley National Laboratory)

  • Marco Osterwalder

    (Lawrence Berkeley National Laboratory
    University of Bern
    Bern University Hospital)

  • Yiwen Zhu

    (Lawrence Berkeley National Laboratory)

  • Han Wu

    (Lawrence Berkeley National Laboratory)

  • Sarah Yasmeen Afzal

    (Lawrence Berkeley National Laboratory
    Stanford University)

  • Matthew J. Blow

    (U.S. Department of Energy Joint Genome Institute)

  • Guy Kelman

    (Lawrence Berkeley National Laboratory
    Hebrew University of Jerusalem)

  • Iros Barozzi

    (Lawrence Berkeley National Laboratory
    Medical University of Vienna
    Imperial College London)

  • Yoko Fukuda-Yuzawa

    (Lawrence Berkeley National Laboratory
    Tohoku University)

  • Jennifer A. Akiyama

    (Lawrence Berkeley National Laboratory)

  • Veena Afzal

    (Lawrence Berkeley National Laboratory)

  • Stella Tran

    (Lawrence Berkeley National Laboratory)

  • Ingrid Plajzer-Frick

    (Lawrence Berkeley National Laboratory)

  • Catherine S. Novak

    (Lawrence Berkeley National Laboratory)

  • Momoe Kato

    (Lawrence Berkeley National Laboratory)

  • Riana D. Hunter

    (Lawrence Berkeley National Laboratory
    Division of Experimental Medicine)

  • Kianna Maydell

    (Lawrence Berkeley National Laboratory)

  • Allen Wang

    (University of California San Diego School of Medicine)

  • Lin Lin

    (University of California San Diego School of Medicine)

  • Sebastian Preissl

    (University of California San Diego School of Medicine
    Faculty of Medicine, University of Freiburg)

  • Steven Lisgo

    (Newcastle University)

  • Bing Ren

    (University of California, San Diego School of Medicine)

  • Diane E. Dickel

    (Lawrence Berkeley National Laboratory
    Octant Inc.)

  • Len A. Pennacchio

    (Lawrence Berkeley National Laboratory
    U.S. Department of Energy Joint Genome Institute
    University of California)

  • Axel Visel

    (Lawrence Berkeley National Laboratory
    U.S. Department of Energy Joint Genome Institute
    University of California)

Abstract

The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during critical stages of craniofacial development. However, a lack of accurate maps of the genomic locations and cell type-resolved activities of craniofacial enhancers prevents their systematic exploration in human genetics studies. Here, we combine histone modification, chromatin accessibility, and gene expression profiling of human craniofacial development with single-cell analyses of the developing mouse face to define the regulatory landscape of facial development at tissue- and single cell-resolution. We provide temporal activity profiles for 14,000 human developmental craniofacial enhancers. We find that 56% of human craniofacial enhancers share chromatin accessibility in the mouse and we provide cell population- and embryonic stage-resolved predictions of their in vivo activity. Taken together, our data provide an expansive resource for genetic and developmental studies of human craniofacial development.

Suggested Citation

  • Sudha Sunil Rajderkar & Kitt Paraiso & Maria Luisa Amaral & Michael Kosicki & Laura E. Cook & Fabrice Darbellay & Cailyn H. Spurrell & Marco Osterwalder & Yiwen Zhu & Han Wu & Sarah Yasmeen Afzal & Ma, 2024. "Dynamic enhancer landscapes in human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46396-4
    DOI: 10.1038/s41467-024-46396-4
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