Dynamic enhancer landscapes in human craniofacial development

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, Matthew J. Blow, Guy Kelman, Iros Barozzi, Yoko Fukuda-Yuzawa, Jennifer A. Akiyama, Veena Afzal, Stella Tran, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Riana D. Hunter, Kianna Maydell, Allen Wang, Lin Lin, Sebastian Preissl, Steven Lisgo, Bing Ren, Diane E. Dickel, Len A. Pennacchio and Axel Visel ()
Additional contact information
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
Cailyn H. Spurrell: Lawrence Berkeley National Laboratory
Marco Osterwalder: Lawrence Berkeley National Laboratory
Yiwen Zhu: Lawrence Berkeley National Laboratory
Han Wu: Lawrence Berkeley National Laboratory
Sarah Yasmeen Afzal: Lawrence Berkeley National Laboratory
Matthew J. Blow: U.S. Department of Energy Joint Genome Institute
Guy Kelman: Lawrence Berkeley National Laboratory
Iros Barozzi: Lawrence Berkeley National Laboratory
Yoko Fukuda-Yuzawa: Lawrence Berkeley National Laboratory
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
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
Steven Lisgo: Newcastle University
Bing Ren: University of California, San Diego School of Medicine
Diane E. Dickel: Lawrence Berkeley National Laboratory
Len A. Pennacchio: Lawrence Berkeley National Laboratory
Axel Visel: Lawrence Berkeley National Laboratory

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-46396-4

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