Dynamic enhancer landscapes in human craniofacial development

Rajderkar, Sudha Sunil; Paraiso, Kitt; Amaral, Maria Luisa; Kosicki, Michael; Cook, Laura E.; Darbellay, Fabrice; Spurrell, Cailyn H.; Osterwalder, Marco; Zhu, Yiwen; Wu, Han; Afzal, Sarah Yasmeen; Blow, Matthew J.; Kelman, Guy; Barozzi, Iros; Fukuda-Yuzawa, Yoko; Akiyama, Jennifer A.; Afzal, Veena; Tran, Stella; Plajzer-Frick, Ingrid; Novak, Catherine S.; Kato, Momoe; Hunter, Riana D.; von Maydell, Kianna; Wang, Allen; Lin, Lin; Preissl, Sebastian; Lisgo, Steven; Ren, Bing; Dickel, Diane E.; Pennacchio, Len A.; Visel, Axel

doi:10.1038/s41467-024-46396-4

Title: Dynamic enhancer landscapes in human craniofacial development

Journal Article · 05 March 2024 · Nature Communications

DOI: https://doi.org/10.1038/s41467-024-46396-4 · OSTI ID:2426867

^[1]; Paraiso, Kitt ^[1];

^[2]; Kosicki, Michael ^[1];

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^[1]; Afzal, Sarah Yasmeen ^[5];

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^[8]; Fukuda-Yuzawa, Yoko ^[9];

^[1]; Afzal, Veena ^[1]; Tran, Stella ^[1]; Plajzer-Frick, Ingrid ^[1]; Novak, Catherine S. ^[1] more »

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Univ. of California, San Diego, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Geneva (Switzerland)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of Bern (Switzerland)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Stanford Univ., CA (United States). Lucile Packard Children’s Hospital
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Hebrew Univ. of Jerusalem (Israel)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Medical University of Vienna (Austria); Imperial College, London (United Kingdom)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Tohoku Univ., Sendai (Japan)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, San Francisco, CA (United States)
Univ. of California, San Diego, CA (United States). School of Medicine
Univ. of California, San Diego, CA (United States). School of Medicine; Univ. of Freiburg (Germany)
Newcastle University, Newcastle upon Tyne (United Kingdom)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Octant Inc., Emeryville, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); University of California, Berkeley, CA (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of California, Merced, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2426867

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 15; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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