Human genetic variation within neural crest enhancers: molecular and phenotypic implications
Open accessAbstract
Developmental gene expression programmes are coordinated by the specialized distal cis-regulatory elements called enhancers, which integrate lineage- and signalling-dependent inputs to guide morphogenesis. In previous work, we characterized the genome-wide repertoire of active enhancers in human neural crest cells (hNCC), an embryonic cell population with critical roles in craniofacial development. We showed that in hNCC, co-occupancy of a master regulator TFAP2A with nuclear receptors NR2F1 and NR2F2 correlates with the presence of permissive enhancer chromatin states. Here, we take advantage of pre-existing human genetic variation to further explore potential cooperation between TFAP2A and NR2F1/F2. We demonstrate that isolated single nucleotide polymorphisms affecting NR2F1/F2-binding sites within hNCC enhancers can alter TFAP2A occupancy and overall chromatin features at the same enhancer allele. We propose that a similar strategy can be used to elucidate other cooperative relationships between transcription factors involved in developmental transitions. Using the neural crest and its major contribution to human craniofacial phenotypes as a paradigm, we discuss how genetic variation might modulate the molecular properties and activity of enhancers, and ultimately impact human phenotypic diversity.
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BAZ1B binding regions are enriched for target sites of major regulators of neural crest and its neural derivatives, among which TFAP2A stands out given its core role in neural border formation and neural crest induction and differentiation through binding and stabilization of neural-crest-specific enhancers with NR2F1, NR2F2, and EP300.
“Thus, BAZ1B binding regions are enriched for target sites of major regulators of NC and its neural derivatives (38, 39), among which TFAP2A stands out given its core role in neural border formation and NC induction and differentiation (40) through the binding and stabilization of NC-specific enhancers, in concert with NR2F1, NR2F2, and EP300 (41).”
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Self-citationGenetic variation within transcriptional regulatory elements and its implications for human disease
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Genome-wide Chromatin Mapping Defines AP2α in the Etiology of Craniofacial Disorders
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Genomic homeostasis and congenital cranio-maxillofacial malformations
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Functional analysis of human enhancers using the zebrafish embryo
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Atlas of cell types and regulatory elements underlying human facial diversity
Erickson, A. G., Gershtein, Y., Galimullina, R., Waern, F., Riba, T., Tesařová, M., Schnyder, D., Li, L., Vaulin, N., Samuelsson, S., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02748-y
- Authors
- Rada-Iglesias, A., Prescott, S. L., & Wysocka, J.
- Affiliations
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Medicine (US)
- Corresponding author
- Wysocka, Joanna
- Venue
- Philosophical Transactions of the Royal Society B Biological Sciences
- Publisher
- The Royal Society
- Published
- 2013-06-19
- Volume
- 368
- Issue
- 1620
- Pages
- 20120360
- ISSN
- 0962-8436 (ISSN-L)
- 1471-2970
- PMC
- PMC3682725
- OpenAlex
- W2162272434
- Cited by
- 24
- References
- 81
- Citations by year
- 2026: 1 · 2025: 4 · 2022: 2 · 2021: 2 · 2020: 2 · 2019: 3 · 2018: 3 · 2017: 2 · 2015: 1 · 2014: 3 · 2013: 1
- FWCI
- 0.16
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Philosophical Transactions of the Royal Society B Biological Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM095555)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- human genetic variation, TFAP2A, NR2F1, NR2F2, cis-regulatory elements, single nucleotide polymorphisms, craniofacial development, developmental gene regulation, enhancer activity
- MeSH terms
- Alleles, Animals, Enhancer Elements, Genetic, Face, Humans, Morphogenesis, Neural Crest, Phenotype, Protein Binding, Genetic Variation, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Transcription Factor AP-2, COUP Transcription Factor I
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