High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development
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Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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A manually curated signature from an extensive literature review validated the cranial identity of the NCSC lines, and clustering by Pearson correlation excluded genotype- or hairpin-specific expression changes.
“As shown in fig. S2A, a manually curated signature from an extensive literature review (23–28) validated the cranial identity of our NCSC lines, while clustering by Pearson correlation excluded the presence of any genotype- or hairpin-specific expression change.”
EGR1 is implicated in cranial development in animal models, and its promoter has been shown to feature a bivalent state in human embryonic cranial neural crest.
“which is implicated in cranial development (in animal models) (33, 34) and whose promoter has been recently shown to feature a bivalent state in human embryonic cranial NC (23, 35).”
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- Authors
- Wilderman, A., VanOudenhove, J., Kron, J., Noonan, J. P., & Cotney, J.
- Affiliations
- UConn Health (US)
- Yale University (US)
- University of Connecticut (US)
- Corresponding author
- Cotney, Justin
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2018-05
- Volume
- 23
- Issue
- 5
- Pages
- 1581-1597
- ISSN
- 2211-1247 (ISSN-L)
- PMC
- PMC5965702
- OpenAlex
- W2801693550
- Cited by
- 139
- References
- 132
- Citations by year
- 2026: 14 · 2025: 21 · 2024: 9 · 2023: 19 · 2022: 16 · 2021: 24 · 2020: 22 · 2019: 11 · 2018: 3
- FWCI
- 9.18
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- SSRN Electronic Journal (acceptedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (acceptedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of Dental and Craniofacial Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Cleft Lip and Palate Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Craniofacial Disorders and Treatments
- Keywords
- craniofacial development, human embryonic development, enhancers, non-coding variants, orofacial clefts, craniofacial anomalies, intronic regulatory elements, gene expression regulation
- MeSH terms
- Embryo, Mammalian, Face, Humans, Skull, Gene Expression Regulation, Developmental, Databases, Nucleic Acid, Epigenesis, Genetic, Embryonic Development
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