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Cell Rep. 2018 May 1;23(5):1581-1597. doi: 10.1016/j.celrep.2018.03.129.

High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development.

Author information

1
Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA.
2
Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA.
3
Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA.
4
Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA. Electronic address: cotney@uchc.edu.

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.

KEYWORDS:

chromatin state; cis-regulatory sequence; cleft lip; cleft palate; craniofacial; development; developmental enhancer; epigenomics; genomics; orofacial clefting; transcriptional enhancer

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