High Resolution Epigenomic Atlas of Early Human Craniofacial Development

Defects in embryonic patterning resulting in craniofacial abnormalities are common birth defects affecting up to 1 in 500 live births worldwide, and are mostly non-syndromic. The regulatory programs that build and shape the craniofacial complex are thought to be controlled by information encoded in the genome between genes and within intronic sequences. Early stages of human craniofacial development have not been interrogated with modern functional genomics techniques, preventing systematic analysis of genetic associations with craniofacial-specific regulatory sequences. Here we describe a comprehensive resource of craniofacial epigenomic annotations and systematic, integrative analysis with a variety of human tissues and cell types. We identified thousands of novel craniofacial enhancers and provide easily accessible genome annotations for craniofacial researchers and clinicians. We demonstrate the utility of our data to find likely causal variants for craniofacial abnormalities and identify a large enhancer cluster that interacts with HOXA genes during craniofacial development.