Genetic studies have shown that distant-acting regulatory sequences (enhancers) embedded in the vast non-coding portion of the human genome play important roles in craniofacial development and susceptibility to craniofacial birth defects. The mechanistic exploration of these distant-acting enhancers continues to be difficult because the genomic location and in vivo function of most craniofacial enhancers remains unknown. As members of FaceBase 1, we generated first sets of annotation and functional data for distal enhancers controlling craniofacial development. These resources proved to be of significant value to the craniofacial research community. However, these efforts captured only a small proportion of the enhancers that are active during craniofacial development in vivo. Here we propose to characterize the gene regulatory landscape of craniofacial development more comprehensively using new and complementary approaches.
The specific aims are: 1) We will map predicted enhancers by ChIP-seq from embryonic mouse and human facial tissues. In preliminary studies, we used ChIP-seq with the enhancer-associated protein p300 to identify several thousand enhancers predicted to be active in the mouse face at e11.5 and in the secondary palate at later stages of development. Using ChIP-seq for a panel of histone modifications (H3K4me1, H3K27ac, H3K27me3), which will require less tissue and increase the sensitivity of enhancer discovery by an order of magnitude, we will obtain higher-resolution data from all subregions of the developing mouse face at three stages of development (e11.5, e13.5, e15.5). We will complement this mouse-based effort with ChIP-seq on human embryonic face tissue to identify human-specific craniofacial enhancers not functionally conserved in mice. 2) In initial studies we characterized ~200 craniofacial enhancers in vivo in transgenic reporter assays. Taking advantage of protocols and collaborations established during FaceBase 1, we will continue to generate critically needed in vivo transgenic assays accompanied by optical projection tomography to characterize enhancers residing in new craniofacial loci identified by FaceBase 2 investigators and outside groups. This will include testing of enhancer variants associated with craniofacial malformations. The datasets, vectors and transgenic embryos produced through our efforts will be made available as resources to the craniofacial research community. We are deeply committed to our ongoing collaborative interactions with the Hub and other Spoke projects, contributing to and taking advantage of the unique research opportunities enabled through the FaceBase program.

Public Health Relevance

The human genome contains mainly DNA that does not code for proteins, and recent studies suggest that this non-coding sequence encompasses important genetic regulatory switches that play a central role in development and disease, including contributing to normal facial variation and common birth defects of the face. It is currently difficult to study these non-coding regulatory sequences important to development, as their location and function in the genome remains largely unknown. This application will use new technologies to map the regulatory sequences controlling craniofacial development and characterize their contributions to normal facial structure and to facial birth defects, generating valuable resources to drive scientific advancement and improve clinical care in this important field.

National Institute of Health (NIH)
National Institute of Dental & Craniofacial Research (NIDCR)
Research Project--Cooperative Agreements (U01)
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Special Emphasis Panel (ZDE1-MH (25))
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Scholnick, Steven
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Lawrence Berkeley National Laboratory
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Ye, Wenduo; Song, Yingnan; Huang, Zhen et al. (2016) A unique stylopod patterning mechanism by Shox2-controlled osteogenesis. Development 143:2548-60
Rosin, Jessica M; Li, Wenjie; Cox, Liza L et al. (2016) A distal 594 bp ECR specifies Hmx1 expression in pinna and lateral facial morphogenesis and is regulated by the Hox-Pbx-Meis complex. Development 143:2582-92
Kvon, Evgeny Z; Kamneva, Olga K; Melo, Uirá S et al. (2016) Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell 167:633-642.e11
Dickel, Diane E; Barozzi, Iros; Zhu, Yiwen et al. (2016) Genome-wide compendium and functional assessment of in vivo heart enhancers. Nat Commun 7:12923
Brinkley, James F; Fisher, Shannon; Harris, Matthew P et al. (2016) The FaceBase Consortium: a comprehensive resource for craniofacial researchers. Development 143:2677-88
Spurrell, Cailyn H; Dickel, Diane E; Visel, Axel (2016) The Ties That Bind: Mapping the Dynamic Enhancer-Promoter Interactome. Cell 167:1163-1166
Barozzi, Iros; Visel, Axel; Dickel, Diane E (2016) Fishing for Function in the Human Gene Pool. Trends Genet 32:392-4
Lidral, Andrew C; Liu, Huan; Bullard, Steven A et al. (2015) A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1. Hum Mol Genet 24:3895-907
Lupiáñez, Darío G; Kraft, Katerina; Heinrich, Verena et al. (2015) Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161:1012-25
Dickel, Diane E; Zhu, Yiwen; Nord, Alex S et al. (2014) Function-based identification of mammalian enhancers using site-specific integration. Nat Methods 11:566-71

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