Clefts of the lip and palate are among the most common craniofacial birth defects. They can co-occur with other symptoms as part of Mendelian disorders, but the majority of cases are non-syndromic and have a complex etiology. In some cases disrupted protein-coding genes have been identified as contributors to orofacial clefting risk. However, accumulating evidence from genome-wide association studies (GWAS) indicates that sequence variation in non-coding regions also strongly contributes to a variety of clinical disorders including orofacial clefting. While it is speculated that many of these variants affect disease through impacting on functional properties of distant-acting transcriptional enhancers, only very few isolated examples of such regulatory variation have been identified. This is likely due to the fact that the genomic location and function of the vast majority of distant-acting enhancers in the human genome remains unknown. To address the pressing need to identify on a genomic scale enhancers that are involved in face and palate development and likely relevant for clefting etiology, we propose here an integrated genomic and transgenic mouse strategy to identify craniofacial enhancers and characterize their activities. Specifically, we will use a ChlP-seq approach to identify genome-wide sets of enhancers that are active in mouse face and palate tissues at embryonic stages that are relevant for orofacial clefting. We will use a transgenic mouse enhancer screen to validate and characterize 130 of these enhancer predictions in detail by determining their in vivo activity patterns. Furthermore, we will identify disease-associated GWAS variants that map to craniofacial enhancers that we will have discovered. We will then test and compare the variant and normal sequences in the transgenic enhancer assay for differences in their in vivo activities. All of the genomic and in vivo datasets, as well as molecular reagents developed through these experiments will be made available to other investigators through the Face Base program in order to maximize their availability and accelerate the progress of biomedical and clinical studies of mid-face and palate development and orofacial clefting.

Public Health Relevance

We propose to identify DNA elements that regulate the activity of individual genes during face and palate development and to define their function in transgenic mouse experiments. We will also examine in detail subsets of these regulatory elements that are altered in cleft lip and palate patients to elucidate their role in these disorders. This research is of direct relevance to NlDCR's mission as it is expected to further our understanding of the genetic basis of craniofacial development and disorders.

National Institute of Health (NIH)
National Institute of Dental & Craniofacial Research (NIDCR)
Research Project--Cooperative Agreements (U01)
Project #
Application #
Study Section
Special Emphasis Panel (ZDE1-JH (24))
Program Officer
Scholnick, Steven
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Lawrence Berkeley National Laboratory
Organized Research Units
United States
Zip Code
Chatterjee, Sumantra; Kapoor, Ashish; Akiyama, Jennifer A et al. (2016) Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. Cell 167:355-368.e10
Hay, Deborah; Hughes, Jim R; Babbs, Christian et al. (2016) Genetic dissection of the ?-globin super-enhancer in vivo. Nat Genet 48:895-903
Cordeddu, Viviana; Yin, Jiani C; Gunnarsson, Cecilia et al. (2015) Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome. Hum Mutat 36:1080-7
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
Fakhouri, Walid D; Rahimov, Fedik; Attanasio, Catia et al. (2014) An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects. Hum Mol Genet 23:2711-20
Osterwalder, Marco; Speziale, Dario; Shoukry, Malak et al. (2014) HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme. Dev Cell 31:345-357
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
Wu, Han; Nord, Alex S; Akiyama, Jennifer A et al. (2014) Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet 10:e1004610
Gordon, Christopher T; Attanasio, Catia; Bhatia, Shipra et al. (2014) Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence. Hum Mutat 35:1011-20
Nord, Alex S; Blow, Matthew J; Attanasio, Catia et al. (2013) Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155:1521-31

Showing the most recent 10 out of 15 publications