Identification of candidate genomic regulatory elements involved in oral clefts

Project Summary/Abstract Disturbances in the molecular pathways that control lip and palate development during embryogenesis can lead to oral clefts, but knowledge of the regulatory interactions involved in modulating the expression of genes in these pathways remains limited. Because enhancers are critical to the spatiotemporal regulation of gene expression during embryogenesis, those that are active in craniofacial tissues during lip and palate development are likely to control the expression of genes relevant to oral clefts. The overall goal of the proposed research is to identify interactions between enhancers, transcription factors that bind the enhancers, and target genes of the enhancers in lip and palate development and oral clefts. Aim 1 is to identify the subset of enhancers that drive gene expression overall in human embryonic palatal mesenchyme cells. The transcription factors with binding site motifs that are enriched in the enhancers will be identified, and binding of the transcription factors within the enhancers in human embryonic palatal mesenchyme cells will be confirmed using assays of chromatin immunoprecipitation followed by sequencing. Aim 2 is to identify enhancers that regulate transcription specifically within human embryonic palatal mesenchyme cells, because such enhancers are more likely to be involved in craniofacial-specific processes during development. Enhancers that can distinguish between human embryonic palatal mesenchyme cells and other types of tissues and cells will be considered palate-specific enhancers. The palate specificity of a subset of the enhancers will be confirmed using in vitro assays.