Potter. Global Gene Expression Atlas of Craniofacial Development

The objective is to create a global gene expression atlas of craniofacial development. The central thesis is that a combination of laser capture microdissection, and FACS, combined with microarrays and next generation sequencing can be used to efficiently achieve this goal. Microarrays, for example, with essentially complete gene representation can be used to rapidly determine the expression levels of every gene in laser capture microdissected elements of craniofacial development. A single experiment, therefore, provides a comprehensive analysis of the gene expression status of one component and a limited number of experiments examining each structure and cell type can create an atlas. A combination of structure, lectin staining, and transgenic GFP expression will be used to precisely identify specific compartments and lineages, including cells driving neural crest induction, nasal placodes and pits, lateral and medial facial eminences, neural crest and paraxial mesoderm cells, maxilla and mandibular processes, signaling centers, and the structures of palatogenesis. Next generation sequencing provides a digital readout of gene expression levels, cross-validates microarray data, gives additional valuable information concerning alternative processing, and can detect expression of genes not represented on arrays. We propose, therefore, to combine the use of microarray and nexgen sequencing in the creation of the craniofacial gene expression atlas. In addition, there are target amplification technologies that make possible the global analysis of gene expression in even single cells, which we propose to use to define molecular level heterogeneity present in the different cells of individual components. Using integrative bioinformatics analysis methodologies, gene expression modules reflective of variously differentiating components will be linked to gene networks implicated by shared structural, functional, and interactome features of the hundreds of genes already known to play individual roles in craniofacial development.