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A fundamental question in biology is how the myriad of specialized cell behaviors observed in a multicellular organism is encoded by a single genome sequence, and which gene regulatory mechanisms orchestrate the spatiotemporal deployment and maintenance of these cell type-specific programs. Decades of genetic and, more recently, genomic analyses have identified multiple layers of regulation, including specific molecular players and their interactions. This regulation ultimately results in cell-specific gene expression profiles that define coordinated cell cooperation at the tissue and whole-organism levels. However, the diversity and evolutionary dynamics of cell types remain almost complete...