Summary The long term goal of this project is to understand how members of large transcription factor families, which share a DNA binding domain and typically have very similar DNA binding specificities, execute highly specific functions in vivo. The primary focus of this proposal is on the Hox family of homeodomain transcription factors, which play critical roles during animal embryogenesis, organ development, and appendage specification in both vertebrates and invertebrates. When these transcription factors mis-regulate their target genes, either due to mutations in their protein-coding sequences or in their target DNA binding sites, developmental defects and many human diseases, from cancer to diabetes, can result. For the next funding period this project will bridge the gap between understanding how these factors specifically recognize their binding sites in vitro, often in conjunction with cofactors, and how they execute their specific functions in vivo. This will be accomplished using whole genome approaches with tagged and mutant Hox factors and by visualizing these proteins and their binding sites in living cells. Additional efforts will be to identify and characterize newly discovered novel cofactors and mechanisms, such as post-translational modifications of Hox proteins, that can alter their DNA binding specificities and/or transcriptional regulatory activities in vivo. In all cases, these experiments will be grounded in identifying and understanding how Hox proteins regulate their bona fide target genes, which allow them to orchestrate entire developmental programs, such as the development of legs and wings.