SUMMARYThe ventrally expressed secreted polypeptide endothelin1 (Edn1) patterns the skeleton derived from the first two pharyngeal arches into dorsal, intermediate and ventral domains. Edn1 activates expression of many genes, including hand2 and Dlx genes. We wanted to know how hand2/Dlx genes might generate distinct domain identities. Here, we show that differential expression of hand2 and Dlx genes delineates domain boundaries before and during cartilage morphogenesis. Knockdown of the broadly expressed genes dlx1a and dlx2a results in both dorsal and intermediate defects, In zebrafish, dlx3b and dlx5a are redundantly required for patterning specifically within intermediate domain-derived skeleton (Walker et al., 2006). By contrast, zebrafish hand2 nulls exhibit loss of lower jaws, but not upper jaws . hand2 is expressed ventral to nkx3.2, a marker of the jaw joint region . In zebrafish, hand2 mutants, nkx3.2 expands ventrally, indicating that hand2 patterns lower jaw identity in part by repressing jaw joint identity . However, it was unclear whether hand2 represses intermediate domain identity, because hand2 mutants consistently lose jointed-jaw skeleton .Fate-mapping experiments have indicated approximately where skeletal patterning domains arise within early pharyngeal arches Crump et al., 2004;Eberhart et al., 2006). However, these fate maps lacked the precision to directly connect early gene expression patterns to later skeletal shapes. Here, we present expression patterns that allow us to precisely define the dorsal, intermediate and ventral domains within zebrafish pharyngeal arches. We propose that the ventral domain comprises the hand2-expressing pharyngeal arch region, and the skeletal elements that are formed in this region. The ventral domain contains most of Meckel's and ceratohyal cartilages, and the dentary bone. The intermediate domain is the region of pharyngeal arches that expresses all Dlx genes, besides dlx2b (which is not expressed in anterior arches). Expression of the most restricted Dlx gene, dlx4a, reveals the borders of the intermediate domain. The intermediate domain includes the jaw joint region, and the second arch joint region, as well as the opercle and branchiostegal bones. Arch mesenchymal expression of dlx3b and dlx4b is also restricted to the intermediate domain. The dorsal domain is the region of the pharyngeal arch dorsal to dlx4a expression. Because dlx2a is expressed throughout the arch dorsoventral axis, co-labeling of dlx2a and dlx4a reveals the dorsal domain. The dorsal domain contains most of the palatoquadrate cartilage, including the distinctive pterygoid process, the hyomandibular cartilage and the maxillary bone. dlx5a and dlx6a expression does not correspond to a single domain.In addition to defining D-I-V domains, this report examines the functional requirements for D-I-V patterning. We show that along with dlx3b and dlx5a, dlx4b is also redundantly required for intermediate domain skeleton. We report a transgenic revealing the expression pattern of trps1, a gen...