(A) Graph of the percentage of observed CHARGE-like phenotypes across the different zebrafish morphants. Significance was determined by chi-square tests. (B–I) Lateral and ventral views of representative cartilage staining in the chd7/fbxl10 double morphants compared to controls (B) at 4 dpf including morphants with normal phenotypes (C), mild malformations of the ceratohyal (D), and chd7/fbxl10 double morphants with severe ceratohyal malformations and ceratobranchial cartilage were undetectable (E). (F) Graph of the frequency of the observed craniofacial cartilage phenotypes in the developing zebrafish. Zebrafish were categorized on the severity of the craniofacial cartilage defect. “Malformed” morphants had all cartilages present but displayed morphological changes in the ceratohyal. “Underdeveloped” morphants had no detectable ceratobranchial arches in addition to a malformed ceratohyal. A morphant was categorized “Absent” with no detectable anterior and branchial arches. A highly underdeveloped neurocranium was present in these morphants. (G–H) Lateral views of representative P-H3 stained zebrafish Std and chd7/fbxl10 morphants at 25 hpf. (I) Quantification of the area occupied by P-H3 positive cells in chd7 morphants (re-plotted from Figure 4C) and chd7/fbxl10 morphants relative to P-H3 positive cells in Std morphants (n = 7). (J) Representative image of the amplified PCR products of both wild-type and morphant chd7 transcripts from 8 hpf across the panel of morphants. Significant p-values in all graphs are noted p < 0.05 (*), p < 0.01 (**), p < 0.001 (***). AC = auditory capsule, CB = ceratobranchial, CH = ceratohyal, EP = ethmoid plate, ME = Meckel’s cartilage, PQ = palatoquadrate.