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The molecular genetic mechanisms of cartilage construction are incompletely understood. Zebrafish embryos homozygous for jellyfish (jef)mutations show craniofacial defects and lack cartilage elements of the neurocranium, pharyngeal arches, and pectoral girdle similar to humans with campomelic dysplasia. We show that two alleles of jef contain mutations in sox9a, one of two zebrafish orthologs of the human transcription factor SOX9. A mutation induced by ethyl nitrosourea changed a conserved nucleotide at a splice junction and severely reduced splicing of sox9a transcript. A retrovirus insertion intosox9a disrupted its DNA-binding domain. Inhibiting splicing of thesox9a transcript in wild-type embryos with splice site-directed morpholino antisense oligonucleotides produced a phenotype like jefmutant larvae, and caused sox9a transcript to accumulate in the nucleus; this accumulation can serve as an assay for …