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Covalent variation is a general property of transcription factors in the sea urchin embryo.

Nine different transcription factors of the Strongylocentrotus purpuratus embryo, belonging to diverse structural families, were examined by high-resolution, two-dimensional gel electrophoresis. These factors had all been cloned previously, and antibodies against the recombinant proteins were available. The factors were visualized immunologically in nuclear extracts from 24-hour blastula-stage embryos. Remarkably, every one of the nine factors displayed multiple charge variants. Three factors, SpZ12-1, SpP3A2, and SpRunt-1, were studied at different stages of embryonic development. The prevalence and distribution of the variant isoforms of all three factors differed at each stage examined; and in all cases the complexity of the variants was greatest in the 24-hour blastula-stage extracts. The most complex set of variants was observed for SpP3A2, and phosphatase treatment demonstrated that some but not all, of the covalent modifications defining these variants are phosphorylations. As the transcription factors were chosen for this study merely on the basis of the availability of antibodies, we conclude that deployment of transcription factors in sea urchin embryos generally involves their covalent modification.