Specific sequences within single-stranded regions in the sea urchin embryo genome

Naturally occurring single-stranded regions in native DNA isolated from sea urchin embryos at the morula stage were removed by digestion with S1 nuclease. Renaturation experiments show that this nuclease removes a portion of the repetitive sequences renaturing between Cot 10(-2) and 20 including about two-thirds of the histone genes. The latter was shown by hybridization of S1-treated morula DNA to either sea urchin 9 S polysome RNA (containing histone mRNA) or to Escherichia coli plasmid DNA carrying sea urchin histone genes. Hybridization of sea urchin DNA to strand-separated recombinant histone gene DNA shows that it is the histone gene antisense strand that is missing from the gapped regions of the native DNA from morulae. Present and previous data support the conclusion that a portion of the single-stranded regions are not in random positions in the embryo genome and do not result from the unwinding of DNA in vivo at replication sites.