Interspersed sequence organization and developmental representation of cloned poly(A) RNAs from sea urchin eggs

A random primed complementary DNA (cDNA) clone library constructed from total maternal poly(A) RNA of sea urchin eggs was screened with two cloned genomic repetitive sequence probes. Sets of cDNA clones reacting with each of these repetitive sequences were recovered. Most of the cloned transcripts included both single copy and repeat sequence elements. Except for the shared repeat sequence element, both the repetitive and single copy regions of the members of each set of clones failed to crossreact. Single copy probes linked to the repeats on the cloned maternal RNAs are represented in an asymmetric manner. It follows that many different genomic members of a given dispersed repeat sequence family are represented in the maternal RNA. RNA gel blots carried out with several repeat probes display about 10 to 20 prominent maternal poly(A) RNAs containing transcripts of each repetitive sequence family. The interspersed maternal transcripts are 3000 to 15,000 bases in length. Maternal transcripts reacting with single copy probes derived from the cloned cDNAs persist during embryonic development, and in some cases appear to be augmented by similar, newly synthesized embryo transcripts. Two examples were found in which additional transcripts of different length appear at specific developmental stages. The transcribed single copy regions are highly polymorphic in the genomes of different individual sea urchins, and comparisons of closely related sea urchin species showed that both the prevalence and length of specific maternal transcripts change rapidly during evolution. Nucleotide sequences of two homologous repeat elements occurring on different cloned transcripts displayed translation stop codons in every possible reading frame. These repeat sequences display structural features suggesting that there has been evolutionary transposition into transcription units active during oogenesis. The repeat elements and their flanking single copy regions reside either in very long 3' or 5'-terminal sequences, or in unprocessed intervening sequences in the maternal poly(A) RNA. These findings lead us to the proposal that the majority of the cytoplasmic poly(A) RNA in echinoderm eggs and early embryos is similar in form to RNAs that occur in the nucleus rather than to the messenger RNA of later cells.