Studies of repetitive sequence transcripts in the sea urchin

The nature of transcripts from repetitive DNA sequences in the sea urchin, Strongylocentrotus purpuratus, is investigated. Hybridization experiments utilizing individual cloned repeat sequences, as well as fractions of total repetitive DNA, indicate that the expression of repeat sequences in RNA is specifically regulated in development. A different set of repeat families is highly represented in each of three RNA populations examined, the nuclear RNAs of gastrula stage embryos and adult intestine tissue, and the total RNA of eggs. Essentially all the genomic repeat families are represented in each RNA, but the prevalence of transcripts representing different repeat families can vary by more than two orders of magnitude in a given RNA. Both complementary strands of most repeat families are represented at similar levels, raising the possibility that RNA-RNA repeat duplex formation occurs in the cell. Two cloned repeat sequences examined were both found primarily on large transcripts in the nuclear RNA, and many of the nuclear repeat transcripts are believed to occur on long interspersed RNA molecules. Several lines of evidence indicate that most repeat sequences in the egg RNA are contained on transcripts with the properties of maternal messenger RNA. A large fraction of the repeat-containing transcripts are polyadenylated. Most of the repeats are found on long transcripts, while in the genome, these repeats are short and interspersed with single-copy sequences. The repeat-containing RNAs are isolated and directly shown to consist of short repeats linked to longer single-copy sequences. These interspersed egg RNAs are shown to include nearly all of the diverse single-copy sequences of total egg RNA, most of which are believed to be message sequences. Several implications of these findings are discussed. Particularly interesting is the conclusion that the single-copy maternal message sequences must be associated primarily with a restricted group of the diverse genomic repeat families. The message sequences thus fall into several hundred sets, each containing transcripts from a different repeat family.