Individual repetitive DNA sequence families of the sea urchin Strongylocentrotus purpuratus were investigated with regard to their genomic organization, the internal structure of their members, and the structural and developmental characteristics of their RN A transcripts.
Analysis by gel blot hybridization and reassociation kinetics of cloned genomic DNA fragments containing members of three specific repeat families reveals a different pattern of organization in each case. One family is organized into long regions of repeated DNA, usually containing several members of the family in a tandem or clustered arrangement. A second family exists as long repeated elements occurring only once in a local genomic region. The third family consists of short repetitive sequence elements which are generally flanked on either side by single-copy sequences.
The internal structure of eight cloned repetitive sequence elements was examined by determination of their nucleotide sequences. The lack of sequence homology among the eight elements indicates that they are representative of distinct repeat families. For the most part they consist of complex sequence internally, with a minor fraction of the length of five of the eight occupied by direct or inverse sequence repetitions. Six of the eight sequences are not translatable. Comparison of the nucleotide sequences of three different members of the same repeat family reveals that they are not simply colinear sequence variants, but that they differ in the presence and/or arrangement of small sequence subelements.
Hybridization with cloned repetitive sequence elements was used to demonstrate that the level of representation of specific repeat sequences is quantitatively similar in the egg RNA of two sea urchin species, S. purpuratus and S. franciscanus.
Egg and embryo polyadenylated RNAs bearing specific repetitive sequences were analyzed by cDNA cloning, DNA and RNA gel blot hybridization, and DNA sequencing. It was found that the two complements of a given repeat are carried on different sets of polyadenylated transcripts, which are generally quite long (> 3 kilobases, with an estimated number average length of 5-6 kilobases). Within these transcripts, specific short repetitive sequence elements are found interspersed either with single-copy sequences or with other repeat sequences. It is demonstrated by sequencing that one such repeat-containing region is not translatable. The sets of polyadenylated transcripts deriving from several individual repeat families undergo substantial quantitative and probably qualitative modulation during early sea urchin development. Analysis of specific transcripts with single-copy probes from repeat-containing cDNA clones indicates that the embryo genome is transcribed to produce at least some of the same interspersed RNAs as are stored in the oocyte during oogenesis. Finally, the transcripts bearing specific repeat sequences in the polyadenylated egg RNA of two related sea urchin species were found to be qualitatively dissimilar.
