The transposable element family TU of the sea urchin Strongylocentrotus purpuratus, a higher eucaryote, has recently been described (D. Liebermann, B. Hoffman-Liebermann, J. Weinthal, G. Childs, R. Maxson, A. Mauron, S. N. Cohen, and L. Kedes, Nature [London] 306:342-347, 1983). A member of this family, TU4, has an insertion, called ISTU4, of non-TU DNA. ISTU4 is a member of a family of repetitive sequences, which are present in some 1,000 copies per haploid S. purpuratus genome (B. Hoffman-Liebermann, D. Liebermann, L. H. S. N. Cohen, Mol. Cell. Biol. 5:991-1001, 1985). We analyzed this insertion to determine whether it is itself a transposable element. The nucleotide sequence of ISTU4 was determined and showed an unusual structure. There are four, -150 nucleotides long, imperfect direct repeats followed by a single truncated version of these repeats. This region is bounded at either side by -100-nucleotide-long sequences that are not related to each other or to the repeats. Nucleotide sequences at the boundaries of ISTU4-homologous and flanking regions in five genomic clones show that ISTU4 represents a family of sequences with discrete ends, which we call Tsp elements. We showed that the genomic locus that carries a Tsp element in one individual was empty in other individuals and conclude that Tsp elements are a new and different type of transposable element. Tsp elements lack two features common to most other transposable elements: Tsp integration does not result in the duplication of host DNA, and there are no inverted repeats at their termini, although short inverted repeats are present at a distance from the termini.Transposable elements have been well studied at the molecular level in a variety of organisms, such as Escherichia coli and other bacteria, maize, yeast, and various Drosophila species (3,8,10). In these systems transposable elements may often have a profound influence on expression of nearby structural genes. The elements can not only inactivate normally active genes but also activate silent genes or alter the level of expression of active ones. This report describes a new family of transposable elements, which we have named Tsp elements, in the genome of the sea urchin Strongylocentrotus purpuratus. The Tsp family was discovered because one of its members is inserted within a member of the TU transposable element family (9).A number of features of the TU family are relevant to an understanding of the present paper. TU elements are transposable elements present in some 400 copies in the genome of the sea urchin species S. purpuratus. This family was originally identified because one of its members, TU1, had integrated into a histone H2B processed pseudogene (12). Subsequent work has extensively characterized the TU family of transposable elements (9, 12). TU elements fall into several classes. A major class (-40%), of which TUl is an example, is rather uniform in structure. The elements of this class consist of several domains (see Fig. 1, upper panel). The termini of the elements are formed...

Sequences homologous to various structural domains of the Strongylocentrotus purpuratus TU family of transposons are present in sea urchin species closely related to S. purpuratus and were found in close proximity to each other in linkage patterns that differed for different species. Sequence homologs of the inverted repeat outer domain (IVR-OD) segment were, in addition, present in a sea urchin related only distantly to S. purpuratus and in all other eucaryotic organisms surveyed. In humans, a polymorphic hybridization pattern was seen for genomic DNA obtained from different individuals. Sequence comparisons revealed that repeated sequence motifs similar to those making up the 15-base-pair direct repeat unit of the IVR-OD domain of the TU elements exist in the IVRs of transposons identffied in Drosophila melanogaster and maize and in the transcription control regions of certain eucaryotic viral and cellular genes. The remarkable evolutionary conservation of IVR-OD homologs may reflect a biological role for these sequences in DNA transposition, the regulation of gene expression, or both.Transposable genetic elements have been shown to be widespread in the biological world (see reference 49 for a review; 3, 13, 14, 45, 55) where they can affect gene expression (8,28,29,33) and may generate genetic diversity (2,5,6,10,15,16,52). Recently, we reported the discovery of a heterogeneous family of modularly structured transposons, the TU elements, in the genome of the sea urchin Strongylocentrotus purpuratus (31, 24). TU1, the initially isolated TU element, consists of an internal (M) segment bracketed by long terminal inverted repeat (IVR) segments; these are divided into structurally distinct inner and outer domains-the latter characterized by a series of tandem repeat units 15 base pairs in length. Other members of the TU element family, which were isolated from an S. purpuratus genomic DNA library on the basis of their homology with the outer domain (OD) of the TUl IVR, include M segments that are not present in TUL. The M segments of TU elements contain sequences that also are found, unassociated with the IVRs, at many other genomic locations. The inclusion of different segments of genomic DNA within different TU elements and the dispersion of TU element sequence domains to multiple locations of the S. purpuratus genome have suggested that these elements may play a role in the rearrangement of genomic DNA segments.The structural heterogeneity of the TU family, the reiterated sequence motif of its IVR-OD segment, and the unique modularity of TU element structure have prompted us to investigate the occurrence of TU-related sequences in the DNAs of other sea urchin species, as well as in other eucaryotes. In this communication, we report that the IVR-OD sequences that define the TU element family in S. purpuratus a) have homologs even in a sea urchin species related only distantly to S. purpuratus (i.e., Lytechinus pictus) and can be found in more closely related sea urchins in close physical proximity to segments ho...