Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs.

Some previously unidentified short interspersed repetitive elements (SINEs) and long interspersed repetitive element (LINEs) were isolated from various higher elasmobranchs (sharks, skates, and rays) and characterized. These SINEs, members of the HE1 SINE family, were tRNA-derived and were widespread in higher elasmobranches. The 3'-tail region of this SINE family was strongly conserved among elasmobranchs. The LINEs, members of the HER1 LINE family, encoded an amino acid sequence similar to that encoded by the chicken CR1 LINE family, and they contained a strongly conserved 3'-tail region in the 3' untranslated region. This tail region of the HER1 LINE family was almost identical to that of the HE1 SINE family. Thus, the HE1 SINE family and the HER1 LINE family provide a clear example of a pair of SINEs and LINEs that share the same tail region. Conservation of the secondary structures of the tail regions, as well as of the nucleotide sequences, between the HE1 SINE family and HER1 LINE family during evolution suggests that SINEs utilize the enzymatic machinery for retroposition of LINEs through the recognition of higher-order structures of the conserved 3'-tail region. A discussion is presented of the parasitism of SINEs on LINEs during the evolution of these retroposons.     

Utilization of the IR hybrid dysgenesis system in Drosophila to test in vivo mobilization of synthetic SINEs sharing 3' homology with the I factor

The current model of short interspersed nuclear element (SINE) mobility suggests that these non-coding retroposons are able to recruit for their own benefits the enzymatic machinery encoded by autonomous long interspersed nuclear elements (LINEs). The recent characterization of potential SINE-LINE partner pairs that share common 3' end sequences concurs with this model and has led to a potent picture of tRNA-derived SINEs consisting of a tripartite functional structure (Mol. Cell. Biol. 16 (1996) 3756; Mol. Biol. Evol. 16 (1999) 1238; Proc. Natl. Acad. Sci. USA 96 (1999) 2869). This structure consist of a 5' polIII tRNA-related promoter region, a central conserved domain and a variable 3' region with homology to the 3' end of LINEs, believed to be essential to direct recognition by the LINE proteins. To test this model in vivo, we have designed synthetic SINEs possessing this 'canonical' structure, including 3' homology to the 3' UTR of the LINE I factor from Drosophila. These synthetic elements were introduced in a Drosophila reactive strain, and SINE retroposition was assessed following dysgenic crosses that are known to induce high levels of I factor germinal transposition. In the progeny from the dysgenic crosses 3400-4000 flies were analyzed but no retroposed copy of the chimeric SINEs was detected, indicating that what is assumed to be a typical SINE structure is not sufficient per se to allow efficient trans-mobilization of our synthetic SINEs by an actively amplifying partner LINE. Alternatively, the apparent absence of natural fly SINEs may underline intrinsic properties of fly biology that are incompatible with the genesis and/or propagation of SINE-like elements.     

SINEs: Short interspersed repeated elements of the eukaryotic genome

Much of the eukaryotic genome is composed of a variety of repetitive sequences. Amongst these, there are two kinds of retroposons (sequence elements derived from nonviral cellular RNA): SINEs (short interspersed elements) and LINEs (long interspersed elements). Amplification of SINEs occurs in a single germ cell, and the members of SINEs spread and become fixed in populations through genetic drift. SINEs can be regarded as phylogenetic landmarks: they are specific to one species, a few species, a genus or in some cases a family, indicating a specific time of amplification during evolution. Recent studies concerning the structure and origin of many SINEs revealed that retroposons are more widespread in animal genomes than was previously thought.     

L1 repeat elements in the human epsilon-G gamma-globin gene intergenic region: sequence analysis and concerted evolution within this family

We have deduced the sequence of a composite long interspersed repeated DNA in primates and herein describe its relationship to a complex repeat element (L1Heg) located in the interval linking the human epsilon- and G gamma-globin genes. The main element of L1Heg is 3' truncated and interrupted by the insertion of the 3' end of a second L1 element. Transposition of L1Heg into this intergenic locus generated a 62-bp duplication of flanking sequences. In contrast, insertion of the second repeat may have been mediated by homology between donor and target sequences. The main repeat represents a novel class of abundant elements whose sequences have diverged from other rodent and primate LINES approximately 1.3 kb downstream from the 5' terminus of L1Heg. Comparison of L1Heg with the sequences of two other related L1 members revealed a complex set of rearrangements confined within a region that resembles the long terminal repeats of other types of retroposons. The boundaries of conversion-like events were defined on the basis of the clustering of nucleotide sequence variants common to two or more nonallelic 3' L1H elements. Several of these events are apparently initiated or resolved within a common 150-bp region that coincides with the 3' terminus of a pan-mammalian open reading frame. This analysis showed that concerted genetic interactions and random drift both contribute appreciably to sequence variation within this set of L1H members.     

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

Many SINEs and LINEs have been characterized to date, and examples of the SINE and LINE pair that have the same 3' end sequence have also increased. We report the phylogenetic relationships of nearly all known LINEs from which SINEs are derived, including a new example of a SINE/LINE pair identified in the salmon genome. We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes.     

Identification of a long stretch of homopurine.homopyrimidine sequence in a cluster of retroposons in the human genome

A cluster of nine retroposons of four different types in a 6221 base EcoRI DNA fragment was isolated from a human fetal liver genomic library using a human nucleophosmin (B23) cDNA as a probe. These retroposons are: (1) a solitary HERV-K long terminal repeat upstream from; (2) a nucleophosmin processed pseudogene; (3) six Alu repeated sequences interspersed in both directions; and (4) a truncated Kpn repeated sequence integrated by an Alu monomer and the HERV-K long terminal repeat. Sequence analysis shows that the nucleophosmin pseudogene contains a long stretch (135 base-pairs) of homopurine.homopyrimidine (Pur.Pyr) sequence. S1 and P1 nuclease digestion indicated that this sequence was able to adopt a non-B-DNA triplex structure under either acidic or neutral conditions. This finding is the first example of the association of a potential DNA triplex structure with a cluster of retroposons.     

A new family of repetitive, retroposon-like sequences in the genome of the rainbow trout

We have identified a new family of interspersed, moderately repetitive DNA elements, termed the RSg-1 family, in the genome of the rainbow trout. Two of the elements examined here are situated upstream of sequences which code for trout nuclear proteins; a protamine gene (p101) and the clustered histone H4 gene. Sequence comparison of various RSg-1 elements indicated a high degree of nucleotide sequence homology between different members of the family. These repetitive elements exhibit well defined 3' ends which contain poly(A) segments preceded by the consensus polyadenylation signal AATAAA. Sequences flanking the 3' end of the poly(A) tract also conform to a consensus sequence. A similar sequence is also found flanking the 5' terminus of the element in the protamine clone p101, and thus may represent a target-site duplication generated upon insertion of the element into the genome. These characteristics, together with the heterogeneous nature of the 5' ends of the elements, are reminiscent of processed pseudogenes and retroposons such as the mammalian L1 family of interspersed repetitive elements.     

Evidence that chicken CR1 elements represent a novel family of retroposons.

We report the first precise delineation of a chicken CR1 element and show that it is flanked by a 6-base-pair target site duplication that occurred when this repetitive element transposed. The 3' end of this CR1 element is defined by an 8-base-pair imperfect direct repeat, and we infer that this sequence represents the 3' end of all intact CR1 elements. In contrast, the 5' ends are not unique, and we argue that this variation existed at the time each element transposed. We also provide evidence that CR1 elements transposed into preferred target sites. CR1 elements therefore appear to represent a novel class of passive retroposons.