Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs.

Several novel (sub)families of SINEs were isolated from the genomes of cetaceans and artiodactyls, and their sequences were determined. From comparisons of diagnostic nucleotides among the short interspersed repetitive elements (SINEs) in these (sub)families, we were able to draw the following conclusions. (1) After the divergence of the suborder Tylopoda (camels), the CHRS family of SINEs was newly created from tRNA(Glu) in a common ancestor of the lineages of the Suina (pigs and peccaries), Ruminantia (cows and deer), and Cetacea (whales and dolphins). (2) After divergence of the Suina lineage, the CHR-1 SINE and the CHR-2 SINE were generated successively in a common ancestor of ruminants, hippopotamuses, and cetaceans. (3) In the Ruminantia lineage, the Bov-tA SINE was generated by recombination between the CHR-2 SINE and Bov-A. (4) In the Suina lineage, the CHRS-S SINE was generated from the CHRS SINE. (5) In this latter lineage, the PRE-1 family of SINEs was created by insertion of part of the gene for tRNA(Arg) into the 5' region of the CHRS-S family. The distribution of a particular family of SINEs among species of artiodactyls and cetaceans confirmed the most recent conclusion for paraphyly of the order Artiodactyla. The present study also revealed that a newly created tRNA(Glu)-derived family of SINEs was subjected both to recombination with different units and to duplication of an internal sequence within a SINE unit to generate, during evolution, a huge superfamily of tRNA(Glu)-related families of SINEs that are now found in the genomes of artiodactyls and cetaceans.     

Artiodactyl interspersed DNA repeats in cetacean genomes

Interspersed repeats that emerged at different evolutionary times are informative in mammalian phylogeny. Here we show that the ancient short interspersed elements (SINEs) ARE1 and ARE2 are abundantly present in the genomes of artiodactyls and cetaceans but not in other mammalian genomes. This supports the classification of the cetaceans with the artiodactyls by a shared character that is unlikely to be the result of convergence. Received: 16 October 1996 / Accepted: 13 December 1996     

Evolutionary applications of MIRs and SINEs

It is believed that short interspersed elements (SINEs) are irreversibly inserted into genomes. We use this concept to try to deduce the evolution of whales using sequence and hybridization studies. The observation that microsatellites are associated with SINEs lead us to screen sequences surrounding cetacean microsatellites for artiodactyl-derived SINEs. Two sequences that were thought to be cetacean SINEs and the bovine SINE were aligned for comparison to sequences flanking microsatellites from ungulates. The bovine SINE was observed only in ruminants while CetSINE1 and 2 were found in mammals. Hybridization studies using these three SINEs revealed that CetSINE1 was found in all ungulates and cetaceans with the strongest hybridization signal observed in the hippopotamus and beluga; CetSINE2 hybridized to all ungulate suborders, while the bovine SINE was only observed in Ruminantia. It is proposed that these putative SINEs are not 'generic' SINEs but mammalian-wide interspersed repeats (MIRs). Caution is urged: what initially appears to be a SINE may instead be a MIR and have reduced evolutionary resolving power.     

SINE Retrotransposition During the Evolution of the Pecoran Ruminants

SINE retrotransposition events have proven their value as phylogenetic markers in several eukaryotic taxa at different taxonomic levels. The genomes of ruminants contain three related SINE elements, Bov-tA, Bov-A2, and Bov-B. To estimate the time points of retrotransposition of individual copies of these SINEs, we designed PCR primers on database sequences containing SINE insertions in cattle, sheep, or goat genomes and tested for the presence of these copies in the genomes of other ruminants. It was checked by sequencing whether length variation of the PCR products reflected a SINE retrotransposition. One Bov-B and nine Bov-tA insertions were shared by cattle, sheep, goat, and giraffe, indicating an early retrotransposition event before the radiation of the Pecora, while three other Bov-tA and two Bov-B elements were apparently inserted later. The ruminant α-lactalbumine gene contains a hotspot of early and more recent Bov-tA insertions, a Bov-tA replacement as well as a recent Bov-B insertion. Three Bov-A2 insertions were found to be shared only by the Bovidae, the Bovini, and the Bos and Bison species, respectively, indicating that most Bov-A2 insertions are relatively recent. The time elapsed since the retrotransposition was also reflected in the degeneration of the direct repeats that flank SINE inserts. We suggest that retrotransposition of SINEs may serve as phylogenetic markers in the ruminant families, subfamilies, and even tribes. In addition, sequencing of SINE insertions revealed several other unique deletions/insertions that also may be informative for phylogenetic reconstructions of ruminants. Received: 19 January 2001 / Accepted: 6 June 2001     

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes

Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families.     

CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1

Short interspersed repetitive elements (SINEs) are widely distributed among the genomes of eukaryotes. We proposed previously that a SINE should be defined by the presence of a region homologous to a tRNA or to 7SL RNA, together with A-box and B-box promoter sequences, in order to distinguish SINEs from other short repetitive sequences, such as short segments of LINEs (long interspersed repetitive elements; Okada et al. Gene 205, 229–243, 1997). Numerous SINE sequences have been deposited to date in DNA databases. In some cases, however, designation of a particular sequence is problematic when the short repetitive sequence has been defined as a SINE without reference to the presence or absence of promoter elements specific for RNA polymerase III. We demonstrate here that four different sequences, namely, ARE1p, ARE2p, CetSINE1, and CetSINE2, each of which has been reported as a SINE, are, in fact, only partial sequences of members of a new subfamily of L1. We also demonstrate that members of this subfamily are distributed specifically among the genomes of cetartiodactyls. Received: 3 May 2000 / Accepted: 22 August 2000     

Predicting mammalian SINE subfamily activity from A-tail length

Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) elements, a rodent-specific SINE derived from tRNA(Ala), are preferentially associated with A-tails over 50 bases in the rat genome, as predicted. Furthermore, these studies detected a subfamily of ID elements that has made over 15,000 copies that is younger than any previously reported ID subfamily. We use PCR analysis of genomic loci to demonstrate that all subfamily members tested inserted after the divergence of Rattus norvegicus from Rattus rattus. We also found evidence that the rodent B1 family of elements is much more active currently in mouse than in rat. These data provide useful estimates of recent activity from all of the mammalian retrotransposons, as well as allowing identification of the most recent insertions for use as population and speciation markers in those species. Both the current rat ID and mouse B1 elements that are active have small, specific interruptions in their 3' A-tail sequences. We suggest that these interruptions stabilize the length of the A-tails and contribute to the activity of these subfamilies. We present a model in which the dynamics of the 3' A-tail may be a central controlling factor in SINE activity.     

CAN—a pan-carnivore SINE family

Short retroposons or short interspersed elements (SINEs) constituting 5–10% genome have been isolated from various organisms. CAN SINEs initially found in American mink were named after dogs (Canis), and the range of their distribution in the genomes of carnivores and mammals in general remained topical. Here we demonstrate CAN sequences in representatives of all carnivore families, but not beyond carnivores, on the basis of sequence bank search and genomic PCR. Analysis of their distribution supports division of carnivores into caniform (dogs, mustelids, raccoons, bears, and pinnipeds) and feliform (cats, civets, and hyenas) lineages. CAN structure is considered in the context of their function and evolution. Received: 13 July 2001 / Accepted: 18 September 2001     

MyrSINEs: a novel SINE family in the anteater genomes

Recent rapid generation of genomic sequence data has allowed many researchers to perform comparative analyses in various mammalian species. However, characterization of transposable elements, such as short interspersed repetitive elements (SINEs), has not been reported for several mammalian groups. Because SINEs occupy a large portion of the mammalian genome, they are believed to have contributed to the constitution and diversification of the host genomes during evolution. In the present study, we characterized a novel SINE family in the anteater genomes and designated it the MyrSINE family. Typical SINEs consist of a tRNA-related, a tRNA-unrelated and an AT-rich (or poly-A) region. MyrSINEs have only tRNA-related and poly-A regions; they are included in a group called t-SINE. The tRNA-related regions of the MyrSINEs were found to be derived from tRNA^Gly. We demonstrate that the MyrSINE family can be classified into three subfamilies. Two of the MyrSINE subfamilies are distributed in the genomes of both giant anteater and tamandua, while the other is present only in the giant anteater. We discuss the evolutionary history of MyrSINEs and their relationship to the evolution of anteaters. We also speculate that the simple structure of t-SINEs may be a potential evolutionary source for the generation of the typical SINE structure.     

Evolutionary diversity and potential recombinogenic role of integration targets of Non-LTR retrotransposons

Short interspersed elements (SINEs) make up a significant fraction of total DNA in mammalian genomes, providing a rich substrate for chromosomal rearrangements by SINE-SINE recombinations. Proliferation of mammalian SINEs is mediated primarily by long interspersed element 1 (L1) non-long terminal repeat retrotransposons that preferentially integrate at DNA sequence targets with an average length of approximately 15 bp and containing conserved endonucleolytic nicking signals at both ends. We report that sequence variations in the first of the two nicking signals, represented by a 5'-TT-AAAA consensus sequence, affect the position of the second signal thus leading to target site duplications (TSDs) of different lengths. The length distribution of TSDs appears to be affected also by L1-encoded enzyme variants because targets with the same 5' nicking site can be of different average lengths in different mammalian species. Taking this into account, we reanalyzed the second nicking site and found that it is larger and includes more conserved sites than previously appreciated, with a consensus of 5'-ANTNTN-AA. We also studied potential involvement of the nicking sites in stimulating recombinations between SINEs. We determined that SINEs retaining TSDs with perfect 5'-TT-AAAA nicking sites appear to be lost relatively rapidly from the human and rat genomes and less rapidly from dog. We speculate that the introduction of DNA breaks induced by recurring endonucleolytic attacks at these sites, combined with the ubiquitousness of SINEs, may significantly promote recombination between repetitive elements, leading to the observed losses. At the same time, new L1 subfamilies may be selected for "incompatibility" with preexisting targets. This provides a possible driving force for the continual emergence of new L1 subfamilies which, in turn, may affect selection of L1-dependent SINE subfamilies.     

Analysis of the human Alu Ya-lineage

The Alu Ya-lineage is a group of related, short interspersed elements (SINEs) found in primates. This lineage includes subfamilies Ya1-Ya5, Ya5a2 and others. Some of these subfamilies are still actively mobilizing in the human genome. We have analyzed 2482 elements that reside in the human genome draft sequence and focused our analyses on the 2318 human autosomal Ya Alu elements. A total of 1470 autosomal loci were subjected to polymerase chain reaction (PCR)-based assays that allow analysis of individual Ya-lineage Alu elements. About 22% (313/1452) of the Ya-lineage Alu elements were polymorphic for the insertion presence on human autosomes. Less than 0.01% (5/1452) of the Ya-lineage loci analyzed displayed insertions in orthologous loci in non-human primate genomes. DNA sequence analysis of the orthologous inserts showed that the orthologous loci contained older pre-existing Y, Sc or Sq Alu subfamily elements that were the result of parallel forward insertions or involved in gene conversion events in the human lineage. This study is the largest analysis of a group of "young", evolutionarily related human subfamilies. The size, evolutionary age and variable allele insertion frequencies of several of these subfamilies makes members of the Ya-lineage useful tools for human population studies and primate phylogenetics.     

Characterization of species-specifically amplified SINEs in three salmonid species—Chum salmon,pink salmon,and kokanee: The local environment of the genome may be important for the generation of a dominant source gene at a newly retroposed locus

Short interspersed repetitive elements (SINEs), known as theHpaI family, are present in the genomes of all salmonid species (Kido et al.,Proc. Natl. Acad. Sci. USA 1991, 88: 2326–2330). Recently, we showed that the retropositional efficiency of the SINE family in the lineage of chum salmon is extraordinarily high in comparison with that in other salmonid lineages (Takasaki et al.,Proc. Natl. Acad. Sci. USA 1994, 91: 10153–10157). To investigate the reason for this high efficiency, we searched for members of theHpaI SINE family that have been amplified species-specifically in pink salmon. Since the efficiency of the species-specific amplification in pink salmon is not high and since other members of the same subfamily of SINEs were also amplified species-specifically in pink salmon, the actual sequence of this subfamily might not be the cause of the high retropositional efficiency of SINEs in chum salmon. Rather, it appears that a highly dominant source gene for the subfamily may have been newly created by retroposition, and some aspect of the local environment around the site of retroposition may have been responsible for the creation of this dominant source gene in chum salmon. Furthermore, a total of 11 sequences ofHpaI SINEs that have been amplified species-specifically in three salmon lineages was compiled and characterized. Judging from the distribution of members of the same-sequence subfamily of SINEs in different lineages and from the distribution of the different-sequence subfamilies in the same lineage, we have concluded that multiple dispersed loci are responsible for the amplification of SINEs. We also discuss the additional possibility of horizontal transmission of SINEs between species. The availability of the sets of primers used for the detection of the species-specific amplifications of the SINEs provides a convenient and reliable method for identification of these salmonid species.     

BoS: A Large and Diverse Family of Short Interspersed Elements (SINEs) in Brassica oleracea

Short interspersed elements (SINEs) are nonautonomous non-LTR retrotransposons that populate eukaryotic genomes. Numerous SINE families have been identified in animals, whereas only a few have been described in plants. Here we describe a new family of SINEs, named BoS, that is widespread in Brassicaceae and present at ∼2000 copies in Brassica oleracea. In addition to sharing a modular structure and target site preference with previously described SINEs, BoS elements have several unusual features. First, the head regions of BoS RNAs can adopt a distinct hairpin-like secondary structure. Second, with 15 distinct subfamilies, BoS represents one of the most diverse SINE families described to date. Third, several of the subfamilies have a mosaic structure that has arisen through the exchange of sequences between existing subfamilies, possibly during retrotransposition. Analysis of BoS subfamilies indicate that they were active during various time periods through the evolution of Brassicaceae and that active elements may still reside in some Brassica species. As such, BoS elements may be a valuable tool as phylogenetic makers for resolving outstanding issues in the evolution of species in the Brassicaceae family.     

Newly discovered young CORE-SINEs in marsupial genomes

Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.