Bov-B-mobilized SINEs in vertebrate genomes

Two new short retroposon families (SINEs) have been found in the genome of springhare Pedetes capensis (Rodentia). One of them, Ped-1, originated from 5S rRNA, while the other one, Ped-2, originated from tRNA-derived SINE ID. In contrast to most currently active mammalian SINEs mobilized by L1 long retrotransposon (LINE), Ped-1 and Ped-2 are mobilized by Bov-B, a LINE family of the widely distributed RTE clade. The 3' part of these SINEs originates from two sequences in the 5' and 3' regions of Bov-B. Such bipartite structure of the LINE-derived part has been revealed in all Bov-B-mobilized SINEs known to date (AfroSINE, Bov-tA, Mar-1, and Ped-1/2), which distinguishes them from other SINEs with only a 3' LINE-derived part. Structural analysis and the distribution of Bov-B LINEs and partner SINEs supports the horizontal transfer of Bov-B, while the SINEs emerged independently in lineages with this LINE.     

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.     

SINEs of a nearly perfect character

Mobile elements have been recognized as powerful tools for phylogenetic and population-level analyses. However, issues regarding potential sources of homoplasy and other misleading events have been raised. We have collected available data for all phylogenetic and population level studies of primates utilizing Alu insertion data and examined them for potentially homoplasious and other misleading events. Very low levels of each potential confounding factor in a phylogenetic or population analysis (i.e., lineage sorting, parallel insertions, and precise excision) were found. Although taxa known to be subject to high levels of these types of events may indeed be subject to problems when using SINE analysis, we propose that most taxa will respond as the order Primates has--by the resolution of several long-standing problems observed using sequence-based methods.     

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.     

Ancient SINEs from African endemic mammals

Afrotheria is a newly recognized taxon comprising elephants, hyraxes, sea cows, aardvarks, golden moles, tenrecs, and elephant shrews, each of which originated in Africa. Although some members of this taxon were once classified into distantly related groups, recent molecular studies have demonstrated their close relationships. It was suggested that this group emerged as a result of physical isolation of the African continent during the successive breakup events of Gondowanaland. In this study, a novel family of SINEs, designated AfroSINEs, was isolated and characterized from the genomes of afrotherians. This SINE family is distributed exclusively among the afrotherian species, confirming their monophyletic relationships. Furthermore, a distinct subfamily, which shares a deletion in the middle region of the SINE, was identified. The distribution of this subfamily is apparently restricted to the genomes of hyraxes, elephants, and sea cows, suggesting monophyly of these three groups, which was previously proposed as Paenungulata. We characterized the structures of the AfroSINEs from all afrotherian representatives by PCR, and we discuss how they were generated as well as the phylogenetic relationships of their host species.     

B1 SINEs in different rodent families

B1 SINEs were studied in 22 families covering all major rodent lineages. The number of B1 copies considerably varies, from 1 x 10(4) in Geomyidae to 1 x 10(6) in Myodonta. B1 sequences can be divided into three main structural variants: B1 with a 20-bp tandem duplication (found in Gliridae, Sciuridae, and Aplodontidae), B1 with a 29-bp duplication (found in other families), and proto-B1 without duplication (pB1). These variants can be further subdivided according to their characters, including specific 7-, 9-, or 10-bp deletions. Different B1 subfamilies predominate in different rodent families. The analysis of B1 variants allowed us to propose possible pathways for the evolution of this SINE in the context of rodent evolution.     

SINEs of speciation: tracking lineages with retroposons

The value of short interspersed elements (SINEs) for diagnosing common ancestry is being expanded to examine the differential sorting of lineages through the course of speciation events. Because most SINEs are neutral markers of identical descent, are not precisely excised from the genome and have a known ancestral condition, they are advantageous for reconciling gene trees and species trees with minimal phylogenetic error. A population perspective on SINE evolution combined with coalescence theory provides a context for investigating the phenomenon of ancestral polymorphism and its role in producing incongruent SINE insertion patterns among multiple loci. Studies of human Alu repeats demonstrate the value of young polymorphic SINEs for assessing human genomic diversity and tracking ancient demographics of human populations, whereas incongruent insertion patterns revealed by older fixed SINE loci, such as those in African cichlid fishes, contain information that might help identify ancient radiations that are otherwise obscured by accumulated mutations in sequence data. Here, we review the utility of retroposons for inferring common ancestry, discuss limits to the method, and clarify confusion by providing examples from the literature that illustrate how discordant multi-locus insertion patterns of retroelements can indicate lineage-sorting events that should not be misinterpreted as phylogenetic noise.     

SINEs, evolution and genome structure in the opossum

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.     

植物基因组中的非LTR反转录转座子SINEs和LINEs

反转录转座子是基因组进化的推动者之一。分为LTR和非LTR两种类型。前者是真核基因组的主要组分,结构和转座方式与逆转录病毒类似。后者是最初发现于动物基因组新近发现在植物基因组中也广泛存在的新型重复序列,包括LINEs(long interspersed nuclear elements)和SINEs(short interspersed nuclear elements)两个亚型。它们大多因自身或受宿主基因组的调控而失去转座活性。其转座机理目前还不十分清楚,推测LINEs可以自主转座,SINEs依赖其他转座子被动转座。种系分析认为LINEs可能是最古老的反转录转座子,SINEs的起源未知。文章对以上内容进行了归纳和讨论。     

Porcine SINEs: Characterization and use in species-specific amplification

A porcine repetitive DNA sequence has been isolated from an intron of the glucose phosphate isomerase gene. The copy number of this and related sequences was estimated to be approximately 10(5) copies per genome. The sequence possesses all the characteristics of short interspersed elements (SINEs) described in other mammals: The repeat is 300 bp in length, has an poly(A)stretch, and contains insertion duplication sites. Homology to seven other porcine sequences, which also have the characteristics of SINEs, has been demonstrated. Primer oligonucleotides, based on conserved regions in the SINE sequences, have been synthesized. Using these primers, PCR-mediated specific amplification of porcine sequences was demonstrated from pig x mouse and pig x hamster hybrid cell lines. Cloning and sequencing of some amplified porcine sequences verify that the sites of priming are SINE sequences.     

Inverse PCR-Based Method for Isolating Novel SINEs from Genome

Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA^Ala molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA^Ala-derived region at the 5′ end, a tRNA-unrelated region, and AT-rich region at the 3′ end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA^Ala gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA^Ala. The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.     

5S rRNA-derived and tRNA-derived SINEs in fruit bats

Most short retroposons (SINEs) descend from cellular tRNA of 7SL RNA. Here, four new SINEs were found in megabats (Megachiroptera) but neither in microbats nor in other mammals. Two of them, MEG-RS and MEG-RL, descend from another cellular RNA, 5S rRNA; one (MEG-T2) is a tRNA-derived SINE; and MEG-TR is a hybrid tRNA/5S rRNA SINE. Insertion locus analysis suggests that these SINEs were active in the recent fruit bat evolution. Analysis of MEG-RS and MEG-RL in comparison with other few 5S rRNA-derived SINEs demonstrates that the internal RNA polymerase III promoter is their most invariant region, while the secondary structure is more variable. The mechanisms underlying the modular structure of these and other SINEs as well as their variation are discussed. The scenario of evolution of MEG SINEs is proposed.