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Results for “Short Interspersed Nucleotide Elements”

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PubMed2000

Phylogenetic analysis of retroposon family as exemplified on human chromosome 13: further evidence for recent proliferation.

The retroposon SINE-R.C2 was first identified as a human-specific insertion in the complement C2 gene. In our previous study, SINE-R type retroposons, derived from the endogenous retrovirus HERV-K family, have been found to be hominoid specific. In this report on human chromosome 13, we identified eighteen new SINE-R retroposons resembling those we have previously reported on the sex chromosomes and on chromosomes 7 and 17. Phylogenetic analysis using the neighbor-joining method revealed that four SINE-R retroposons (13-16, 21, 23, 25) on chromosome 13 were closely related to the human-specific retroposon SINE-R.C2, with a high degree of sequence homology (95-97%). Such elements differ from the HERV-K10. LTR sequence from which they are derived in being deleted for the promoter region. Therefore while the evidence adds to the case that some classes of SINE-R element have continued to proliferate in hominid and hominoid evolution and may, as in the case of Fukuyama type muscular dystrophy, be a cause of insertional mutagenesis, they are less likely than the HERV-K10 LTR to have a positive effect on host gene activity.

Chromosomes, Human, Pair 13↗

PubMed2002

Quantitative PCR detection of pork in raw and heated ground beef and pâté.

Quantitative estimates are important to establish whether pork adulteration in ground beef and pâté is accidental or intentional. A PCR procedure has been developed and evaluated to quantify pork in heated and nonheated meat and pâtés by densitometry using a specific and sensitive repetitive DNA element. Thirty, twenty-five, and twenty PCR cycles were carried out to find the best standard curve and correlation between pork content and band intensity. Twenty cycles showed the best results, quantifying degree contamination up to 1% pork in beef (heated and nonheated) and pork in duck pâté with a minimum error. Finally, fraud was found in commercial pâtés.

Animals↗

PubMed2004

Phylogenetic footprint analysis of IGF2 in extant mammals.

Genomic imprinting results in monoallelic gene transcription that is directed by cis-acting regulatory elements epigenetically marked in a parent-of-origin-dependent manner. We performed phylogenetic sequence and epigenetic comparisons of IGF2 between the nonimprinted platypus (Ornithorhynchus anatinus) and imprinted opossum (Didelphis virginiana), mouse (Mus musculus), and human (Homo sapiens) to determine if their divergent imprint status would reflect differences in the conservation of genomic elements important in the regulation of imprinting. We report herein that IGF2 imprinting does not correlate evolutionarily with differential intragenic methylation, nor is it associated with motif 13, a reported IGF2-specific "imprint signature" located in the coding region. Instead, IGF2 imprinting is strongly associated with both the lack of short interspersed transposable elements (SINEs) and an intragenic conserved inverted repeat that contains candidate CTCF-binding sites, a role not previously ascribed to this particular sequence element. Our results are the first to demonstrate that comparative footprint analysis of species from evolutionarily distant mammalian clades, and exhibiting divergent imprint status is a powerful bioinformatics-based approach for identifying cis-acting elements potentially involved not only in the origins of genomic imprinting, but also in its maintenance in humans.

Amino Acid Sequence↗

PubMed2000

The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine specific SINE elements.

The alpha-actin gene of channel catfish (Ictalurus punctatus) was cloned and sequenced. The gene has a similar organization and exhibited a high level of sequence similarity to those from other vertebrate animals. The upstream region of the alpha-actin gene included a TATA box, a CAAT box, three E-boxes, and a CArG box. Nested deletion segments containing these transcriptional motifs were fused to the reporter gene chloramphenicol acetyl transferase (CAT). Transfection of the clones into C2C12 cells indicated that all these motifs are required for transcriptional activities. The channel catfish alpha-actin gene is associated with two distinct short interspersed repetitive elements (SINEs). The first SINE element showed high levels of sequence similarity to the zebrafish Mermaid element, while the second SINE element is not similar to the Mermaid element except for an 8bp sequence CCCCGTGC suggesting their evolutionary linkage. However, the second SINE element appeared to co-exist with the Mermaid element in most cases and therefore was designated as the Merman element. Approximately 9000 copies and 1200 copies of the Mermaid and Merman elements exist per haploid channel catfish genome, respectively. BLAST searches indicated that both the Mermaid and the Merman elements were frequently associated with gene sequences, mostly those of aquatic animals, suggesting their evolutionary origin in association with aquatic organisms and their function in shaping the evolution of genomes in aquatic animals.

Actins↗

PubMed2002

A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes.

Through the sequence analysis of 27 imprinted human genes and a set of 100 control genes we have developed a novel approach for identifying candidate imprinted genes based on the differences in sequence composition observed. The imprinted genes were found to be associated with significantly reduced numbers of short interspersed transposable element (SINE) Alus and mammalian-wide interspersed repeat (MIR) repeat elements, as previously reported. In addition, a significant association between imprinted genes and increased numbers of low-complexity repeats was also evident. Numbers of the Alu classes AluJ and AluS were found to be significantly depleted in some parts of the flanking regions of imprinted genes. A recent study has proposed that there is active selection against SINE elements in imprinted regions. Alternatively, there may be differences in the rates of insertion of Alu elements. Our study indicates that this difference extends both upstream and downstream of the coding region. This and other consistent differences between the sequence characteristics of imprinted and control genes has enabled us to develop discriminant analysis, which can be used to screen the genome for candidate imprinted genes. We have applied this function to a number of genes whose imprinting status is disputed or uncertain.

Female↗

PubMed2001

Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure.

Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.

Animals↗

PubMed2001

Transcriptional activation of short interspersed elements by DNA-damaging agents.

Short interspersed elements (SINEs), typified by the human Alu repeat, are RNA polymerase III (pol III)-transcribed sequences that replicate within the genome through an RNA intermediate. Replication of SINEs has been extensive in mammalian evolution: an estimated 5% of the human genome consists of Alu repeats. The mechanisms regulating transcription, reverse transcription, and reinsertion of SINE elements in genomic DNA are poorly understood. Here we report that expression of murine SINE transcripts of both the B1 and B2 classes is strongly upregulated after prolonged exposure to cisplatin, etoposide, or gamma radiation. A similar induction of Alu transcripts in human cells occurs under these conditions. This induction is not due to a general upregulation of pol III activity in either species. Genotoxic treatment of murine cells containing an exogenous human Alu element induced Alu transcription. Concomitant with the increased expression of SINEs, an increase in cellular reverse transcriptase was observed after exposure to these same DNA-damaging agents. These findings suggest that genomic damage may be an important activator of SINEs, and that SINE mobility may contribute to secondary malignancy after exposure to DNA-damaging chemotherapy.

Animals↗

PubMed2005

Short interspersed elements (SINEs) are a major source of canine genomic diversity.

SINEs are retrotransposons that have enjoyed remarkable reproductive success during the course of mammalian evolution, and have played a major role in shaping mammalian genomes. Previously, an analysis of survey-sequence data from an individual dog (a poodle) indicated that canine genomes harbor a high frequency of alleles that differ only by the absence or presence of a SINEC_Cf repeat. Comparison of this survey-sequence data with a draft genome sequence of a distinct dog (a boxer) has confirmed this prediction, and revealed the chromosomal coordinates for >10,000 loci that are bimorphic for SINEC_Cf insertions. Analysis of SINE insertion sites from the genomes of nine additional dogs indicates that 3%-5% are absent from either the poodle or boxer genome sequences--suggesting that an additional 10,000 bimorphic loci could be readily identified in the general dog population. We describe a methodology that can be used to identify these loci, and could be adapted to exploit these bimorphic loci for genotyping purposes. Approximately half of all annotated canine genes contain SINEC_Cf repeats, and these elements are occasionally transcribed. When transcribed in the antisense orientation, they provide splice acceptor sites that can result in incorporation of novel exons. The high frequency of bimorphic SINE insertions in the dog population is predicted to provide numerous examples of allele-specific transcription patterns that will be valuable for the study of differential gene expression among multiple dog breeds.

Animals↗

PubMed2005

Probing the secondary structure of salmon SmaI SINE RNA.

SmaI is a short interspersed element (SINE) of the salmon genome, and is derived from tRNA(Lys). We probed the secondary structure of SmaI SINE RNA by enzymatic cleavage and found that the RNA structure comprises three separate domains. The 5'-terminal region (the 5' domain) forms a tRNA-like cloverleaf structure, whereas the 3'-terminal region (the 3' domain) forms an extended stem-loop. The loop region is thought to be recognized by the reverse transcriptase (RT) encoded by the long interspersed element (LINE). The two structural domains are linked by a single-stranded region (the linker domain). Our melting profile analyses indicated the presence of two structural domains having different thermal stabilities, thus supporting the domain composition described above. Based on these results, we discuss the structural generality and evolutionary advantage of the domain composition of SINE RNA.

Animals↗

PubMed1999

Physical distribution of SINE elements in the chromosomes of Atlantic salmon and rainbow trout.

SINE sequences are interspersed throughout virtually all eukaryotic genomes. In the family Salmonidae three families of SINEs have been identified. In this work we have attempted to characterize and locate by means of fluorescent in situ hybridization (FISH) one of these families (HpaI) in the genome of Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). Our results show that these SINEs are interspersed throughout all the chromosome pairs except for the heterochromatin-positive areas, generating a banding pattern that could be useful for chromosome identification in both species.

Animals↗

PubMed2003

B1 and related SINEs in mammalian genomes.

Although B1 and Alu were the first discovered Short Interspersed Elements (SINEs), the studies of these genomic repeats were mostly limited to mice and humans and little data on their presence in other animals were available. Here we report the presence of these SINEs in a wide range of rodents (in all 15 tested families) as well as primates and tree-shrews and their absence in other mammals. Distribution pattern of these SINEs in mammals supports close relationship between rodents and primates as well as tree-shrews. Sequence analysis of these elements, apparently descending from cellular 7SL RNA indicates their rearrangements such as dimerization (Alu), quasi-dimerization (B1), acquiring a tRNA-related unit (B1-dID), extended deletions, etc., preceding their active expansion in the genomes. The revealed common pattern of microenvironment of some rearrangement hot spots in SINEs (internal duplications and deletions) suggests involvement of short direct repeats in the mechanism of such rearrangements. This hypothesis allows us to explain short rearrangements in these and other short retroposons.

Animals↗

PubMed2004

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.

Animals↗

PubMed2005

A retroposon analysis of Afrotherian phylogeny.

Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed.

Amino Acid Sequence↗

PubMed2006

A SINE family widely distributed in the plant kingdom and its evolutionary history.

The distribution and evolution of Au SINE in plants were examined. Au SINE is a short interspersed element first identified in Aegilops umbellulata, a close relative of wheat. The Au SINE was previously found in species such as wheat, maize, tobacco, and tomato, but not in rice. In this study, we first searched public databases, and next examined the presence of Au in a broad range of plant species by PCR using internal primers of Au. Although Au is likely to be absent from many species including rice, it was identified in many Gramineae, Solanaceae, and Fabaceae species, and also in a basal angiosperm species, Asimina triloba. Phylogenetic studies suggest that Au SINE originated before the divergence of monocots and eudicots. Au SINE sequences of Asimina, Triticum, Zea, Nicotiana, Lotus, Medicago, and Glycine were aligned and compared. Although sequences of Au were highly conserved among distantly related species, every Au element in Glycine had a 16 bp deletion and its 3' end differed from sequences of other species. This type of Au could only be found in G. max, and not in other species including other Fabaceae species such as M. truncatula and L. japonicus. This is the first report of a plant SINE family present in multiple lineages, and the evolution of Au SINE in the plant kingdom, especially in Gramineae and Fabaceae is discussed.

Asimina↗

PubMed2006

Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents.

A new short interspersed element (SINE) was isolated from the genome of desert kangaroo rat (Dipodomys deserti) using single-primer PCR. This SINE consists of two monomers: the left monomer (IDL) resembles rodent ID element and other tRNAAla(CGC)-derived SINEs, whereas the right one (Geo) shows no similarity with known SINE sequences. PCR and hybridization analyses demonstrated that IDL-Geo SINE is restricted to the rodent superfamily Geomyoidea (families Geomyidea and Heteromyidea). Isolation and analysis of IDL-Geo from California pocket mouse (Chaetodipus californicus) and Botta's pocket gopher (Thomomys bottae) revealed some species-specific features of this SINE family. The structure and evolution of known dimeric SINEs are discussed.

Animals↗

PubMed1999

Rapid SINE-mediated detection of cisplatin:DNA adduct formation in vitro and in vivo in blood.

Cisplatin (cis-dichlorodiammine platinum II) is one of the most effective antitumor agents to date. Its usefulness is limited, however, by toxicity to healthy tissues, most notably, its nephrotoxicity. To maximize the chemotherapeutic potential of cisplatin and minimize its adverse effects, it is imperative to monitor formation of cisplatin:DNA adducts throughout treatment. We developed a novel, highly sensitive, SINE (Short Interspersed DNA Element)-mediated. PCR-based assay for detection of cisplatin adducts in vitro and in vivo, in DNA from mouse blood cells. The assay relies on the abundance, dispersion and conservation of SINEs in mammalian genomes. The B1 elements at a copy number of 50,000-80,000 are the most abundant SINEs in the mouse genome. Due to their strong sequence conservation, primers complementary to the B1 consensus sequence anneal to the majority of their targets in the genome and allow simultaneous amplification of long random segments of genomic DNA. Thus, in conjunction with the fact that cisplatin adducts block the progression of thermostable polymerase, B1 element-anchored PCR makes a sensitive tool for assessing the overall integrity of the transcribed regions in the mouse genome. The high sensitivity of the assay allows detection of DNA damage at the low cisplatin dosage of 1-8 mg/kg that is considered as sub-chemotherapeutic in experimental animal models. The sensitivity range therefore, makes this assay suitable for the development of predictive correlation for both, the efficacy of treatment as well as induction of nephrotoxicity.

3T3 Cells↗

PubMed2005

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals.

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed element (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR element is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Animals↗

PubMed2006

A SINE-based dichotomous key for primate identification.

For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA samples from evolutionarily divergent primate species. For each node of a combined phylogenetic tree (56 species; n=8 [Hominids]; 11 [New World monkeys]; 21 [Old World monkeys]; 2 [Tarsiformes]; and, 14 [Strepsirrhines]), we tested loci (>400 in total) from prior phylogenetic studies as well as newly identified elements for their ability to amplify in all 56 species. Ultimately, 195 loci were selected for inclusion in this Alu-based key for primate identification. This dichotomous SINE-based key is best used through hierarchical amplification, with the starting point determined by the level of initial uncertainty regarding sample origin. With newly emerging genome databases, finding informative retrotransposon insertions is becoming much more rapid; thus, the general principle of using SINEs to identify organisms is broadly applicable.

Animals↗