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PubMed2004

Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats.

Recent genomic analyses revealed many kinds of tandem repeats of specific sequences. Some of them are related to genetic diseases, but their biological functions and structures are still unknown. Two X-ray structures of a short DNA fragment d(gcGA[G]1Agc) show that four base-intercalated duplexes are assembled to form an octaplex at a low K+ concentration, in which the eight G5 residues form a stacked double G-quartet in the central part. At a higher K+ concentration, however, the octaplex is split into just two halves. These structural features suggest a folding process of eight tandem repeats of d(ccGA[G]4Agg), according to a double Greek-key motif. Such a packaging of the repeats could facilitate slippage of a certain sequence during DNA replication, to induce increase or decrease of the repeats.

Base Sequence↗
PubMed1999

Sequence analysis and population data of short tandem repeat polymorphisms at loci D8S639 and D11S488.

Short tandem repeat loci are ideal markers for forensic and paternity case work. A high degree of polymorphism, as determined by gross length measurement, is very often due to complex underlying sequence variation. In the present study, we have studied the sequence structure and population genetics of two short tandem repeat polymorphisms at loci D8S639 and D11S488 in German Caucasians from the region of Hesse. Sequence data revealed a considerable polymorphism at both loci. Locus D8S639 is characterized by a tetranucleotide (AGAT)n repeat pattern with (GAT) and (AGGT) repeats dispersed throughout several alleles. These microvariations lead to alleles differing by one base pair or alleles of identical size. At locus D8S639 we observed 17 allelic lengths comprising 25 different alleles. Alleles at locus D11S488 possess a compound repeat region consisting of (AAAG)n and (GAAG)n repeats. At locus D11S488 we observed 15 allelic lengths with a total of 24 alleles. Allelic lengths increased in size by 4bp increments corresponding to the addition of one tetranucleotide repeat unit. Population data of loci D8S639 and D11S488 revealed a high polymorphism with heterozygosity rates of 0.85 (D8S639) and 0.91 (D11S488).

Alleles↗
PubMed2000

Variable number of tandem repeat loci in the mitochondrial genomes of beets.

We found four unrelated tandem repeat loci (TR1, TR2, TR3 and TR4) in the mitochondrial genomes of beets, with the TR1 locus embedded within a three-membered family of recombining repeat sequences (the rrn26-repeat). TR1 is composed of an array of 32-bp tandem repeats, the number of which varies from 2 to 13 among the seven beet genotypes examined. It is interesting to note that TR1 has 7-bp direct repeats flanking the array, which may be involved in the generation of the tandem repeat array. Such striking features are shared by the remaining TR loci, and this is thus the first description of minisatellite nucleotide sequences from a higher-plant mitochondrial genome.

Base Sequence↗
PubMed2004

Evaluation of variable number tandem repeat (VNTR) loci in molecular typing of Mycobacterium bovis isolates from Ireland.

Various sets of short tandem repeats such as the exact tandem repeats (ETRs), mycobacterial interspersed repetitive units (MIRUs) and variable number tandem repeat (VNTR) loci, have recently been described as effective tools in strain typing M. tuberculosis complex isolates, representative of global diversity. This study extends our previous study, evaluating the discrimination of a further 17 MIRU_VNTR loci individually and comparing the resolution of published VNTR sets and spoligotyping using a panel of 47 local M. bovis field isolates, including known epidemiologically linked isolates and 9 M. tuberculosis complex reference isolates. Individual loci differed greatly in their discrimination. The discriminatory capacity of novel combinations of the most discriminating VNTR loci was also assessed. In the panel of 47 M. bovis isolates, 17 unique profiles were resolved using VNTR set 1, whilst the MIRUs and ETRs resolved the panel into 11 and 6 profiles, respectively. A novel combination of 10 highly discriminatory VNTRs was determined, which resolved 30 unique profiles. The configuration of a multi-locus VNTR-based assay and its ability to provide a flexible, convenient and high-resolution genotyping method is discussed. We suggest a panel of VNTR markers which may be widely suitable for molecular epidemiological studies of M. bovis. However, the number and combination of informative VNTR markers selected needs to be determined empirically with reference to locally prevalent strains and will depend on the epidemiological study requirements.

Alleles↗
PubMed2005

Functional specificity of Candida albicans Als3p proteins and clade specificity of ALS3 alleles discriminated by the number of copies of the tandem repeat sequence in the central domain.

Candida albicans strain SC5314 contains two ALS3 alleles, which differ in sequence with respect to the number of copies of the 108 bp tandem repeat sequence within the central domain of the coding region. One allele (ALS3(12)) has 12 tandem repeat copies while the other (ALS3(9)) has 9 copies. Wild-type C. albicans (ALS3(12)/ALS3(9)) and those containing various ALS3 alleles (ALS3(12)/als3Delta(9), als3Delta(12)/ALS3(9) and als3Delta(12)/als3Delta(9)) were assayed for adhesion to monolayers of cultured vascular endothelial and pharyngeal epithelial cells. These assays showed obvious adhesive function for the larger Als3p protein, compared to a minor contribution to adhesion from the smaller protein. These functional differences in strain SC5314 prompted examination of ALS3 allelic diversity across the five major genetic clades of C. albicans. This analysis focused on the number of copies of the tandem repeat sequence within the central domain of the coding region and showed a range of alleles encoding from 6 to 19 tandem repeat copies. Clades differed with respect to prevalent ALS3 alleles and allele distribution, but were similar for the mean number of tandem repeat copies per ALS3 allele. Analysis of allelic pairing showed clade differences and the tendency for C. albicans strains to encode one longer and one shorter ALS3 allele. The allelic variability observed for ALS3 and its functional consequences observed in strain SC5314 highlight the importance of understanding ALS allelic diversity in order to draw accurate conclusions about Als protein function.

Alleles↗
PubMed1995

Synthesis and conformational investigation of tandem repeat sequence in RNA polymerase II.

The largest subunit of RNA polymerase II has a very interesting sequence in the C-terminus; that is, a tandem repeat sequence of Ser-Pro-Thr-Ser-Pro-Ser-Tyr consisted of proline residues and three kinds of residues having side-chain hydroxyl groups. Although lack of this tandem repeat is a lethal event in vivo, its functional role is unclear. The sequential polypeptide corresponding to this tandem repeat, poly(Ser-Pro-Thr-Ser-Pro-Ser-Tyr), was synthesized and its conformation was investigated by circular dichroism comparing to the monomeric heptapeptide. In addition, the theoretical conformational analysis based on the molecular mechanics was tried for the heptapeptide in the repeating unit and the periodic polyheptapeptide corresponding to the tandem repeat sequence. These results suggested the possibility that the tandem repeat contains a kind of super conformation composed of the repetitive turn structure in the native state. The characteristic repetitive turn structure would be the key of its function mechanism.

Amino Acid Sequence↗
PubMed1999

Reconstructing the duplication history of a tandem repeat.

One of the less well understood mutational transformations that act upon DNA is tandem duplication. In this process, a stretch of DNA is duplicated to produce two or more adjacent copies, resulting in a tandem repeat. Over time, the copies undergo additional mutations so that typically, multiple approximate tandem copies are present. An interesting feature of tandem repeats is that the duplicated copies are preserved together, making it possible to do "phylogenetic analysis" on a single sequence. This involves using the pattern of mutations among the copies to determine a minimal or a most likely history for the repeat. A history tries to describe the interwoven pattern of substitutions, indels, and duplication events in such a way as to minimize the number of identical mutations that arise independently. Because the copies are adjacent and ordered, the history problem can not be solved by standard phylogeny algorithms. In this paper, we introduce several versions of the tandem repeat history problem, develop algorithmic solutions and evaluate their performance. We also develop ways to visualize important features of a history with the goal of discovering properties of the duplication mechanism.

Algorithms↗
PubMed2003

Neither inverted repeat T-DNA configurations nor arrangements of tandemly repeated transgenes are sufficient to trigger transgene silencing.

Transgene expression was analysed in Arabidopsis T-DNA transformants carrying defined numbers and arrangement of different reporter genes. All transgenes were placed under the control of the strong constitutive CaMV 35S promoter. High, stable transgene expression was observed in plants containing two copies of the beta-glucuronidase (GUS) gene, two or four copies of the green fluorescent protein (GFP) gene and two, four or six copies of the streptomycin phosphotransferase (SPT) gene. Thus, the mere presence of multiple promoter and/or transgene sequences did not result in gene silencing. In none of the cases analysed were tandem repeat arrangements of transgenes and/or inverted repeat (IR) T-DNA structures sufficient to trigger silencing of the different reporter genes. Instead, post-transcriptional gene silencing (PTGS) correlated with the copy number of the highly expressed transgenes. Twelve copies of the SPT and four copies of the GUS gene triggered silencing. Silencing is frequently associated with repetitive T-DNA structures. We favour the idea that in many cases this may be attributed to the high transgene doses rather than the repeat arrangements themselves.

Arabidopsis↗
PubMed2001

JC virus regulatory region tandem repeats in plasma and central nervous system isolates correlate with poor clinical outcome in patients with progressive multifocal leukoencephalopathy.

JC virus (JCV), the causative agent of progressive multifocal leukoencephalopathy (PML), has a hypervariable regulatory region (JCV RR). A conserved archetype form is found in the urines of healthy and immunocompromised individuals, whereas forms with tandem repeats and deletions are found in the brains of PML patients. Type I JCV RR, seen in MAD-1, the first sequenced strain of JCV, contains two 98-bp tandem repeats each containing a TATA box. Type II JCV RR has additional 23-bp and 66-bp inserts or fragments thereof and only one TATA box. We cloned and sequenced JCV RR from different anatomic compartments of PML patients and controls and correlated our findings with the patients' clinical outcome. Twenty-three different sequences were defined in 198 clones obtained from 16 patients. All 104 clones with tandem repeats were type II JCV RR. Patients with poor clinical outcome had high proportions of JCV RR clones with both tandem repeats in plasma (54%) and brain or cerebrospinal fluid (85%). In those who became survivors of PML, archetype sequences predominated in these anatomic compartments (75 and 100%, respectively). In patients with advanced human immunodeficiency virus infection without PML, only 8% of JCV RR clones obtained in the plasma contained tandem repeats. These data suggest that the presence of tandem repeats in plasma and CNS JCV RR clones is associated with poor clinical outcome in patients with PML.

Brain↗
PubMed1997

uvrD mutations enhance tandem repeat deletion in the Escherichia coli chromosome via SOS induction of the RecF recombination pathway.

It has previously been shown that recombination between tandem repeats is not significantly affected by a recA mutation in Escherichia coli. Here, we describe the activation of a RecA-dependent recombination pathway in a hyper-recombination mutant. In order to analyse how tandem repeat deletion may proceed, we searched for mutants that affect this process. Three hyper-recombination clones were characterized and shown to be mutated in the uvrD gene. Two of the mutations were identified as opal mutations at codons 130 and 438. A uvrD::Tn5 mutation was used to investigate the mechanism of deletion formation in these mutants. The uvrD-mediated stimulation of deletion was abolished by a lexAind3 mutation or by inactivation of either the recA, recF, recQ or ruvA genes. We conclude that (i) this stimulation requires SOS induction and (ii) tandem repeat recombination in uvrD mutants occurs via the RecF pathway. In uvrD+ cells, constitutive expression of SOS genes is not sufficient to stimulate deletion formation. This suggests that the RecF recombination pathway activated by SOS induction is antagonized by the UvrD protein. Paradoxically, we observed that the overproduction of UvrD from a plasmid also stimulates tandem repeat deletion. However, this stimulation is RecA independent, as is deletion in a wild-type strain. We propose that the presence of an excess of the UvrD helicase favours replication slippage. This work suggests that the UvrD helicase controls a balance between different routes of tandem repeat deletion.

Adenosine Triphosphatases↗
PubMed2006

Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis.

BACKGROUND: The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary. RESULTS: Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats. CONCLUSION: In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.

Automation↗
PubMed1992

Characterization of a porcine variable number tandem repeat sequence specific for the glucosephosphate isomerase locus.

A variable number of tandem repeat from a porcine glucosephosphate isomerase intron has been isolated and sequenced. The repeat has a unit size of 39 bp, is highly conserved and is present in at least 14 copies. Flanking sequences show a sequence periodicity of 53-54 bp and some sequence homology to the 39 bp repeat. A considerable part of the genomic DNA has been lost during subcloning and is considered to be deletion prone or refractory to propagation in E. coli. The tandem repeat is locus specific and detects at least six alleles in BamHI digested porcine DNA. No homology to other tandem repeat sequences has been found.

Animals↗
PubMed1982

Host-specific activation of transcription by tandem repeats from simian virus 40 and Moloney murine sarcoma virus.

The simian virus (SV40) 72-base pair (bp) tandem repeated sequences have recently been shown to function as activators or enhancers of early viral transcription. A recombinant viral genome was recently constructed by inserting 72-bp tandem repeats from the Moloney murine sarcoma virus (MSV) in place of the 72-bp repeats of SV40. Although this genome replicates in monkey kidney cells, its rate of large tumor antigen expression and replication is considerably slower than that of wild-type SV40. In mouse cells, however, equivalent levels of large tumor antigen appear to be expressed from both wild-type and recombinant genomes, suggesting a relationship between the level of enhancer activity and the host cell. To confirm this observation, we have applied a sensitive quantitative assay for gene expression based on the conversion of chloramphenicol to its acetylated forms. The gene encoding the enzymatic function chloramphenicol acetyltransferase was inserted into two vectors in which the enhancer sequences from SV40 or MSV were placed adjacent to the early SV40 promoter. The SV40 tandem repeats appear to activate gene expression to significantly higher levels in monkey kidney cells, but the MSV repeats are more active in two lines of mouse cells. These findings suggest that the tandem repeat elements may interact with host-specific molecules and, furthermore, may constitute one of the elements determining the host range of these eukaryotic viruses.

Acetyltransferases↗
PubMed2005

Effective display of metallothionein tandem repeats on the bioadsorption of cadmium ion.

To increase the level of adsorption of heavy metal ions in surface-engineered yeasts, a yeast metallothionein (YMT) was tandemly fused and displayed by means of an alpha-agglutinin-based display system. The display of the YMT and its tandem repeats was examined by immunofluorescent labeling. The adsorption and recovery of Cd(2+) on the cell surface was increasingly enhanced with increasing number of tandem repeats. All Cd(2+)-binding sites in the YMT tandem repeats were suggested to be completely occupied. To investigate the relationship between cell-surface adsorption and protection against heavy metal ion toxicity, the tolerance of these surface-engineered yeasts to Cd(2+) was examined by growing in Cd(2+)-containing liquid medium. The rate of growth was found to be dependent on the number of displayed tandem repeats of YMT. These results suggest that the characteristics of surface-engineered yeasts as a bioadsorbent were dependent on the ability of the displayed proteins to bind metal ions, and the adsorption of heavy metal ions on the cell surface plays a major role in the ability of the cells to resist the toxic effects of metal ions.

Adsorption↗
PubMed2000

The 5S rRNA genes in Macaca fascicularis are organized in two large tandem repeats.

The 5S rRNA genes in Macaca fascicularis are organized in tandem repeats which are unusually large and complex. The tandem repeats consist of a 7.3 kb DNA fragment with two 5S rRNA genes linked to a 4.3 kb fragment with one gene. The total number of genes in the repeats is 50-100 per haploid genome. The 5S rDNA has an external promoter, the D box, in the same position relative to transcription start as the human gene but is transcribed less efficiently than a human 5S rRNA gene in a HeLa cell extract.

Animals↗
PubMed2004

Lineage-specific tandem repeats riding on a transposable element of MITE in Xenopus evolution: a new mechanism for creating simple sequence repeats.

Xstir is a repetitive DNA sequence element that is extremely amplified as a common component of two different structures: a tandem repeat (Xstir array) and a MITE (miniature inverted-repeat transposable element) in the genome of Xenopus laevis. To elucidate the origin and evolutionary history of Xstir-related sequences, we investigated their species specificity among three Xenopus species (X. laevis, X. borealis, and X. tropicalis). Analyses by sequence alignment and digestion with restriction enzymes of genomic Xstir-related sequences revealed that the MITE (Xmix MITE) was well conserved among the three Xenopus species, with small lineage-specific differences. On the other hand, the tandem repeat element (tropXstir) in X. tropicalis was different from the Xstir that X. laevis and X. borealis have in common. Both sequences of Xstir and tropXstir were, however, different segments of the Xmix MITE. The results suggest that these tandem repeats were formed by partial tandem duplication of the MITE internal sequence in each lineage of X. tropicalis and of X. borealis/X. laevis after their branching. A molecular mechanism for creating and elongating the tandem repeats from the MITE is proposed.

Animals↗
PubMed1993

Instability of repeats of the von Willebrand factor gene variable number tandem repeat sequence in intron 40.

The von Willebrand factor gene contains a highly polymorphic variable number tandem repeat sequence (VNTR) in intron 40. We observed the spontaneous mutation to a new length allele. Sequence analysis revealed that the change in length corresponds to one tetranucleotide repeat unit. This observation emphasizes the risk of errors in family studies and prenatal diagnosis due to VNTR instability.

DNA↗
PubMed1996

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Base Sequence↗