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PubMed2000

Allele frequencies of 13 short tandem repeats in population samples from the Iberian Peninsula and northern Africa.

The 13 short tandem repeat (STR) loci D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 as well as the amelogenin locus, contained in AmpFlSTR Profiler Plus and/or AmpFlSTR Cofiler and/or AmpFlSTR Green I PCR amplification kits, were studied in four populations from the Iberian Peninsula, Basques, Catalans, Andalusians and Portuguese and two North African populations (Moroccan Arabs and Berbers). The aim of the study was to obtain accurate allele frequency data and other genetic parameters of forensic interest on the main representative human groups living in Iberia and Morocco using an automated method and commercial amplification kits.

Africa, Northern↗
PubMed1996

High-resolution capillary array electrophoretic sizing of multiplexed short tandem repeat loci using energy-transfer fluorescent primers.

Short tandem repeat regions (STRs) from the polymorphic loci VWFA, THO1, TPO and CSF were amplified by the multiplex polymerase chain reaction (PCR) and analyzed by capillary array electrophoresis with fluorescence detection of energy transfer (ET) labels. The fluorescent ET primers are labeled with one fluorescein at the 5' end and a second fluorescein at the position of the 7th or 9th (modified) base to produce fragments that fluoresce in the green (lambda max = 525 nm). M13 A-track sequencing fragments, used as an internal sizing standard, were generated with a universal primer that has a donor fluorescein at the 5' end and a rhodamine acceptor at the position of the 11th (modified) base to produce fragments fluorescing in the red (> 590 nm). The labeled DNA fragments were excited at 488 nm, and the fluorescence was detected with a two-color confocal fluorescence scanner. Separations were performed on arrays of hollow fused silica capillaries filled with denaturing and replaceable hydroxyethyl cellulose sieving matrices. Separations were complete in less than 50 min, and single base resolution as well as reproducible STR sizing was achieved. The relative standard deviation in sizing was below 0.6%. This work establishes the feasibility of high-resolution, high-speed and high-throughput STR typing of single-stranded DNA fragments using capillary array electrophoresis.

Bacteriophage M13↗
PubMed1997

Typing of the short tandem repeat D8S347 locus with different fluorescence markers.

The short tandem repeat (STR) locus D8S347 was analyzed by capillary electrophoresis. Sequencing data and a population study of 203 individuals from a southwestern German population are presented. We detected 12 different alleles, 340-388 bp in length, and found 40 different genotypes. The heterozygosity index was 85.7%. Futhermore, we investigated the consequences of different fluorescent dyes, namely 6-FAM, HEX, and ROX, on the ABI-calculated fragment sizes of defined (i.e., sequenced) alleles (348-376 bp in length). 6-FAM-labeled fragments appear to be smaller than the corresponding HEX- or ROX-labeled fragments. On average, 6-FAM-labeled fragments differ by 3.52 bp from the sequencing data, HEX-labeled ones by 2.04 bp, and ROX-labeled ones by 1.42 bp. Generally, small alleles differ less from the expected sequencing data than larger ones.

Chromosome Mapping↗
PubMed1997

A new allele at the short tandem repeat locus HumF13A01.

We investigated the (AAAG)n short tandem repeat (STR) polymorphism HumF13A01 an Austrian Caucasoid population sample (n = 674). PCR amplified fragments were detected on an automatic A.L.F. DNA sequencer using laser-induced fluorescence. A total of 14 alleles could be identified including a new 179 bp allele which was designated allele 3. Sequence determination of allele 3 confirmed the typing results by revealing three continuous copies of the core repeat, whereas in sequencing of 54 additional alleles no further variants or microheterogeneities could be observed. The population data showed no significant deviation from Hardy-Weinberg equilibrium.

Austria↗
PubMed2001

An efficient algorithm for finding short approximate non-tandem repeats.

We study the problem of approximate non-tandem repeat extraction. Given a long subject string S of length N over a finite alphabet Sigma and a threshold D, we would like to find all short substrings of S of length P that repeat with at most D differences, i.e., insertions, deletions, and mismatches. We give a careful theoretical characterization of the set of seeds (i.e., some maximal exact repeats) required by the algorithm, and prove a sublinear bound on their expected numbers. Using this result, we present a sub-quadratic algorithm for finding all short (i.e., of length O(log N)) approximate repeats. The running time of our algorithm is O(DN(3pow(epsilon)-1)log N), where epsilon = D/P and pow(epsilon) is an increasing, concave function that is 0 when epsilon = 0 and about 0.9 for DNA and protein sequences.

Algorithms↗
PubMed1996

An efficient method for generation and subcloning of tandemly repeated DNA sequences with defined length, orientation and spacing.

Tandemly repeated DNA sequences generated from single synthetic oligonucleotide monomers are useful for many purposes. With conventional ligation procedures low yields and random orientation of oligomers makes cloning of defined repeated sequences difficult. We solved these problems using 2 bp overhangs to direct orientation and random incorporation of linkers containing restriction sites during ligation. Ligation products are amplified by PCR using the linker oligonucleotides as primers. Restriction digestion of the PCR products generate multimer distributions whose length is controlled by the monomer/linker ratio. The concatenated DNA fragments of defined length, orientation and spacing can be directly used for subcloning or other applications without further treatment.

Base Sequence↗
PubMed1993

The cAMP response element in the rat thyrotropin receptor promoter. Regulation by each decanucleotide of a flanking tandem repeat uses different, additive, and novel mechanisms.

A decanucleotide tandem repeat (TR) sequence, between -162 and -140 base pairs (bp) of the minimal thyrotropin receptor promoter, decreases gene expression by repressing constitutive enhancer activity of its cAMP response element (CRE). Each decanucleotide acts additively. CRE-binding proteins and liver or thyroid nuclear extracts footprint a region including the CRE and the 3' decanucleotide, -148 to -124 bp; nuclear proteins interacting with the 3' decanucleotide protect a smaller region -148 to -135 bp. Separate groups of nuclear proteins interact with the CRE and the 3' decanucleotide; mutations of the CRE affect protein interactions with the 3' decanucleotide and the converse. Nuclear proteins bind to single- or double-stranded 3' decanucleotide DNA; those interacting with the CRE bind only double-stranded DNA. The repressor action of the 5' decanucleotide is associated with an interaction between the coding strand and a single-stranded binding protein in liver and thyroid nuclear extracts. The 5' decanucleotide is in a CT-rich region with S1 nuclease hypersensitivity, near perfect mirror images, and direct repeats. The data therefore indicate that each TR decanucleotide modulates CRE constitutive enhancer activity by different but additive mechanisms, competition versus interaction with a single-stranded binding protein, and each interacts with different nuclear proteins that are not thyroid-specific. The same region in the human thyrotropin receptor represses CRE constitutive enhancer activity by the same mechanisms, despite a nonidentical sequence and no overt TR.

Animals↗
PubMed1993

Immunogenicity in mice of tandem repeats of an epitope from herpes simplex gD protein when expressed by recombinant adenovirus vectors.

The antigenic and immunogenic potential was examined of human adenovirus type 5 (Ad) recombinants carrying and expressing from one to four tandem repeats of a linear neutralizing epitope from the gD protein of herpes simplex virus type 1 (HSV-1) as a fusion with the beta-galactosidase protein. The fusion proteins produced by these Ad vectors in infected cell culture reacted with a herpes simplex virus (HSV) epitope-specific monoclonal antibody to a degree dependent on the number of epitope repeats in the protein. Mice immunized by intraperitoneal injection of the Ad vectors developed an anti-HSV immune response as measured by ELISA and by HSV-1 neutralization assays. The mean antibody titre induced by a single injection of the Ad vector increased with the number of epitope repeats expressed by the recombinant. Any animal that had developed a serum-neutralizing titre of at least 1:80 survived challenge with a normally lethal dose of HSV-2 administered by the intraperitoneal route. Recombinant vectors expressing four repeats of the HSV epitope were as effective in antibody induction and protection as an adenovirus vector carrying and expressing the entire HSV gD protein. These results suggest that the expression of tandem repeats of appropriate epitopic sequences by adenovirus vectors may provide a safe and effective method of immunizing against HSV infection.

Adenoviruses, Human↗
PubMed2001

Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline.

BACKGROUND: The injection of double-stranded RNA (dsRNA) has been shown to induce a potent sequence-specific inhibition of gene function in diverse invertebrate and vertebrate species. The homology-dependent posttranscriptional gene silencing (PTGS) caused by the introduction of transgenes in plants may be mediated by dsRNA. The analysis of Caenorhabditis elegans mutants impaired with dsRNA-mediated silencing and studies in plants implicate a biological role of dsRNA-mediated silencing as a transposon-repression and antiviral mechanism. RESULTS: We investigated the silencing of testis-expressed Stellate genes by paralogous Su(Ste) tandem repeats, which are known to be involved in the maintenance of male fertility in Drosophila melanogaster. We found that both strands of repressor Su(Ste) repeats are transcribed, producing sense and antisense RNA. The Stellate silencing is associated with the presence of short Su(Ste) RNAs. Cotransfection experiments revealed that Su(Ste) dsRNA can target and eliminate Stellate transcripts in Drosophila cell culture. The short fragment of Stellate gene that is homologous to Su(Ste) was shown to be sufficient to confer Su(Ste)-dependent silencing of a reporter construct in testes. We demonstrated that Su(Ste) dsRNA-mediated silencing affects not only Stellate expression but also the level of sense Su(Ste) RNA providing a negative autogenous regulation of Su(Ste) expression. Mutation in the spindle-E gene relieving Stellate silencing also leads to a derepression of the other genomic tandem repeats and retrotransposons in the germline. CONCLUSIONS: Homology-dependent gene silencing was shown to be used to inhibit Stellate gene expression in the D. melanogaster germline, ensuring male fertility. dsRNA-mediated silencing may provide a basis for negative autogenous control of gene expression. The related surveillance system is implicated to control expression of retrotransposons in the germline.

Adenosine Triphosphatases↗
PubMed2000

[Screening of all types of alleles of (A-C)n dinucleotide tandem repeat sequence of aldose reductase gene].

The screening method of seven alleles (Z-6, Z-4, Z-2, Z, Z + 2, Z + 4 and Z + 6) in the (A-C)n dinucleotide tandem repeat sequence was studied. These alleles constitute a microsatellite DNA marker upstream of the transcription initiation site on the aldose reductase gene. At first, genoimic DNAs were isolated from leucocyte pellets, and the region containing the dinucleotide repeats was amplified by PCR with a pair of amplification primers that flanked 132-144 bp region. Then, the PCR products of the DNA samples whose alleles belonged to homozygotes were selected, purified, and sequenced directly in order to find out the types of alleles. Finally, using Z-2 allele as a marker, the samples containing Z-2 allele were detected by 12% fromamide-urea gel electrophoresis together with silver-staining. This method is simple, quick and accurate. It facilitates the screening of a large number of samples and is also suitable for identification of other dinucleotide tandem repeat sequences.

Aldehyde Reductase↗
PubMed2002

Tandem repeat polymorphism of the CYP2E1 gene: an association study with esophageal cancer and lung cancer.

BACKGROUND: Cytochrome P-450 (CYP) enzymes have been shown to play important roles in chemical carcinogenesis. Reports have indicated that polymorphism in CYP1A1, CYP1A2, CYP2A6, CYP2E1, and CYP2D6 are associated with an altered risk of developing cancers of the lung, bladder, liver, and colon. CYP2E1 plays an important role in alcohol metabolism and participates in the metabolic activation of various carcinogens, such as N-nitrosodimethylamine. Recently, we found repeated sequences that consist of four alleles (A1, A2, A3, and A4) and six genotypes (A1/A2, A2/A2, A2/A3, A2/A4, A3/A4 and A4/A4) of the CYP2E1 gene. In the present study, we investigated whether these polymorphisms are associated with lung cancer and esophageal cancer. METHODS: DNA was isolated from blood samples of 192 healthy control subjects, 85 patients with lung cancer, and 82 patients with esophageal cancer in Japanese males. DNA samples were amplified by polymerase chain reaction in the 5'-flanking region of the CYP2E1 gene and in exon 12 in the ALDH2 gene. The tandem repeat polymorphisms were examined using DNA fragment analysis. Missense mutations in exon 12 of the ALDH2 gene were examined using fluorescence-based single strand conformational change polymorphism analysis. Written informed consent was obtained from all the subjects. RESULTS: In the CYP2E1 gene 5'-flanking region polymorphism, patients with esophageal cancer showed significantly higher frequency of the A4/A4 genotype compared with the control subjects (p = 0.02), but no difference was found in patients with lung cancer. The frequencies of the mutant ALDH2*2 allele were significantly higher in patients with esophageal cancer (27.7%) than in healthy control subjects (7.3%; p< 0.0001; habitual alcohol drinkers). CONCLUSIONS: The distribution of genotypes and allele frequencies of the tandem repeats of the 5'-flanking region of the CYP2E1 gene was significantly different in patients with esophageal cancer.

5' Flanking Region↗
PubMed1995

Molecular analysis of a putative transposable retroelement from the Zea genus with internal clusters of tandem repeats.

The molecular characterization of a recently discovered family of long repetitive sequences, termed ZLRS, is described. These elements belong to the class of moderate dispersed repetitive DNA and are specific to the Zea genus. An 8089-bp sequence from a Zea diploperennis ZLRS element have been elucidated. Sequence analysis reveals the presence of a long terminal repeat-like region, two clusters of different tandem repeats and several ORFs. On these grounds, ZLRS could be considered a new member of the superfamily of transposable retroelements. Tandems are present in the majority of ZLRS elements, they show an important stem-loop secondary structure predicted by the computer and their sequence conservation suggests a functional role.

Amino Acid Sequence↗
PubMed1989

The virulence-associated gonococcal H.8 gene encodes 14 tandemly repeated pentapeptides.

H.8 is a virulence-associated, surface-exposed immunogenic macromolecule composed of lipid and protein, common to Neisseria gonorrhoeae and Neisseria meningitidis. The H.8 DNA sequence predicted a 6.9 kD peptide comprising 14 tandemly repeated pentameric sequences. Ten were identical: Pro, Ala, Ala, Glu, Ala. Also predicted was a lipoprotein leader consensus sequence which probably specified acylation since the Escherichia coli-expressed protein was tightly associated with lipid. Lipid appeared to contribute significantly to H.8 antigen's electrophoretic mobility. This is the first description of a prokaryotic outer membrane protein composed solely of tandem repeats. Furthermore, DNA encoding this repeat appears to have been duplicated and translocated into another neisserial gene encoding an azurin.

Amino Acid Sequence↗
PubMed1988

A highly immunogenic region of a human polymorphic epithelial mucin expressed by carcinomas is made up of tandem repeats.

The nucleotide sequences of partial cDNA clones coding for the core protein of a human polymorphic epithelial mucin were determined, and a large domain was found to consist of a 60-base pair tandem repeat sequence. The cDNA clones were originally selected (Gendler, S. J., Burchell, J. M., Duhig, T., Lamport, D., White, R., Parker, M., and Taylor-Papadimitriou, J. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 6060-6064) using three monoclonal antibodies which show differential reactivity with the mucin produced by normal and malignant breast. Two of the epitopes are exposed in the normally processed and cancer-associated mucin, while one epitope is unmasked only in the cancer-associated mucin (Burchell, J. M., Durbin, H., and Taylor-Papadimitriou, J. (1983) J. Immunol. 131, 508-513; Burchell, J., Gendler, S., Taylor-Papadimitriou, J., Girling, A., Lewis, A., Millis, R., and Lamport, D. (1987) Cancer Res. 47, 5476-5482). We show here that all three antibodies react with a synthetic peptide with an amino acid sequence corresponding to that predicted by the tandem repeat. Identification of the epitopes preferentially expressed on the cancer-associated mucin should allow a directed approach to the development of tumor-specific antibodies using synthetic peptides as immunogens.

Alleles↗
PubMed1983

Sequences homologous to the variant antigen mRNA spliced leader are located in tandem repeats and variable orphons in trypanosoma brucei.

We have examined the organization of genomic sequences homologous to the spliced leader of Trypanosoma brucei variant surface glycoprotein (VSG) mRNA, using a synthetic oligodeoxynucleotide probe. These sequences are highly reiterated in the trypanosome genome and most are located in 1.4 kb units arranged in a direct tandem repeat. However, some of the 1.4 kb sequences are dispersed from the cluster(s) of tandem repeats and are flanked by non-repeat DNA. The number and arrangement of these leader sequence orphons varies among different T. brucei stocks. Within the IsTat serodeme, the arrangement of three of four spliced leader orphons observed with Eco RV digestion was stable during a chronic infection and cyclic transmission through the insect vector. The fourth Eco RV orphon, however, undergoes rearrangement during antigenic variation and life-cycle differentiation.

Animals↗
PubMed1991

Avian tandem repeats: nuclear protein binding sites and the origins of short tandem repetitive DNAS.

A 14 bp repeat isolated from the genome of a Mallard duck (Anas platyrhynchos) and a 13 bp repeat isolated from the genome of a Muscovy duck (Cairina moschata) were both tandem and genus-specific. There were 2.1 x 10(6) copies of the 14 bp repeat in the Mallard duck genome and 1.3 x 10(6) copies of the 13 bp repeat in the Muscovy duck genome. These two repeats were not obviously homologous but each contains different transcription protein binding sites. Experimentally, the two repeats were also observed to bind nuclear proteins specifically. A sequence-selective mechanism for the expansion of short tandem repeats from single ancestral sequences containing nuclear protein binding sites is presented.

Animals↗
PubMed2001

Identification and characterization of variable-number tandem repeats in the Yersinia pestis genome.

Yersinia pestis, the infamous plague-causing pathogen, appears to have emerged in relatively recent history. Evidence of this fact comes from several studies that document a lack of nucleotide diversity in the Y. pestis genome. In contrast, we report that variable-number tandem repeat (VNTR) sequences are common in the Y. pestis genome and occur frequently in gene coding regions. Larger tandem repeat arrays, most useful for phylogenetic analysis, are present at an average of 2.18 arrays per 10 kbp and are distributed evenly throughout the genome and the two virulence plasmids, pCD1 and pMT1. We examined allelic diversity at 42 chromosomal VNTR loci in 24 selected isolates (12 globally distributed and 12 from Siskiyou County, Calif.). Vast differences in diversity were observed among the 42 VNTR loci, ranging from 2 to 11 alleles. We found that the maximum copy number of repeats in an array was highly correlated with diversity (R = 0.86). VNTR-based phylogenetic analysis of the 24 strains successfully grouped isolates from biovar orientalis and most of the antiqua and mediaevalis strains. Hence, multiple-locus VNTR analysis (MLVA) appears capable of both distinguishing closely related strains and successfully classifying more distant relationships. Harnessing the power of MLVA to establish standardized databases will enable researchers to better understand plague ecology and evolution around the world.

Animals↗
PubMed1996

Group B streptococci escape host immunity by deletion of tandem repeat elements of the alpha C protein.

Group B streptococci (GBS) are the most common cause of neonatal sepsis, pneumonia, and meningitis. The alpha C protein is a surface-associated antigen; the gene (bca) for this protein contains a series of tandem repeats (each encoding 82 aa) that are identical at the nucleotide level and express a protective epitope. We previously reported that GBS isolates from two of 14 human maternal and neonatal pairs differed in the number of repeats contained in their alpha C protein; in both pairs, the alpha C protein of the neonatal isolate was smaller in molecular size. We now demonstrate by PCR that the neonatal isolates contain fewer tandem repeats. Maternal isolates were susceptible to opsonophagocytic killing in the presence of alpha C protein-specific antiserum, whereas the discrepant neonatal isolates proliferated. An animal model was developed to further study this phenomenon. Adult mice passively immunized with antiserum to the alpha C protein were challenged with an alpha C protein-expressing strain of GBS. Splenic isolates of GBS from these mice showed a high frequency of mutation in bca--most commonly a decrease in repeat number. Isolates from non-immune mice were not altered. Spontaneous deletions in the repeat region were observed at a much lower frequency (6 x 10(-4)); thus, deletions in that region are selected for under specific antibody pressure and appear to lower the organism's susceptibility to killing by antibody specific to the alpha C protein. This mechanism of antigenic variation may provide a means whereby GBS evade host immunity.

Animals↗