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PubMed1998

Population genetic study of four short tandem repeat loci in the Belgian population, using capillary electrophoresis.

Allele frequencies of four short tandem repeat loci (HumCD4, HumTH01, HumD21S11 and HumSE33) were investigated in a sample of 395 unrelated Belgian individuals using multiplex polymerase chain reaction and capillary electrophoresis. Automated laser fluorescence was used to detect four fluorescent dyes, enabling the use of an internal standard within each lane. With this method rapid typing with high resolution was obtained and the different alleles were grouped on a statistical base. All loci meet Hardy-Weinberg expectations. The allelic frequency data, together with the constructed allelic ladder, can be used in paternity testing and personal identification in the medical and forensic sciences.

Belgium↗
PubMed1993

A continuous linkage map of 22 short tandem repeat polymorphisms on human chromosome 12.

A continuous linkage map consisting of 22 short tandem repeat polymorphisms has been constructed for human chromosome 12 using 23 non-CEPH pedigrees. The markers were distributed at an average distance of 9.35 cM (3.1-33.9 cM). Eighteen of the markers could be positioned uniquely with a likelihood of > 1000:1. The physical locations of some of the markers suggest that the map covers 85-95% of the chromosome. This framework map of 18 markers has a female length of 213 cM and a male length of 131 cM. Female recombination frequencies were greater than male recombination frequencies except in the distal portion of the short arm. The map provides confirmatory evidence for orders established previously on CEPH pedigrees and uniquely positions 4 additional markers (CD4, ATPSB, D12S56, PLA2).

Chromosome Mapping↗
PubMed1988

GATA tandem repeats detect minisatellite regions in blowfly DNA (Diptera: Calliphoridae).

A DNA probe containing GATA tandem repeats detected numerous dispersed minisatellite regions in the genomes of the blowflies Chrysomya rufifacies and Calliphora erythrocephala. These regions seemed to be actively transcribed into poly(A)+ RNA in a tissue-specific manner. When genomic DNA of blastoderm embryos was compared with adult genomic DNA some loci hybridizing to GATA displayed a marked stage-specific variation in length. In Calliphora, a small sex-linked dimorphism of GATA mini-satellite-associated restriction fragments was observed.

Animals↗
PubMed1989

Expression of synthetic calcitonin genes in plasmid vectors containing tandemly repeated non-overlapping ribosome binding sites.

1. Expression plasmids containing non-overlapping tandemly repeated ribosome binding sites (RBS) were constructed in order to stabilize mRNA and enhance translation. 2. Two synthetic genes (human calcitonin tetramer gene and a fusion gene human gamma-interferon-human calcitonin) were cloned in these vectors and the effect of multiplicity of Shine-Dalgarno (S/D) sequence on heterologous gene expression was studied. 3. It was found that duplication and triplication of RBS had no effect on the stability of mRNA but led to a strong decrease in the level of recombinant protein and mRNA in the cell. 4. Plasmids bearing four times repeated S/D sequences gave longer-lived mRNAs and maintained a level of protein and mRNA very close to the values obtained with a single S/D containing plasmids.

Base Sequence↗
PubMed2004

Germline mutation rates at tandem repeat loci in DNA-repair deficient mice.

Mutation rates at two expanded simple tandem repeat (ESTR) loci were studied in the germline of non-exposed and irradiated severe combined immunodeficient (scid) and poly(ADP-ribose) polymerase (PARP-1-/-) deficient male mice. Non-exposed scid and PARP-/- male mice showed considerably elevated ESTR mutation rates, far higher than those in wild-type isogenic mice and other inbred strains. The irradiated scid and PARP-1-/- male mice did not show any detectable increases in their mutation rate, whereas significant ESTR mutation induction was observed in the irradiated wild-type isogenic males. ESTR mutation spectra in the scid and PARP-1-/- strains did not differ from those in the isogenic wild-type strains. Considering these data and the results of previous studies, we propose that a delay in repair of DNA damage in scid and PARP-1-/- mice could result in replication fork pausing which, in turn, may affect ESTR mutation rate in the non-irradiated males. The lack of mutation induction in irradiated scid and PARP-1-/- can be explained by the high cell killing effects of irradiation on the germline of deficient mice.

Animals↗
PubMed2000

Genetic variation at nine short tandem repeat loci in Chamorros and Filipinos from Guam.

Allele distributions for nine tetrameric short tandem repeat (STR) loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA and vWA were determined in Chamorros and Filipinos residing in Guam. There was little evidence for departures from Hardy-Weinberg expectations (HWE) in any of the populations. Based on the exact test, the only locus that departs significantly from HWE is D8S1179 (p=0.005, Chamorros; p=0.030, Filipinos). There is little evidence for association of alleles between the loci in these databases. The number of pairwise locus departures from expectations is no more than would be expected by chance. The allelic frequency data are similar to comparable published data within the same population group (e.g., a comparison of Filipinos with Filipinos) and significantly different compared with other major population groups, such as African Americans, Caucasians, and Hispanics. The F(ST) estimate over all nine STR loci is 0.0090.

Journal Article↗
PubMed1981

Non-nucleosomal packaging of a tandemly repeated DNA sequence at termini of extrachromosomal DNA coding for rRNA in Tetrahymena.

A tandemly repeated DNA hexanucleotide sequence, 5'C-C-C-C-A-A3', that occurs at the termini of extrachromosomal DNA molecules coding for rRNA (rDNA) in Tetrahymena macronuclei was examined to determine whether it is packaged as nucleosomes. This repeated DNA sequence comprises the terminal few hundred base pairs at each end of the linear rDNA molecules. Digestion of macronuclei with micrococcal nuclease showed that this DNA sequence is protected from digestion but is left, following digestion, as a single but broad size class of DNA fragments several hundred base pairs long, under conditions in which bulk macronuclear DNA and rDNA were digested to fragments that were multiples of approximately 200 base pairs in length. The repeated C-C-C-C-A-A was found protected as fragments longer than the bulk macronuclear DNA digestion products at all times during digestion. Together with putative associated protein(s), this protected DNA was soluble after lysis of micrococcal nuclease-digested macronuclei at low salt concentrations but was insoluble in 0.075--0.2 M KCl, regardless of the extend of digestion. The size and solubility properties of the repeated C-C-C-C-A-A DNA nucleoprotein complex after micrococcal nuclease digestion of macronuclei are clearly distinguishable from those of nucleosomes, and it is inferred that this DNA sequence in macronuclei is packaged in chromatin by proteins other than histones.

Cell Nucleus↗
PubMed1987

Role in translation of a triple tandemly repeated sequence in the 5'-untranslated region of human thymidylate synthase mRNA.

A triple tandem repeat (TTR) consisting of 90 nucleotides exists immediately upstream of the ATG initiator codon in human thymidylate synthase (TS) cDNA (pcHTS-1). To investigate the role of the TTR in the expression of the TS cDNA, we used pcHTS-1 to construct mutant cDNA clones in which part of the TTR was deleted or an additional element was inserted. The mutant cDNA plasmid was introduced into murine TS-negative mutant cells and the relative translation efficiencies of the mutant cDNAs were determined by measuring the transient expression of TS activity and the amount of TS mRNA transcribed. The translation efficiency in transient expression of the mutants was increased by deletions covering all the first two repeated elements, and the part of the third closest to the ATG initiator codon, but was not affected by deletions of only parts of the first two repeated elements at the 5' end. The translation efficiency was also not affected by insertion of an additional repeated element into the TTR. These results suggest that the first two repeated elements at the 5' end both have inhibitory effects on translation of the TS mRNA, probably due to the unique structural feature of this element.

Animals↗
PubMed1996

Distribution of tandem repeat polymorphism within minisatellite MS621 (D5S110).

The minisatellite MS621 (D5S110) is a highly polymorphic tandem repeat locus which maps to the distal region of human chromosome 5p. Major repeat unit variants at D5S110 differ not by base substitutions but by differences in the repetition of an 11 bp sequence motif found within each repeat. The two major classes of repeat unit thus contain two ('dimeric' = D-type) or three ('trimeric' = T-type) copies of this short motif. Mapping the distribution of these D- and T-type repeat units within alleles has allowed the analysis of the structural basis of allelic variation and of one de novo mutation. In contrast to previous studies of some other highly polymorphic minisatellites, this analysis provided no clear evidence for polarized variability at D5S110.

Animals↗
PubMed2005

Comparative nucleotide sequence analysis of polymorphic variable-number tandem-repeat Loci in Mycobacterium ulcerans.

We analyzed a set of variable-number tandem-repeat (VNTR) loci to assess their nucleotide sequence diversity in isolates of three Mycobacterium ulcerans genotypes. Sequence variants in two loci resulted in intraspecies resolution of Southeast Asian and Asian genotypes in contrast to a homogenous sequence composition among African isolates. Nucleotide sequence polymorphism in repeat units can enhance discrimination of VNTR loci.

Bacterial Typing Techniques↗
PubMedDate not supplied

Data on six short-tandem repeat polymorphisms in an autochthonous Basque population.

Population data studies for six short-tandem repeat loci (HUMCSF1P0, HUMTPOX, HUMTH01, HUMHPRTB, HUMFES/FPS, and HUMvWF) were carried out on a sample of 326 autochthonous Basques. Comparing with other European samples, we found the highest frequencies known so far for allele 11 of the HUMCSF1P0 locus (0.380), allele 10 of the HUMFES/FPS locus (0.384), and allele 17 of the HUMvWF locus (0.329). On the other hand, we found the lowest frequencies recorded in Europe for allele 12 of the HUMCSF1P0 locus (0.291), allele 7 of the HUMTH01 locus (0.128), and allele 11 of the HUMFES/FPS system (0.317). These results support the hypothesis that the Basque population is a remnant of early European settlers.

Ethnicity↗
PubMedDate not supplied

[Variable tandem repeat VcA of Vibrio cholerae].

Computer analysis revealed seven potential variable-number tandem-repeat (VNTR) loci in the Vibrio cholerae genome. Specific primers were designed to amplify locus VcA located on chromosome 2 and containing a TGCTGT repeat. The locus was found in all tested strains from a V. cholerae strain collection, the repeat number varying 3 to 23. In total, 14 VcA alleles were observed. The VcA locus was proposed as a marker for the molecular typing of V. cholerae strains.

Algorithms↗
PubMed1991

Antisense RNA inhibition of expression of a pair of tandemly repeated genes results in a delay in cell-cell adhesion in Dictyostelium.

Two tandem genes code for a protein recognized by antibodies to gp24, a small surface protein implicated in cell-cell adhesion of Dictyostelium discoideum. However, these genes do not appear to code for gp24 itself. We have transformed cells with a cloned vector that directs the synthesis of antisense RNA from one of the pair of tandemly repeated genes during the first 4 hr of development. During this period, gp24 protein fails to accumulate and the cells do not become mutually adhesive. Antisense RNA encoded by this vector is unstable and rapidly disappears after synthesis stops. gp24 protein then accumulates and the cells acquire cell-cell adhesion and proceed through development.

Actins↗
PubMed1996

[Forensic application of two short tandem repeat (STR) polymorphic markers, FES and HUMTH01].

This paper reports polymorphisms of two short tandem repeats (STR) in the human c-fes/proto-oncogene (FES) and the human tyrosine hydroxylase gene (HUMTH01), and their application to paternity cases. Genomic DNA samples from 213 unrelated Japanese individuals and from 30 paternity cases were subjected to the polymerase chain reaction (PCR) and then the amplified products were electrophoresed in denaturing polyacrylamide sequencing gels. Allelic bands were detected with autoradiography. Seven alleles differing in the numbers of the repeat units were observed at both loci. Heterozygosity (%) and polymorphism information context were calculated, being 69% and 0.641 FES, and 70% and 0.647 for HUMTH01. The allele frequencies of the two STRs in this study were found to be similar to those previously reported on Asians but different from those in Caucasians and Blacks. When the STRs were applied to 30 paternity cases that had been already tested by using conventional markers, there were no discrepancies between the results of the STRs and of conventional markers. Furthermore, the two STRs could be successfully coamplified in multiplex PCR. These results suggest that the two STRs are useful in forensic work in Japan.

Alleles↗
PubMed1998

Italian population data on the polymarker system and on the five short tandem repeat loci CSF1PO, TPOX, TH01, F13B, and vWA.

A population study on five short tandem repeat (STR) loci and five sequence specific polymorphism loci was performed on unrelated Italian Caucasians. Separation and detection of the amplified STR fragments were carried out by high resolution vertical denaturing polyacrylamide gel electrophoresis (PAGE) and silver staining, respectively. The sequence specific loci were analyzed using the AmpliType PM Typing Kit (Perkin Elmer, Foster City, CA). All loci, except Gc (p = 0.031), meet Hardy-Wienberg expectations. In addition, there is no evidence for association of alleles between pairs of loci. The combined power of discrimination for the five STR loci is 0.9999862 and for the PM loci is 0.99503. The results suggest that these loci may be useful for human identification cases in Italy.

Alleles↗
PubMed1998

Genetic variation at the short tandem repeat loci HumvWA, HumFXIIIB, and HumFES/FPS in the Egyptian and Yemenian populations.

The short tandem repeat systems (STRs) HumvWA, HumFXIIIB, and HumFES/FPS were amplified in a triplex polymerase chain reaction (PCR) on blood samples from 100 unrelated Yemenians and 100 unrelated Egyptians. The samples were analyzed by native horizontal discontinual electrophoresis. No deviations from Hardy-Weinberg equilibrium were detected. The mean exclusion chances for Egyptians and Yemenians were 0.634 and 0.591 (vWA), 0.530 and 0.531 (FXIIIB), and 0.573 and 0.583 (FES); the discriminating powers were 0.937 and 0.924 (vWA), 0.900 and 0.899 (FXIIIB), and 0.918 and 0.921 (FES); and the observed heterozygosity rates were 0.84 and 0.72 (vWA), 0.73 and 0.83 (FXIIIB), and 0.81 and 0.80 (FES). No significant differences were found between the two Arab populations, but the differences between both Arab populations and a European population for HumFES and FXIIIB and between the Yemenian sample and a European sample for vWA were significant. No evidence of linkage disequilibrium between any of the three STRs tested was found.

Alleles↗
PubMed1998

Population study of the short tandem repeat polymorphisms HumTH01, HumvWA31, HumFESFPS and HumF13A01 in Sicily (Southern Italy).

Population genetic studies were carried out on randomly selected and unrelated healthy individuals from Sicily (n = 140-150 individuals) using the short tandem repeat (STR) systems HumTH01, HumvWA31, HumFESFPS and HumF13A01. After vertical electrophoresis on polyacrylamide denaturing gels 6 alleles could be identified for TH01, 9 for vWA31, 7 for FESFPS and 11 for F13A01. No significant deviations from Hardy-Weinberg were observed.

Alleles↗
PubMed2005

Cancer cell line identification by short tandem repeat profiling: power and limitations.

Cancer cell lines are used worldwide in biological research, and data interpretation depends on unambiguous attribution of the respective cell line to its original source. Short-tandem-repeat (STR) profiling (DNA fingerprinting) is the method of choice for this purpose; however, the genetic stability of cell lines under various experimental conditions is not well defined. We tested the effect of long-term culture, subcloning, and generation of drug-resistant subclones on fingerprinting profiles in four widely used leukemia cell lines. The DNA fingerprinting profile remained unaltered in two of them (U937 and K562) throughout 12 months in culture, and the vast majority of subclones derived therefrom by limiting dilution after long-term culture revealed the same profile, indicating a high degree of stability and clonotypic homogeneity. In contrast, two other cell lines (CCRF-CEM and Jurkat) showed marked alterations in DNA fingerprinting profiles during long-term culture. Limiting dilution subcloning revealed extensive clonotypic heterogeneity with subclones differing in up to eight STR loci from the parental culture. Similar heterogeneity was observed in subclones generated by selection culture for drug resistance where DNA fingerprinting proved useful in identifying possible resistance mechanisms. Thus, common tissue culture procedures may dramatically affect the fingerprinting profile of certain cell lines and thus render definition of their origin difficult.

Apoptosis↗