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PubMed1989

A B-cell-specific nuclear protein that binds to DNA sites 5' to immunoglobulin S alpha tandem repeats is regulated during differentiation.

Immunoglobulin heavy-chain switching is effected by recombination events between sites associated with tandemly repeated switch sequences located 5' to immunoglobulin heavy-chain genes. Using the band mobility shift assay, we have identified two distinct sites 5' to the alpha heavy-chain switch sequence with affinity for a single B-cell-specific DNA-binding protein, S alpha-BP. S alpha-BP was present in nuclear extracts from pre-B and B cells but was not detected in extracts from plasmacytomas, B-cell hybridomas, T-cell lymphomas, or a macrophage cell line. It was also not detectable in other nonlymphoid cells tested. Evidence suggests there are S alpha-BP-binding sites near other immunoglobulin switch sequences. As with the S alpha sites, these sites appear to be distinct from the consensus tandem repeats characteristic of immunoglobulin switch sequences. The possible functions of S alpha-BP on contacting its binding sites are discussed in the context of immunoglobulin heavy-chain switch recombination.

Animals↗

PubMedDate not supplied

Polymorphic tandem repeats in the thymidylate synthase gene is associated with its protein expression in human gastrointestinal cancers.

BACKGROUND: Thymidylate synthase (TS) is a target enzyme of 5-fluorouracil (5-FU), and the TS gene has a polymorphic tandem repeated sequence in the 5'-untranslated region. We investigated the polymorphism on the repeat length of the TS gene and its relation to the number of 5-fluoro-dUMP (FdUMP) binding sites in human gastrointestinal cancers. MATERIALS AND METHODS: Seventy adenocarcinoma samples were used. Twenty-one patients received UFT and 49 patients received no treatment before surgery. Tandem repeat length of TS gene was determined by PCR amplification of genomic DNA. The number of FdUMP binding sites were measured by 3H-FdUMP binding assay. RESULTS: Double- (2R) and triple-repeated (3R) sequences of the TS gene were found in the cancer tissues. Three genotypes of TS were found: 2R/2R (n = 3), 2R/3R (n = 16) and 3R/3R (n = 51). The free TS level for the 3R/3R genotype was significantly higher than for the 2R/3R genotype in UFT (+) group. Similar genotype-dependent difference of TS level was observed in UFT (-) group. CONCLUSIONS: Our results suggest the link between TS genotype and TS protein expression. This link might offer an advantage for selection of patients to receive 5-FU-based chemotherapy.

5' Untranslated Regions↗

PubMed2006

Multiple-locus variable-number tandem repeat analysis of Neisseria meningitidis yields groupings similar to those obtained by multilocus sequence typing.

We identified many variable-number tandem repeat (VNTR) loci in the genomes of Neisseria meningitidis serogroups A, B, and C and utilized a number of these loci to develop a multiple-locus variable-number tandem repeat analysis (MLVA). Eighty-five N. meningitidis serogroup B and C isolates obtained from Dutch patients with invasive meningococcal disease and seven reference strains were analyzed using MLVA and multilocus sequence typing (MLST). MLVA, based on eight VNTR loci with limited variability in the number of repeats, yielded clustering of the strains similar to that obtained by MLST, with congruence between both methods amounting to 69%. The ability to recognize clonal complexes makes MLVA a valuable high-throughput method to serve as a tool complementary to MLST. Four highly variable VNTR loci were used in a second assay to analyze N. meningitidis serogroup C strains collected during an outbreak of meningococcal disease in The Netherlands. Typing based on the latter VNTR loci enabled differentiation of isolates with identical MLST sequence types and grouped epidemiologically related strains.

Bacterial Typing Techniques↗

PubMed2003

Characterization of a novel dimorphism in the 5' flanking region of the short tandem repeat (STR) locus, c-fes/fps (FES).

The FES short tandem repeat (STR) locus contains seven to 14 repeats of the tetranucleotide sequence ATTT. A novel 10 base pair dimorphism in the 5' flanking region of the FES locus was characterized in four broad populations: African-American, Hispanic, Caucasian, and Asian. The absence of the 10 base pair sequence, or (-) allele, was closely linked to FES STR alleles with 10 or fewer repeats. The presence of the 10 base pair sequence, or (+) allele, was closely linked to FES STR alleles with 12 or more repeats. The (-) and (+) alleles occurred equally often in FES STR allele 11. The nucleotide sequence (5'-GGCTGTTTTG-3') of the (+) allele, located 179 base pairs upstream of the FES STR, was determined to be consistent within and among the four populations. Statistical and sequence analysis confirmed the linkage between the two polymorphic sites. The results indicate that the exclusion rate of the FES locus is increased, above that for the STR alone, when both polymorphic characteristics are considered.

5' Flanking Region↗

PubMed2003

Analysis of the polymorphic structure of short tandem repeats locus D18S555.

We analyzed the polymorphic structure of the short tandem repeats (STR) (RRGG) locus D18S555 by DNA sequencing, and examined the distribution of alleles in DNA samples from Japanese and Chinese individuals. DNA sequence analysis showed that the alleles at this locus consisted of deletions or insertions of (gaaagaaagaat), (ggaa), (ggaaggaaggag), (ggaaggagggaaggaaggag), (gggaggaa), and (ggga) 5, with each allele having its own DNA sequence. Analysis of 200 unrelated Japanese and 169 unrelated Chinese subjects identified 11 alleles, of which alleles 4, 6, and 13 occurred with a high frequency. There was no difference in allele frequency between the two ethnic groups. These results indicate that the genotyping of D18S555 alleles requires no sequence analysis, and making the locus applicable to forensic identity.

Asian People↗

PubMed2005

Unusual variant alleles in commonly used short tandem repeat loci.

Unusually large variant alleles were observed in the short tandem repeat (STR) systems D3S1358 and D21S11, both of which are included in the international standard set of loci (ISSOL) and routinely typed in National DNA intelligence databases worldwide. The observed alleles fell within the size range of the adjacent STR marker, which could easily cause problems with respect to correct allele assignments for both loci concerned. We compared the amplification and potential interpretation with three different commercially available kits, which are frequently used in forensic work. PCR products were cloned and sequenced in order to determine the structure of these unusual allele variants and confirm their size and designation (D3S1358 allele 26, D21S11 allele 46). In the locus D21S11 we observed an as yet undescribed partial duplication of the constant region.

Alleles↗

PubMed1998

Reuse of denaturing polyacrylamide gels for short tandem repeat analysis.

Denaturing polyacrylamide gel electrophoretic analysis of amplified polymorphic short tandem repeat (STR) loci using fluorescent markers is a mainstay of forensic and paternity testing. To reduce the drawback of preparing gels or using expensive precast gels, we have developed a simple and rapid method to reuse gels between 2 and 8 times over a period of several days. Following the initial electrophoresis and scan, the original samples are removed from the gel by a 1-1.5-h reverse-electrophoresis step. This step heats the gel for the next set of samples and can be performed several days after the initial electrophoresis. Sample bands remain sharp on subsequent runs, but edge effects (frowning of the outside lanes) become progressively worse and ultimately limit gel reuse. Well distortions and separation of the gel from the plates become problems if the gel is used more than twice. However, degassing the gel solution and bonding the gel to both plates eliminate these problems. Precast gels also can be used multiple times. Using this technique, we have successfully analyzed samples amplified with a nine-locus multiplex system and characterized the separated products using a fluorescent scanner and software.

Acrylic Resins↗

PubMed2005

Shifts in targeting of class switch recombination sites in mice that lack mu switch region tandem repeats or Msh2.

The mechanisms that target class switch recombination (CSR) to antibody gene switch (S) regions are unknown. Analyses of switch site locations in wild-type mice and in mice that lack the Smu tandem repeats show shifts indicating that a 4-5-kb DNA domain (bounded upstream by the Imu promoter) is accessible for switching independent of Smu sequences. This CSR-accessible domain is reminiscent of the promoter-defined domains that target somatic hypermutation. Within the 4-5-kb CSR domain, the targeting of S site locations also depends on the Msh2 mismatch repair protein because Msh2-deficient mice show an increased focus of sites to the Smu tandem repeat region. We propose that Msh2 affects S site location because sequences with few activation-induced cytidine deaminase targets generate mostly switch DNA cleavages that require Msh2-directed processing to allow CSR joining.

Animals↗

PubMed2006

Parentally imprinted allele typing at a short tandem repeat locus in intron 1a of imprinted gene KCNQ1.

A short tandem repeat (STR) in the intron 1a of paternally imprinted gene, KCNQ1, is evaluated as a new probe for use in parentally imprinting allele (PIA) typing. This typing can determine the inheritance of one allele from father by the methylation difference. Allelic and genotypic frequencies of the STR were determined using samples from 175 unrelated Japanese and 170 unrelated Germans. The polymorphism information contents were 0.652 and 0.634 for the Japanese and the Germans, respectively, indicating usefulness in individual identification. This method was applied to five Japanese families consisting of 19 individuals. Genomic DNA was digested by methylation-sensitive restriction endonucleases, HhaI and HapII, followed by PCR amplification using two-step sandwich primer sets and the products were analyzed on polyacrylamide gel electrophoresis. For all of the families, each child's paternal allele given by PIA typing corresponded to one of the two alleles from father, not the two from mother, that were determined by the STR genotyping. The results demonstrate that this STR probe is feasible for use in PIA typing and that its typing method can contribute to paternity testing.

DNA Probes↗

PubMed1999

Efficiency of two different nine-loci short tandem repeat systems for DNA typing purposes.

BACKGROUND: Genotyping based on short tandem repeat (STR) regions is widely used in human identification and parentage testing, in gene mapping studies, and as an approach to studies on the etiopathogenesis and diagnosis of hereditary diseases. We wished to study a new analytical approach that uses capillary electrophoresis and multicolor fluorescence in place of slab gel electrophoresis. METHODS: We evaluated the efficiency for parentage and forensic purposes of the AmpFLSTR Profiler PlusTM typing kit that is used with the ABI Prism 310 Genetic Analyzer (System-2 STR), and that of a widely used panel of nine STRs analyzed with conventional slab-gel electrophoresis followed by radioactive detection (System-1 STR). System-2 STR, based on automated capillary electrophoresis and automated sizing of the alleles by Genotyper 2.0 software, was used to determine the allele frequency of the nine loci in 157 Caucasian subjects from southern Italy. On the basis of the data obtained, we submitted 40 trios to parentage testing. RESULTS: A higher median probability of paternity attribution and power of exclusion were obtained with System-2 STR vs System-1 STR: respectively, 99.99% and 99.95% (P <0.05) for attribution; and five and four excluding loci (P <0.05) for exclusion. The most informative and highly discriminating loci were D18S51, D21S11, and FGA. The combined probability of matching-by-chance for all nine STRs was 1.36 x 10(-12) for System-2 compared with 1.11 x 10(-7) obtained with the other system. The internal standard and allelic ladder of the System-2 STR facilitated accurate and precise genotyping; furthermore, System-2 STR and was faster than the conventional System-1 STR. CONCLUSIONS: The System-2 STR allows rapid testing with higher probabilities of attribution and a higher power of exclusion than with the comparison method with slab-gel electrophoresis.

Alleles↗

PubMed1997

Five cases of forensic short tandem repeat DNA typing.

In medicolegal samples DNA is often broken into fragments. In many cases, only the amplification of short tandem repeated DNA stretches (STRs), which are located in noncoding regions, allows DNA typing of such degraded materials. To demonstrate the high diversity of biological materials which forensic biologists have to deal with, and to outline the success rates and limits of the method, we describe five cases (minute amount of tissue on barrel, tissue in decay, tumor tissue, sperm after multiple rape, stored urine samples) in which forensic DNA typing was successfully performed by use of the short tandem repeats HUMDHFRP2, HUMD8S306, HUMCD4, HUMF13A1, HUMTH01, HUMVWA, and HUMFES.

DNA↗

PubMed1999

The Trypanosoma cruzi trans-sialidase, through its COOH-terminal tandem repeat, upregulates interleukin 6 secretion in normal human intestinal microvascular endothelial cells and peripheral blood mononuclear cells.

The Trypanosoma cruzi trans-sialidase can sensitize mice to become highly susceptible to T. cruzi invasion, through mechanisms that remain unknown. In pursuing this observation, we found that purified trans-sialidase induces the selective release of biologically active interleukin (IL)-6 in naive human intestinal microvascular endothelial cells (HIMECs), peripheral blood mononuclear cells (PBMCs), and bladder carcinoma cells. The trans-sialidase action was independent of its catalytic activity, as demonstrated with a genetically engineered trans-sialidase mutant, an enzymatically active polypeptide, and cocultures of PBMCs with epimastigotes and trypomastigotes. Instead, the trans-sialidase action was reproduced with a recombinant COOH-terminal tandem repeat and with synthetic peptides modeled on the tandem repeat. Most interesting, HIMECs infected with a trypomastigote population expressing trans-sialidase effectively released IL-6, but did not upon infection with the counterpart trypomastigote population expressing low trans-sialidase levels. IL-6 is a key factor in the regulation and symptom formation of infection caused by several types of viruses, such as HIV and influenza A virus. However, the function of IL-6 in protozoan and other parasitic diseases remains unclear. The unique findings presented here suggest that trans-sialidase is a major inducer of IL-6 secretion in T. cruzi infection, independently of immune cell activation. Such IL-6 secretion might underlie some features of Chagas's disease, such as pyrexia, neuroprotection, and fibrosis, and might result in the undermining of normal acquired immunity against T. cruzi.

Amino Acid Sequence↗

PubMed1990

Characterization of a tandemly repeated DNA from the fleshfly Sarcophaga bullata.

In studies on the highly repetitive DNA sequences of the flesh fly Sarcophaga bullata, a 279 bp tandem repeat was cloned and sequenced. A 17 bp stretch within the clone was identical to a motif repeated five times in the satellite DNA of the Bermuda land crab. Southern DNA blotting showed the tandem repeat had a high degree of conservation of MboI sites, but had divergence for EcoRI sites; thus, all repeat units were not identical. The cloned DNA localized to the quinacrine-bright centromeric heterochromatin of the C and E autosomes and to sites on the chromosomal arms. In cases of asynapsis of homologs, the probe localized to euchromatic sites on both homologs or sometimes only on one homolog. The probe also localized near, to, or at a major developmental puff (B9). We conclude that blocks of this short interspersed repetitive DNA occur throughout the Sarcophaga genome in both heterochromatin and euchromatin, and also that the variable position of these sequences suggests they possess a degree of instability.

Animals↗

PubMed2026

Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.

BACKGROUND: Short tandem repeats (STRs) are repetitive DNA sequences with 1–6 nucleotide repeat units, exhibiting high polymorphism due to varying repeat counts. STRs are more variable than SNPs and can cause genetic disorders. With population-scale cattle whole-genome sequencing data available, whole-genome STR identification has attracted new interest, but challenges remain due to the lack of standardized methods, sequencing data limitations, and the diversity of STR-calling tools. This study compared six STR-calling tools: HipSTR, GangSTR, and ExpansionHunter for short-read data, and Straglr, RepeatHMM, and LongTR for Oxford Nanopore (ONT) long-read data—using sequences from five Holstein cattle (two parent–offspring trios with a shared sire). This is the first cattle study to evaluate short- and long-read STR callers using both data types from the same animals. RESULTS: In short-read data, ExpansionHunter identified the highest number of polymorphic STRs (pSTRs) (327,690), followed by HipSTR (205,900) and GangSTR (110,680), with 93,023 loci detected by all three tools. In long-read data, LongTR detected 470,250 pSTRs, RepeatHMM 224,185, and Straglr 90,275, with only 33,253 loci shared among them. Mendelian consistency of STR genotypes in the trio offspring was high (> 0.8) for all short-read tools, with HipSTR and GangSTR highest at 0.98. LongTR was the only long-read tool with high consistency (0.88). Short-read tools also showed higher concordance in STR genotypes among themselves than was observed among long-read tools. However, long-read tools had a clear advantage in detecting large STRs. Relative to computational efficiency, HipSTR and GangSTR (short-reads), and LongTR (long-reads) required less memory and shorter runtimes than the other tools. CONCLUSIONS: Tool selection is critical for accurate whole-genome STR identification in cattle. For short-read data, HipSTR showed relatively high Mendelian consistency and concordance compared to the other tools, while ExpansionHunter was able to detect longer STRs but with lower Mendelian consistency. For long-read data, LongTR demonstrated higher consistency and computational efficiency relative to the other tools. Based on these results, HipSTR and LongTR are suggested as preferred options for short-read and ONT long-read datasets, respectively, in cattle STR analysis. These recommendations are based on the metrics observed in this study, and confirmatory analyses across additional breeds, larger sample sizes, and validated truth sets are encouraged.

Animals↗

PubMed1990

Amplification of a variable number of tandem repeats (VNTR) locus (pMCT118) by the polymerase chain reaction (PCR) and its application to forensic science.

A genetic locus (D1S58, defined by DNA probe pMCT118) that contains a variable number of tandem repeats (VNTR) has been successfully amplified from a very small amount of genomic deoxyribonucleic acid (DNA) by the polymerase chain reaction (PCR). The DNA sequence of the locus was determined and was found to consist of a 16-base consensus sequence and flanking sequences. Oligonucleotide primers complementary to the flanking sequences were synthesized to serve as primers for amplification of MCT118 by the PCR method. Human genomic DNA isolated from blood (2 ng from each sample) was successfully amplified at the MCT118 locus, and polymorphic bands were detectable by ethidium bromide staining after electrophoresis on polyacrylamide gels. Determination of genotypes at this VNTR locus can now be routinely achieved within 24 h, without the need for Southern blots or radioactive materials. Furthermore, the small size (387 to 723 base pairs) of the DNA fragments produced in the PCR amplification permits good resolution of individual alleles that differ by only one repeat unit. The precise specification of the number of tandem repeats present in each allelic fragment is reproducible from one analysis to another.

Alleles↗

PubMed1982

Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units.

The genes coding for the two major small nuclear RNAs in the sea urchin are organized in independent tandem repeating units. The small nuclear RNAs, N1 and N2 were purified from gastrula embryos of Lytechinus variegatus. These RNAs are analogous to the U series of RNA in mammalian cells as judged by their identical 5' termini and the sequence homology of the N1 urchin RNA and U1 mouse RNA. These RNAs were polyadenylated with E. Coli adenylate transferase. A 32PO4 labeled copy of each RNA was made with RNA-dependent DNA polymerase. This copy was used to probe the gene organization of these RNAs by hybridizing to restriction enzyme digests of sperm DNA. Each of these RNAs is coded in a tandemly repeated cluster (at least 30 kb) with a repeat length of 1100-1400 bases. The N1 and N2 clusters are distinct. The N1 repeat has been cloned and the repeating organization confirmed with the cloned gene.

Animals↗

PubMed2000

[Short tandem repeat loci examination after repair of coracoclavicular ligament injury by tissue engineered tendon].

OBJECTIVE: To evaluate the result of clinical application in the repair of coracoclavicular ligament injury by tissue engineered tendon using the technique of short tandem repeat loci examination. METHODS: In september 1999, human embryonic tendon cells and artificial materials were co-cultured in vitro to construct tissue engineered tendon, which repaired coracoclavicular ligament injury. After 6 months of operation, micro-tissue were sampled during the operation of removal of internal fixation, and morphological characteristics were examined by HE staining, DNA of tissues were extracted to examine D3S1754 and Cyar04 gene loci. RESULTS: The shoulder function of the patient was recovered well after operation, and no local or systemic immunological rejection were occurred. The electrophoresis typing showed 13/14 at D3S1754 and 8/9 at Cyar04 in the tissue of tissue engineered tendon, while the autogenous ligament were 13/13 and 8/8 at D3S1754 and Cyar04 loci respectively, which suggested that the tissue engineered tendon was survived in vivo. CONCLUSION: The examination of short tandem repeat loci is a better index to evaluate the survival situation of tissue engineered tissue after transplantation in clinical application.

Acromioclavicular Joint↗

PubMed1987

Some extrachromosomal circular DNAs from Drosophila embryos are homologous to tandemly repeated genes.

In Drosophila melanogaster embryos we have identified three classes of extrachromosomal circular DNA molecules homologous to the three main families of tandemly repeated genes, 5 S, rDNA and histone. 5 S genes are present in circular multimeric molecules containing up to 16 copies of the 375(+/- 7) base-pair repeated unit. Circular molecules homologous to rDNA are also multimeric molecules, which contain up to ten copies of the 240 base-pair tandemly repeated sequence of the non-transcribed spacer. The two major genomic classes of histone units (4800 and 5000 bases) are found only as monomeric circular molecules. No circular intermediate of the I transposable element was detected in embryos laid by F1 dysgenic females produced by the I-R system of hybrid dysgenesis. As far as we know, it is the first time that genes have been identified among extrachromosomal circular molecules independently of any specific amplification phenomenon.

Animals↗