SEARCH · PubMed Health

Results for “Tandem repeats”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2006

Two-step recruitment of RNA-directed DNA methylation to tandem repeats.

Tandem repeat sequences are frequently associated with gene silencing phenomena. The Arabidopsis thaliana FWA gene contains two tandem repeats and is an efficient target for RNA-directed de novo DNA methylation when it is transformed into plants. We showed that the FWA tandem repeats are necessary and sufficient for de novo DNA methylation and that repeated character rather than intrinsic sequence is likely important. Endogenous FWA can adopt either of two stable epigenetic states: methylated and silenced or unmethylated and active. Surprisingly, we found small interfering RNAs (siRNAs) associated with FWA in both states. Despite this, only the methylated form of endogenous FWA could recruit further RNA-directed DNA methylation or cause efficient de novo methylation of transgenic FWA. This suggests that RNA-directed DNA methylation occurs in two steps: first, the initial recruitment of the siRNA-producing machinery, and second, siRNA-directed DNA methylation either in cis or in trans. The efficiency of this second step varies depending on the nature of the siRNA-producing locus, and at some loci, it may require pre-existing chromatin modifications such as DNA methylation itself. Enhancement of RNA-directed DNA methylation by pre-existing DNA methylation could create a self-reinforcing system to enhance the stability of silencing. Tandem repeats throughout the Arabidopsis genome produce siRNAs, suggesting that repeat acquisition may be a general mechanism for the evolution of gene silencing.

Arabidopsis↗

PubMed2005

Evaluating distance functions for clustering tandem repeats.

Tandem repeats are an important class of DNA repeats and much research has focused on their efficient identification, their use in DNA typing and fingerprinting, and their causative role in trinucleotide repeat diseases such as Huntington Disease, myotonic dystrophy, and Fragile-X mental retardation. We are interested in clustering tandem repeats into groups or families based on sequence similarity so that their biological importance may be further explored. To cluster tandem repeats we need a notion of pairwise distance which we obtain by alignment. In this paper we evaluate five distance functions used to produce those alignments--Consensus, Euclidean, Jensen-Shannon Divergence, Entropy-Surface, and Entropy-weighted. It is important to analyze and compare these functions because the choice of distance metric forms the core of any clustering algorithm. We employ a novel method to compare alignments and thereby compare the distance functions themselves. We rank the distance functions based on the cluster validation techniques--Average Cluster Density and Average Silhouette Width. Finally, we propose a multi-phase clustering method which produces good-quality clusters. In this study, we analyze clusters of tandem repeats from five sequences: Human Chromosomes 3, 5, 10 and X and C. elegans Chromosome III.

Algorithms↗

PubMed2003

Maintenance of heterochromatin by RNA interference of tandem repeats.

Tandem repeats are prone to epigenetic silencing regulated by RNA interference. This may be because siRNAs from tandem array transcripts are regenerated by RNA-dependent RNA polymerase (RdRP) and Dicer, but siRNAs from single-copy sequences are exhausted by sequential use of downstream primers by RdRP. This could account for the formation of heterochromatin from tandem repeats.

Heterochromatin↗

PubMed1991

DNA typing and genetic mapping with trimeric and tetrameric tandem repeats.

Tandemly reiterated sequences represent a rich source of highly polymorphic markers for genetic linkage, mapping, and personal identification. Human trimeric and tetrameric short tandem repeats (STRs) were studied for informativeness, frequency, distribution, and suitability for DNA typing and genetic mapping. The STRs were highly polymorphic and inherited stably. A STR-based multiplex PCR for personal identification is described. It features fluorescent detection of amplified products on sequencing gels, specific allele identification, simultaneous detection of independent loci, and internal size standards. Variation in allele frequencies were explored for four U.S. populations. The three STR loci (chromosomes 4, 11, and X) used in the fluorescent multiplex PCR have a combined average individualization potential of 1/500 individuals. STR loci appear common, being found every 300-500 kb on the X chromosome. The combined frequency of polymorphic trimeric and tetrameric STRs could be as high as 1 locus/20 kb. The markers should be useful for genetic mapping, as they are sequence based, and can be multiplexed with the PCR. A method enabling rapid localization of STRs and determination of their flanking DNA sequences was developed, thus simplifying the identification of polymorphic STR loci. The ease by which STRs may be identified, as well as their genetic and physical mapping utility, give them the properties of useful sequence tagged sites (STSs) for the human genome initiative.

Asian People↗

PubMed2005

Comparison of variable number tandem repeat and short tandem repeat genetic markers for qualitative and quantitative chimerism analysis post allogeneic stem cell transplantation.

BACKGROUND: Analysis of donor chimerism has become a routine procedure for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation. Quantitative analysis of chimerism kinetics has been shown to predict graft failure or relapse. In this study, we compared the use of variable number tandem repeats (VNTR) and short tandem repeats (STR) as polymorphic genetic markers in chimerism analysis. This study included qualitative and quantitative assessment of both techniques to assess informative yield and sensitivity. PATIENTS AND METHODS: We analyzed 206 samples representing 40 transplant recipients and their HLA-identical sibling donors. A panel of six VNTR loci, 15 STR loci and 1 sex chromosome locus was used. Amplified VNTR products were visualized in an ethidium bromide-stained gel. STR loci were amplified using fluorescent primers, and the products were analyzed by capillary electrophoresis. RESULTS: VNTR and STR analysis gave comparable qualitative results in the majority of cases. The incidence of mixed chimerism (MC) by STR analysis was 45% compared to 32% in cases evaluated by VNTR analysis. STR markers were more informative; several informative loci could be identified in all patients. Unique alleles for both patient and donor could be identified in all patients by STR versus 32/40 by VNTR analysis. The STR markers were also more sensitive in the detection of chimerism. The size of VNTR alleles and differences between the size of donor and recipient VNTR alleles affected the sensitivity of detection. With both techniques, quantitative assessment of chimerism showed some discrepancies between the estimated and the calculated percentage of donor DNA. Discordance between the two estimates was observed in 8/19 patients with MC. However, sequential monitoring of the relative band intensity of VNTR alleles offered some insight into the direction of change in engraftment over time. CONCLUSION: The higher yield of informative loci with STR and the automated measurement of amplified STR 103 products offered the advantages of more rapid and accurate quantitative assessment of chimerism. The choice between these two techniques depends on the need for quantitative or qualitative information, the availability of equipment, and the cost.

Chimerism↗

PubMed2002

Comparison of short tandem repeat and variable number tandem repeat genetic markers for quantitative determination of allogeneic bone marrow transplant engraftment.

Variable number tandem repeats (VNTRs) were among the first genetic markers used to quantitate bone marrow transplant engraftment. The limitations of PCR-based VNTR markers in distinguishing some donor/recipient pairs has shown the need for additional genetic markers to analyze engraftment. Short tandem repeats (STRs) provide an excellent tool for this purpose because of their high degree of polymorphism and relatively short length. We compared STR analysis results with previous VNTR results for 16 post-transplantation samples from four allogeneic bone marrow transplant patients. Previously analyzed patient samples were chosen to cover the full range of engraftment. DNA samples from each patient were analyzed in a blinded fashion. Good quantitative correlation was found between STR and VNTR results in samples from all four patients. STR markers were informative in one patient for whom PCR-based VNTR markers were not available. Correlation of VNTR and STR methods helps to validate the use of STRs for the quantitative analysis of bone marrow transplant engraftment. This study demonstrates that STR-based human identity testing kits are well suited for engraftment analysis.

Bone Marrow Transplantation↗

PubMed2006

Ten tandem repeats of beta-hCG 109-118 enhance immunogenicity and anti-tumor effects of beta-hCG C-terminal peptide carried by mycobacterial heat-shock protein HSP65.

The beta-subunit of human chorionic gonadotropin (beta-hCG) is secreted by many kinds of tumors and it has been used as an ideal target antigen to develop vaccines against tumors. In view of the low immunogenicity of this self-peptide,we designed a method based on isocaudamer technique to repeat tandemly the 10-residue sequence X of beta-hCG (109-118), then 10 tandemly repeated copies of the 10-residue sequence combined with beta-hCG C-terminal 37 peptides were fused to mycobacterial heat-shock protein 65 to construct a fusion protein HSP65-X10-betahCGCTP37 as an immunogen. In this study, we examined the effect of the tandem repeats of this 10-residue sequence in eliciting an immune by comparing the immunogenicity and anti-tumor effects of the two immunogens, HSP65-X10-betahCGCTP37 and HSP65-betahCGCTP37 (without the 10 tandem repeats). Immunization of mice with the fusion protein HSP65-X10-betahCGCTP37 elicited much higher levels of specific anti-beta-hCG antibodies and more effectively inhibited the growth of Lewis lung carcinoma (LLC) in vivo than with HSP65-betahCGCTP37, which should suggest that HSP65-X10-betahCGCTP37 may be an effective protein vaccine for the treatment of beta-hCG-dependent tumors and multiple tandem repeats of a certain epitope are an efficient method to overcome the low immunogenicity of self-peptide antigens.

Amino Acid Sequence↗

PubMed2006

Tools for the identification of variable and potentially variable tandem repeats.

BACKGROUND: Tandem repeat arrays showing variation between sequences within a population, between strains or across species may have functional effects. The increasing availability of genomic sequence data makes routine description of observed variation possible, creating a need for tools to describe such variability. RESULTS: We present a set of programs that facilitate the identification of tandem repeats showing variation across multiple sequences or genomes, and the prediction of potentially polymorphic tandem repeats. The VNTRfinder (Variable Number of Tandem Repeats finder) program enables the detection of sequence length variation between arrays of inter-specific or intra-specific tandem repeats. In the absence of comparable sequences to explore observed variation, predictions are provided describing which tandem repeats are more likely to be variable, to help guide and focus further experimental evaluation. CONCLUSION: These tools represent a resource for researchers interested in tandem repeats in nucleotide sequences that are most likely to be of clinical and evolutionary interest. The tools are available at http://bioinformatics.rcsi.ie/vntrfinder/. Downloadable versions for UNIX/LINUX and WINDOWS which permit the consideration of longer and more numerous sequences are also available.

Algorithms↗

PubMed1996

Allele frequency distributions at several variable number of tandem repeat (VNTR) and short tandem repeat (STR) loci in a restricted Caucasian population from south Italy and their evaluation for paternity and forensic use.

Allele frequencies at six VNTR loci, 11 STR loci, and at the HLA-DQA1 locus were evaluated in a well-defined population from Campania (South Italy). The allele frequencies of three VNTR loci, 11 STR loci, and the HLA-DQA1 locus were compared with data obtained from a general Caucasian reference population in the USA. The aim of this study was to determine the power of each single locus and group of loci for forensic and paternity testing purposes. Significant differences between the allele frequencies of the two populations were found in two VNTR loci, four STR loci and in the HLA-DQA1 locus. The two populations were in Hardy-Weinberg equilibrium for the STR loci, but as expected, not for some VNTR loci. It was also found that: (i) the discriminatory power of two STR systems (nine and 11 loci, respectively) is similar in the two populations analysed; and (ii) that the allele frequencies for the STR systems of a large reference population can always be applied to subjects of a small subpopulation. In conclusion, for forensic purposes and for paternity testing, most of the 11 STR loci examined can be analysed using allele frequencies from a general Caucasian reference population without typing subpopulations, whereas the VNTR loci must be subtyped.

Adult↗

PubMed1995

Genetic typing with HUMTH01, HUMVWA31A and HUMFES/FPS short tandem repeat loci, D1S80 variable number tandem repeat locus and HLA-DQ alpha of recent and from XII-XIII centuries spongy bone.

The genetic analysis of ancient populations through DNA from bone remains, requires use of short sized loci that can be amplified by polymerase chain reaction (PCR) for which the short tandem repeat (STR) loci are most suitable. These techniques can also be applied to genetic identification in forensic casework. In this study three STR loci, HUMFES/FPS, HUMTH01, and HUMVWA31A, were selected to estimate their usefulness when applied to recent and ancient spongy bone DNA typing. In addition, loci D1S80 and HLA DQ alpha were also tested in the analysis of recent spongy bone DNA. The recent remains studied were constituted by ten spongy bone samples of postmortem material from one individual buried for 1 year. The ancient remains are composed by 8 spongy bone samples from the heads of left femurs from a XII-XIII Centuries Basque Country population. Adequate amplification and typing results could only be obtained with cetyltrimethyl ammonium bromide (CTAB)-extracted DNA, without any further purification after precipitation. Genotypes of the one year post-mortem material and those of his son and his wife were obtained at the D1S80, HLA-DQ alpha, and STR loci. In all these systems, no exclusion was observed, with a combined probability of paternity of 0.9997. This demonstrates the reliability of the obtained results. The genetic typing of HUMTH01 in spongy bone from the XII-XIII Centuries Basque Country individuals was also performed. This will allow the genetic analysis of ancient bone remains and therefore, to carry out evolutionary population studies.

Base Sequence↗

PubMed1994

High sensitive DNA typing approaches for the analysis of forensic evidence: comparison of nested variable number of tandem repeats (VNTR) amplification and a short tandem repeats (STR) polymorphism.

The approach of using nested primers for the APO B variable number of tandem repeats (VNTR) increases the sensitivity of the polymerase chain reaction (PCR) to single cell level. Different experiments and a comparison to the short tandem repeats (STR) system VWA were carried out, to determine the applicability of this method to forensic samples. Nested amplification of the Apo B VNTR was affected by a strong tendency towards preferential amplification of the shorter alleles. This phenomenon was observed for DNA quantities as low as 100 pg and impaired, depending on the allele length, the results for mixed samples. As expected, VWA polymorphism showed less preferential amplification. The high sensitivity of both PCR systems is accompanied by an increased susceptibility to contamination. Using artificially contaminated bloodstains, the bloodstain genotype, the contamination or both genotypes could be found on one piece of evidence. Here a single analysis can lead to an incorrect result. Therefore a strategy for obtaining reliable results should consist of multiple stain extractions and the amplification of different stepped dilutions of the DNA solution.

Base Sequence↗

PubMed2000

Comparison of automated short tandem repeat and manual variable number of tandem repeat analysis of chimerism in bone marrow transplant patients.

Hematopoietic chimerism can be monitored in bone marrow transplant patients at DNA polymorphic sites. In this study, allele detection and quantification by ethidium bromide-stained agarose gels were compared with automated fluorescent sizing on an artificially mixed system and on chimeric post-transplant whole blood and sorted cell populations. A panel of five variable number of tandem repeats (VNTRs) were amplified and quantified visually on an ethidium bromide-stained gel. The ten short tandem repeats (STRs) were amplified as a multiplex polymerase chain reaction (PCR) and fluorescently detected on a DNA sequencer. Fluorescent band intensities were converted to fluorescent peak areas for allele quantification. Using mixed DNA of different proportions, both STRs and VNTRs showed linearity and appeared equally sensitive. However, case studies showed STRs to be more sensitive (<5%) than VNTRs (<10%). The STRs more accurately quantified the minor DNA component at low concentrations.

Alleles↗

PubMed2006

TRDB--the Tandem Repeats Database.

Tandem repeats in DNA have been under intensive study for many years, first, as a consequence of their usefulness as genomic markers and DNA fingerprints and more recently as their role in human disease and regulatory processes has become apparent. The Tandem Repeats Database (TRDB) is a public repository of information on tandem repeats in genomic DNA. It contains a variety of tools for repeat analysis, including the Tandem Repeats Finder program, query and filtering capabilities, repeat clustering, polymorphism prediction, PCR primer selection, data visualization and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench. It provides user storage space and permits collaborators to privately share their data and analysis. TRDB is available at https://tandem.bu.edu/cgi-bin/trdb/trdb.exe.

Animals↗

PubMed2003

Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii).

Alligators and Crocodiles↗

PubMed2002

Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats.

A procedure utilizing Chelex 100, chelating resin, was adapted to extract DNA from dental pulp. The procedure was simple and rapid, involved no organic solvents, and did not require multiple tube transfers. The extraction of DNA from dental pulp using this method was as efficient, or more so, than using proteinase K and phenol-chloroform extraction. In this study, the Chelex method was used with amplification and typing at Y-chromosomal loci to determine the effects of temperature on the sex determination of the teeth. The extracted teeth were incinerated in a dental furnace for 2 minutes at 100 degrees C, 200 degrees C, 300 degrees C, 400 degrees C, and 500 degrees C. After the isolation of DNA from the dental pulp by the Chelex method, alphoid repeats, and short tandem repeats, the human Y chromosome (DYZ3), DYS19, SYS389, DYS390, and DYS393 could be amplified and typed in all samples incinerated at up to 300 degrees C for 2 minutes. The DYS389 locus in some samples could not be amplified at 300 degrees C for 2 minutes. An autopsy case is described in which genotypings of DYS19, DYS390, and DYS393 from dental pulp obtained from a burned body were needed. The data presented in this report suggest that Chelex 100-based DNA extraction, amplification, and typing are possible in burned teeth in forensic autopsy cases.

Chelating Agents↗

PubMed2002

Independently regulated neocentromere activity of two classes of tandem repeat arrays.

Tandem repeat arrays often are found in interstitial (i.e., normally gene-rich) regions on chromosomes. In maize, genes on abnormal chromosome 10 induce the tandem repeats that make up knobs to move poleward on the meiotic spindle. This so-called neocentromere activity results in the preferential recovery, or meiotic drive, of the knobs in progeny. Here we show that two classes of repeats differ in their capacity to form neocentromeres and that their motility is controlled in trans by at least two repeat-specific activators. Microtubule dynamics appear to contribute little to the movement of neocentromeres (they are active in the presence of taxol), suggesting that the mechanism of motility involves microtubule-based motors. These data suggest that maize knob repeats and their binding proteins have coevolved to ensure their preferential recovery in progeny. Neocentromere-mediated drive provides a plausible mechanism for the evolution and maintenance of repeat arrays that occur in interstitial positions.

Carrier Proteins↗

PubMed1997

United States population data on the multiplex short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--and the variable number tandem repeat locus D1S80.

Allele frequencies for three tetrameric short tandem repeat (STR) loci HUMTHO1, TPOX, and CSF1PO and a variable number tandem repeat locus D1S80 were determined in United States Caucasian, African American, and Hispanic sample populations. All loci, except the TPOX locus in the Caucasian sample population, meet Hardy-Weinberg expectations. There is no evidence for association of alleles among the four loci. The allelic frequency data are similar to other comparable data within the same major population group.

Black People↗

PubMed2006

The exact joint distribution of the sum of heads and apparent size statistics of a "tandem repeats finder" algorithm.

Tandem repeats play many important roles in biological research. However, accurate characterization of their properties is limited by the inability to easily detect them. For this reason, much work has been devoted to developing detection algorithms. A widely used algorithm for detecting tandem repeats is the "tandem repeats finder'' (Benson, G., Nucleic Acids Res. 27, 573-580, 1999). In that algorithm, tandem repeats are modeled by percent matches and frequency of indels between adjacent pattern copies, and statistical criteria are used to recognize them. We give a method for computing the exact joint distribution of a pair of statistics that are used in the testing procedures of the "tandem repeats finder'': the total number of matches in matching tuples of length k or longer, and the total number of observations from the beginning of the first such matching tuple to the end of the last one. This allows the computation of the conditional distribution of the latter statistic given the former, a conditional distribution that is used to test for tandem repeats as opposed to non-tandem direct repeats. The setting is a Markovian sequence of a general order. Current approaches to this distributional problem deal only with independent trials and are based on approximations via simulation.

Algorithms↗