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PubMed2006

[Fifteen short tandem repeat polymorphisms in Han race of North China].

OBJECTIVE: To research on the genetic polymorphism distributions of 15 short tandem repeat (STR) loci in Han race of North China and the genetic data of population genetics. METHODS: The capillary electrophoresis and five-color fluorescent multi-amplifying were applied to detect the genotypes of 15 STR loci in 597 unrelated Chinese Han individuals. RESULTS: No significant deviation from the Hardy-Weinberg Equilibrium was observed. High polymorphism was detected in the loci. Statistical analysis was carried out to obtain some parameters of forensic medicine. The heterozygosity of 15 loci was above 0.62. The values of discrimination power (DP) at 15 STRs ranged from 0.802 to 0.967. The values of excluding probability of paternity (EP) ranged from 0.320 to 0.697. The values of probability matching (Pm) ranged from 0.033 to 0.198. The fifteen loci showed an accumulated total discrimination power (TDP) more than 0.999999, a cumulative excluding probability of paternity (CEP) as 0.99999571, and total probability matching to be 8.93 x 10(-18). CONCLUSION: The data indicated that detecting combined 15 STRs is sensitive and reliable, and can be used to forensic and individual identification cases in Chinese group.

Asian People↗
PubMed1990

Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA.

As a model to examine the local distribution of sequence variation within large arrays of tandemly repeated DNA in complex genomes, the long-range organization of alpha-satellite DNA from human chromosome 17 was investigated. Three individual chromosomes, representing different alpha-satellite haplotypes, were segregated into mouse and human somatic cell hybrids and their arrays sized by pulse-field gel electrophoresis. An inventory of the higher-order repeat units found in multiple separate regions of these megabase arrays was obtained using cosmid mapping and two-dimensional gel electrophoresis, a technique that combines the large-scale resolution of pulsed-field gel electrophoresis with the small-scale resolution of conventional gel electrophoresis. These analyses show that alpha-satellite arrays are characterized by the presence of localized homogeneous domains containing only one distinct type of repeat unit. These domains, which consist of sequence variants and/or higher-order repeat length variants, can be up to at least several hundred thousands of bases in length. Both abundant and rare variant repeat units can be localized in these distinct domains, which may correspond to transition states in the evolution of tandem multicopy DNA families. This description of the organization of large arrays of tandem repeats provides insight into mechanisms involved in their homogenization.

Amino Acid Sequence↗
PubMed2003

The tandem-repeat polymorphism of the DC-SIGNR gene does not affect the susceptibility to HIV infection and the progression to AIDS.

DC-SIGNR is a C-type lectin that functions as a transreceptor for HIV-1. The exon 4 of the DC-SIGNR gene comprises a variable number of 69-bp tandem repeats, encoding for parts of the extracellular protein domain. Here, we analyzed the relevance of this gene polymorphism for the interindividual transmission of HIV-1 and the progression to AIDS. A cross-sectional comparison between HIV-1-infected patients (n = 391) and healthy volunteers (n = 134) did not reveal significant differences with regard to the DC-SIGNR allele distribution. Moreover, DC-SIGNR allele frequencies were similar in slowly progressing HIV patients (n = 31) and patients who rapidly progressed to AIDS (n = 46). Additionally, in a cohort of 149 newly HIV-infected patients, no relationship was found between HIV set point viremia and DC-SIGNR genotypes. Thus, the DC-SIGNR tandem-repeat polymorphism in exon 4 does not have a significant impact on the host's susceptibility to HIV and the clinical progression to AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed2000

Tandem repeat of a transcriptional enhancer upstream of the sterol 14alpha-demethylase gene (CYP51) in Penicillium digitatum.

We investigated the mechanism of resistance to demethylation inhibitors (DMI) in Penicillium digitatum by isolating the CYP51 gene, which encodes the target enzyme (P450(14DM)) of DMI, from three DMI-resistant and three DMI-sensitive strains. The structural genes of all six strains were identical, but in the promoter region, a unique 126-bp sequence was tandemly repeated five times in the DMI-resistant strains and was present only once in the DMI-sensitive strains. Constitutive expression of CYP51 in the resistant strains was about 100-fold higher than that in the sensitive strains. We introduced CYP51, including the promoter region, from a DMI-resistant strain into a DMI-sensitive strain, which rendered the transformants DMI resistant and increased CYP51 expression. We also found that if the number of copies of the repeat was reduced to two, resistance and CYP51 expression also decreased. These results indicate that the 126-bp unit acts as a transcriptional enhancer and that a tandem repeat of the unit enhances CYP51 expression, resulting in DMI resistance. This is a new fungicide resistance mechanism for filamentous fungi.

Base Sequence↗
PubMed2004

Tandem repeat hypothesis in imprinting: deletion of a conserved direct repeat element upstream of H19 has no effect on imprinting in the Igf2-H19 region.

Igf2 and H19 are reciprocally imprinted genes on mouse distal chromosome 7. They share several regulatory elements, including a differentially methylated region (DMR) upstream of H19 that is paternally methylated throughout development. The cis-acting sequence requirements for targeting DNA methylation to the DMR remain unknown; however, it has been suggested that direct tandem repeats near DMRs could be involved. Previous studies of the imprinted Rasgrf1 locus demonstrate indeed that a direct repeat element adjacent to a DMR is responsible for establishing paternal allele-specific methylation at the DMR and therefore allelic expression of the Rasgrf1 transcript. We identified a prominent and conserved direct tandem repeat 1 kb upstream of the H19 DMR and proposed that it played a similar role in imprinted regulation of H19. To test our hypothesis, we generated mice harboring a 1.7-kb targeted deletion of the direct repeat element and analyzed fetal growth, allelic expression, and methylation within the Igf2-H19 region. Surprisingly the deletion had no effect on imprinting. These results together with deletions of other repeats close to imprinted genes suggest that direct repeats may not be important for the targeting of methylation at the majority of imprinted loci and that the Rasgrf1 locus may be an exception to this rule.

Animals↗
PubMedDate not supplied

Comparing tandem repeats with duplications and excisions of variable degree.

Traditional sequence comparison by alignment employs a mutation model comprised of two events, substitutions and indels (insertions or deletions) of single positions. However, modern genetic analysis knows a variety of more complex mutation events (e.g., duplications, excisions, and rearrangements), especially regarding DNA. With ever more DNA sequence data becoming available, the need to accurately compare sequences which have clearly undergone more complicated types of mutational processes is becoming critical. Herein we introduce a new method for pairwise alignment and comparison of sequences with respect to the special evolution of tandem repeats: substitutions and indels of single positions and, additionally, duplications and excisions of variable degree (i.e., of one or more repeat copies simultaneously) are taken into account. To evaluate our method, we apply it to the spa VNTR (variable number of tandem repeats) cluster of Staphylococcus aureus, a bacterium of high medical importance.

Algorithms↗
PubMed2002

Evolution of heteroplasmy at a mitochondrial tandem repeat locus in cultured rabbit cells.

Surveys of animal mitochondrial DNA (mtDNA) polymorphism reveal that mtDNA length variation is common. Much of this variation involves non-coding tandem repeat arrays in the main control region of the molecule. Despite a high mutation rate, generating systematic individual mtDNA length heteroplasmy, the number of repeats in a tandem array is maintained within a narrow range in lagomorphs. To investigate the basis for this apparent paradox, we studied the evolution of mtDNA length polymorphism in several rabbit cell clones containing different proportions of mtDNA, with four or five 153-bp repeats. Our data show that equivalent amounts of two mtDNA molecular types are not stable (evolution towards a predominant type being the rule) and that other types remain represented, maintaining the length polymorphism. The data suggest that mtDNA molecules with a longer array of repeats have a replicative advantage that could depend on the nuclear background.

Animals↗
PubMed2004

A 210-kb segment of tandem repeats and retroelements located between imprinted subdomains of mouse distal chromosome 7.

Mammalian genes subject to genomic imprinting often form clusters and are regulated by long-range mechanisms. The distal imprinted domain of mouse chromosome 7 is orthologous to the Beckwith-Wiedemann syndrome domain in human chromosome 11p15.5 and contains at least 13 imprinted genes. This domain consists of two subdomains, which are respectively regulated by an imprinting center. We here report the finished-quality sequence of a 0.6-Mb region encompassing the more centromeric subdomain. The sequence contains four imprinted genes (Ascl2/Mash2, Ins2, Igf2 and H19) and reveals previously unidentified CpG islands and tandem repeats, which may be features of imprinted genes. Most interestingly, a unique 210-kb segment consisting almost exclusively of tandem repeats and retroelements is identified. This segment, located between Th and Ins2, has features of heterochromatin-forming DNA and is highly methylated at CpG sites. The segment exhibits asynchronous replication on the parental chromosomes, a feature of the imprinted domains. We propose that this repeat segment could serve either as a boundary between the two subdomains or as a target for epigenetic chromatin modifications that regulate imprinting.

Animals↗
PubMed2005

Polymorphism of tandem repeat in promoter of 5-lipoxygenase in ASA-intolerant asthma: a positive association with airway hyperresponsiveness.

BACKGROUND: 5-Lipooxygenase (ALOX5) and 5-lipoxygenase-activating protein (ALOX5AP) are known as key enzymes in cysteinyl-leukotriene (cys-LT) production, critical mediators in aspirin acetylsalicyclic acid (ASA)-intolerant asthma (AIA). To date, studies of the promoter region of ALOX5 gene has revealed the potential influence of a variable number of tandem repeats of a Sp1- and Egr1-binding motif, on the transcription rate. METHODS: To understand the pathological process that arises from cys-LT overproduction in AIA, we genotyped ALOX5 Sp1 and ALOX5AP poly(A) repeat promoter polymorphism by fluorescent-based capillary electrophoresis in the Korean population. RESULTS: No significant differences in allele and genotype frequencies of the ALOX5 and ALOX5AP promoter polymorphisms were observed between the three groups. However, there was a strong association of the ALOX5 Sp1 repeat polymorphism with airway hyperresponsiveness (AHR; PC20 methacholine); AIA patients carrying a mutant allele (n > 5 or n < 5 repeats) showed increased AHR compared to AIA patients with wild-type genotype (P=0.003). CONCLUSION: Although the alleles of the ALOX5 and ALOX5AP promoter cannot be considered as a prominent risk factor in the development of AIA, the genetic variant of tandem repeat (GGGCGG; Sp1-binding motif) in ALOX5 promoter is associated with the severity of airway hyperresponsiveness in AIA patients.

5-Lipoxygenase-Activating Proteins↗
PubMed2003

The thymidylate synthase tandem repeat polymorphism is not associated with homocysteine concentrations in healthy young subjects.

Thymidylate synthase (TYMS) and 5,10-methylenetetrahydrofolate reductase (MTHFR) may compete for their common cofactor 5,10-methylenetetrahyhdrofolate (5,10-meTHF). Limiting 5,10-meTHF results in elevated homocysteine, especially in individuals homozygous for the T allele of the MTHFR C677T polymorphism. The TYMS gene has a tandem repeat polymorphism (two repeats or three repeats, designated 2R or 3R, respectively), which may also affect homocysteine concentrations. The 3R allele is subject to increased translational efficiency in vitro and the 3R3R genotype is associated with both decreased serum folate and elevated plasma homocysteine (tHcy) in a population of Singapore Chinese. We assessed the relationship between TYMS genotype and key biochemical and genetic variables in a random sample of 392 healthy young Northwestern European men and women. The tHcy concentrations for 3R3R homozygotes (median 8.5 micromol/l) did not differ significantly from those for 2R2R homozygotes (median 8.7 micromol/l) or 2R3R heterozygotes (median 9.3 micromol/l) in the population as a whole (P=0.43), or in subsets of subjects with low serum folate (P=0.60) or the MTHFR 677TT genotype (P=0.90). Furthermore, there was no trend toward elevated tHcy in 3R3R homozygotes. Similarly, the TYMS tandem repeat polymorphism was not associated with serum folate concentrations. Our findings indicate that the TYMS 3R3R genotype is not a determinant of homocysteine in this sample of healthy young Caucasian adults from Northern Ireland.

Adult↗
PubMed2005

Combined laser-assisted microdissection and short tandem repeat analysis for detection of in situ microchimerism after solid organ transplantation.

Following the transplantation of a solid organ leukocytes of donor origin migrate out of the organ, contributing to a chimeric blood cell population ("peripheral microchimerism"). At the same time, leukocytes and pluripotent precursor cells of the recipient migrate into the organ, creating an "in situ microchimerism." A method is described for the identification of cells with the recipient's genotype in the transplanted organ by combining laser-assisted microdissection and short tandem repeat analysis. The microdissection allows the contamination-free isolation of morphologically and immunohistochemically characterized cells or groups of cells from histological tissue sections. The subsequent analysis of highly polymorphic short tandem repeats enables unequivocal genotyping in nearly all donor-recipient instances. Employing this new methodological approach, we could identify in individual transplanted organs differentiated parenchymal cells of recipient's origin, which most probably are derived from circulating precursor cells from the bone marrow.

Humans↗
PubMed2003

[Polymorphisms of six short tandem repeat loci in Zhejiang She ethnic population and Zhejiang Hans of China].

OBJECTIVE: To investigate genetic polymorphism of six short tandem repeat (STR) loci (D3S1358,D16S539, TH01,TPOX, CSF1PO,D7S820) in Zhejiang She ethnic population and Han population. METHODS: By use of AmpFlSTR Cofiler kit, 6 STR loci in 108 She samples and 102 Han samples were amplified. The PCR products were electrophoresed by ABI Prism 377 sequencer; the data were analyzed by Genescan software. RESULTS: All genotype frequencies of the 6 STR loci in She and Han ethnic groups met Hardy-Weinberg equilibrium. In the She population, the heterozygosities (H) in D3S1358,D16S539,TH01,TPOX, CSF1PO and D7S820 were 0.8028, 0.9148, 0.7522, 0.6728, 0.9123,0.8338, the exclusion of paternity(EP) were 0.4067, 0.6057, 0.4437, 0.3200, 0.5250, 0.5358, discrimination power (DP) were 0.6690, 0.7841, 0.6447, 0.5382, 0.7298, 0.7296.The combined DP, PE and polymorphism information content were 0.9991,0.9805,0.9988 respectively. There were significant differences at D3S1358, D16S539 and TPOX loci, compared with Hans. CONCLUSION: She population has its own STR allele distribution characteristic. The above data obtained from She population can be used not only in genetic researches and population investigation, but also in human identity and paternity testing.

China↗
PubMed2003

High-density map of short tandem repeats across the human major histocompatibility complex.

The human genome contains one short tandem repeat (STR) roughly every 2,000 base pairs. They are particularly useful markers for gene mapping and disease association studies due to their high degree of polymorphism and ubiquitous frequency throughout the genome. The major histocompatibility complex (MHC) has been the focus of many disease association studies, and the recent availability of the entire sequence of the complex has logarithmically expanded the density of potential markers for fine mapping disease loci. Here we present a complete assessment of the available STRs within a 3.8-Mb genomic segment encompassing the MHC. Of 443 potential STRs identified by computer analysis and tested for variation in a single sample containing pooled DNA from 36 individuals, 249 polymorphic STRs located throughout the complex were identified. The class of repeat (di-, tri-, etc.), precise nucleotide position, position relative to known genes, PCR conditions, and D6S numbers for the 249 polymorphic STRs are provided as a resource for selecting appropriate markers to use in future studies of MHC molecular genetics and disease association.

Base Sequence↗
PubMed2001

[Variability of short tandem repeats on the human Y chromosome].

Nine rare (biallelic) mutations and six short tandem repeats (STR) mapping to the nonrecombining portion of the Y chromosome were genotyped in 734 males from different geographical regions inhabited by the contemporary Armenian population. The analysis of molecular variance (AMOVA) showed that 48.9% of total STR genetic variation was explained by the differences between the haplogroups isolated based on biallelic polymorphism, whereas only 1.3% of genetic variation could be attributed to the differences between the geographic groups.

Armenia↗
PubMed2000

Tandem repeat of C/EBP binding sites mediates PPARgamma2 gene transcription in glucocorticoid-induced adipocyte differentiation.

Bone marrow stromal stem cells differentiate into many different types of cells including osteoblasts and adipocytes. Long-term glucocorticoid treatment decreases osteoblastic activity but increases adipocytes. We investigated the mechanism of glucocorticoid-induced PPARgamma2 transcription. Treatment of human bone marrow stromal cells with dexamethasone induced the differentiation of these cells into adipocytes as measured by oil-red O staining, and Northern blot analysis showed that dexamethasone strongly induced PPARgamma2 mRNA expression in cells cultured in adipocyte induction medium. Moreover, the mRNA of C/EBPdelta, an adipocyte-promoting transcription factor, was also induced by dexamethasone in the presence of induction medium. Gel mobility shift assays using purified GST-C/EBPdelta fusion protein showed that C/EBPdelta specifically binds to a 40-base pair DNA element from PPARgamma2 promoter, which was found to contain a tandem repeat of C/EBP binding sites. Transfection studies in mouse mesenchymal C3H10T1/2 cells showed that it is the tandem repeat of the C/EBP binding site in PPARgamma2 promoter region that regulates dexamethasone-mediated PPARgamma2 gene activation. We conclude that glucocorticoid-induced adipogenesis from bone marrow stromal cells is mediated through a reaction cascade in which dexamethasone transcriptionally activates C/EBPdelta; C/EBPdelta then binds to PPARgamma2 promoter and transactivates PPARgamma2 gene expression. This activated master regulator, in turn, initiates the adipocyte differentiation.

Adipocytes↗
PubMed2004

Comparative genetics of functional trinucleotide tandem repeats in humans and apes.

Several human neurodegenerative disorders are caused by the expansion of polymorphic trinucleotide repeat regions. Many of these loci are functional short tandem repeats (STRs) located in brain-expressed genes, and their study is thus relevant from both a medical and an evolutionary point of view. The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion (therefore, an insight into evolutionary medicine) and to unravel whether any human-specific feature may be identified in brain-expressed genes involved in human disease. We analyzed the variability of the normal range of seven expanding STR CAG/CTG loci (SCA1, SCA2, SCA3-MJD, SCA6, SCA8, SCA12, and DRPLA) and two nonexpanding polymorphic CAG loci (KCNN3 and NCOA3) in humans, chimpanzees, gorillas, and orangutans. The study showed a general conservation of the repetitive tract and of the polymorphism in the four species and high heterogeneity among loci distributions. Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest variance, although only for the expanding loci, suggesting a relationship between variability levels and expansion potential. The sequence analysis shows high levels of sequence conservation among species, a lack of correspondence between interruption patterns and variability levels, and signs of conservative selective pressure for some of the STR loci. Only two loci (SCA1 and SCA8) show a human specific distribution, with larger alleles than the rest of species. This could account, at the same time, for a human-specific trait and a predisposition to disease through expansion.

Analysis of Variance↗
PubMed1982

A tandem repeat gene in a picornavirus.

Three closely related genes for the small genome-linked protein (VPg) of picornaviruses have been identified by sequence analysis as a tandem repeat in the genome of Foot and Mouth Disease Virus (FMDV), strain O1K. This unusual structure was also found in the genome of strain C1O, belonging to a different FMDV serotype. Predicted biochemical properties of the three VPg gene products are in excellent agreement with the data from protein analysis of a heterogeneous VPg population from a third FMDV serotype, strain A10 (1). Taken together, these data indicate that the VPgs from all three genes function equally well in vivo. This is the first report of a tandem repeat gene in a viral genome.

Amino Acid Sequence↗
PubMed2004

Short tandem repeat polymorphism and cancer risk: influence of laboratory analysis on epidemiologic findings.

Short tandem repeats (STR) are common polymorphisms in the genome. The length of STR may influence gene transcription, exhibiting diverse phenotypes. Two STRs, one trinucleotide repeats in the androgen receptor (AR) gene and one dinucleotide repeats in the insulin-like growth factor-I (IGF-I) gene, have been studied for their role in cancer, and the results are conflicting. Although there are many reasons for inconsistent findings, laboratory issues are often overlooked. DNA sizing analysis is regularly used to determine the length of STR, but its analytic validity has not been evaluated in epidemiologic studies. To examine if sizing analysis can reliably determine dinucleotide STR, we compared the method with direct DNA sequencing in analyzing CA repeats in the IGF-I gene in a small case-control study. The study enrolled 75 breast cancer cases and 75 age- and race-matched controls. DNA was extracted from buffy coats and was analyzed for CA repeats by both DNA sizing and direct sequencing. Our comparison indicated that these methods detected the same number of repeats in the short allele but not in the long allele. There was a substantial discrepancy between the methods in determining homozygous alleles. Although the two methods showed <10% of samples having an exact match on the number of repeats in both alleles, both techniques were able to detect a genotype-phenotype correlation and a racial disparity in the genotype. An association between breast cancer risk and IGF-I genotype was found in sequencing analysis but not in sizing analysis. Overall, the comparison suggests that laboratory analysis of dinucleotide STR may not be as reliable as originally thought. This unreliability in STR analysis may result in inconsistent study findings.

Adult↗