Genomes and Genes
Summary: The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.
- Kunnas T, Lehtimaki T, Karhunen P, Laaksonen R, Janatuinen T, Vesalainen R, et al. Estrogen receptor genotype modulates myocardial perfusion in young men. J Mol Med (Berl). 2004;82:821-5 pubmed..Our results suggest that adenosine-stimulated myocardial perfusion is lower in subjects with ESR1 long alleles than the other TA repeat genotypes. ..
- Salaun L, Linz B, Suerbaum S, Saunders N. The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori. Microbiology. 2004;150:817-30 pubmed..putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Here a comparative analysis of the two genomes is reported and an updated and expanded list of 46 ..
- Duhagon M, Smircich P, Forteza D, Naya H, Williams N, Garat B. Comparative genomic analysis of dinucleotide repeats in Tritryps. Gene. 2011;487:29-37 pubmed publisher..Thus, we perform a comparative analysis of the occurrence, length and location of dinucleotide repeats (DRs) in the Tritryp genomes and their putative associations with known biological processes...
- Chung U, Lee H, Yoo J, Park M, Shin K. Mitochondrial DNA CA dinucleotide repeats in Koreans: the presence of length heteroplasmy. Int J Legal Med. 2005;119:50-3 pubmedThe mitochondrial DNA HV3 region contains CA dinucleotide repeats which display length polymorphism...
- Ng T, Lam C, Lam D, Chiang S, Tam P, Wang D, et al. AC and AG dinucleotide repeats in the PAX6 P1 promoter are associated with high myopia. Mol Vis. 2009;15:2239-48 pubmed..No sequence alterations in the coding or splicing regions showed an association with high myopia. Two dinucleotide repeats, (AC)(m) and (AG)(n), in the P1 promoter region were found to be highly polymorphic and significantly ..
- Hui J, Hung L, Heiner M, Schreiner S, Neumüller N, Reither G, et al. Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing. EMBO J. 2005;24:1988-98 pubmed..HnRNP L was detected specifically bound to these diverse CA elements. These data demonstrated that intronic CA sequences constitute novel and widespread regulatory elements of alternative splicing. ..
- Cuadrado A, Cardoso M, Jouve N. Physical organisation of simple sequence repeats (SSRs) in Triticeae: structural, functional and evolutionary implications. Cytogenet Genome Res. 2008;120:210-9 pubmed publisher..The importance of SSRs in plant breeding and their possible role in chromosome structure, function and evolution is discussed. ..
- Sharma V, Kumar N, Brahmachari S, Ramachandran S. Abundance of dinucleotide repeats and gene expression are inversely correlated: a role for gene function in addition to intron length. Physiol Genomics. 2007;31:96-103 pubmed..which are negative cis modulators of transcription, and transcriptional levels and other commonly occurring dinucleotide repeats, is required...
- McNeil J, Smith K, Hall L, Lawrence J. Word frequency analysis reveals enrichment of dinucleotide repeats on the human X chromosome and [GATA]n in the X escape region. Genome Res. 2006;16:477-84 pubmed..Results identify previously unknown sequence differences on the human X chromosome. Notably, the dinucleotide repeats [AT]n, [AC]n, and [AG]n are significantly enriched across the X chromosome compared with autosomes...
- Schlotterer C, Ritter R, Harr B, Brem G. High mutation rate of a long microsatellite allele in Drosophila melanogaster provides evidence for allele-specific mutation rates. Mol Biol Evol. 1998;15:1269-74 pubmed..This hypermutable allele has 28 dinucleotide repeats and is among the longest microsatellite reported in D. melanogaster. The allele-specific mutation rate of 3...
- Schug M, Hutter C, Wetterstrand K, Gaudette M, Mackay T, Aquadro C. The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol Biol Evol. 1998;15:1751-60 pubmed..Our estimate of mutation rate for a total of 49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only slightly higher than the estimate from our earlier study...
- Lerat E, Capy P, Biémont C. The relative abundance of dinucleotides in transposable elements in five species. Mol Biol Evol. 2002;19:964-7 pubmed
- Boyer J, Yamada N, Roques C, Hatch S, Riess K, Farber R. Sequence dependent instability of mononucleotide microsatellites in cultured mismatch repair proficient and deficient mammalian cells. Hum Mol Genet. 2002;11:707-13 pubmed..This observation implies that the replication fidelity is lower in G(17) repeats. ..
- Yamada N, Smith G, Castro A, Roques C, Boyer J, Farber R. Relative rates of insertion and deletion mutations in dinucleotide repeats of various lengths in mismatch repair proficient mouse and mismatch repair deficient human cells. Mutat Res. 2002;499:213-25 pubmed..Results of these direct studies on microsatellite mutations in cultured cells should be useful for refinement of mathematical models for microsatellite evolution. ..
- Borstnik B, Pumpernik D. Tandem repeats in protein coding regions of primate genes. Genome Res. 2002;12:909-15 pubmed..The trinucleotide repeats cover slightly more than 0.3% of the protein coding regions of genes. ..
- Bachtrog D, Agis M, Imhof M, Schlotterer C. Microsatellite variability differs between dinucleotide repeat motifs-evidence from Drosophila melanogaster. Mol Biol Evol. 2000;17:1277-85 pubmed..Similar differences in mutation rates were obtained by an alternative method which estimates microsatellite mutation rates from their genomic length distribution. ..
- Ikeda Y, Oda S, Abe T, Ohno S, Maehara Y, Sugimachi K. Features of microsatellite instability in colorectal cancer: comparison between colon and rectum. Oncology. 2001;61:168-74 pubmed..In the rectum, there was no tumour with the type B/MSI-H phenotype. These findings suggest that cancers occurring in the colon and the rectum have a differential molecular background for carcinogenesis. ..
- Kunnas T, Holmberg Marttila D, Karhunen P. Analysis of estrogen receptor dinucleotide polymorphism by capillary gel electrophoresis with a population genetic study in 180 Finns. Hum Hered. 1999;49:142-5 pubmedWe developed a suitable method for analysing dinucleotide repeats found in the upstream of human alpha-estrogen receptor (ER) gene by applying capillary electrophoresis and automatic analysis...
- Ellegren H. Heterogeneous mutation processes in human microsatellite DNA sequences. Nat Genet. 2000;24:400-2 pubmed..Expansions are more common than contractions among dinucleotide repeats, whereas no such trend is evident among tetranucleotide repeats...
- Toth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000;10:967-81 pubmed..Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed. ..
- Eckert K, Yan G. Mutational analyses of dinucleotide and tetranucleotide microsatellites in Escherichia coli: influence of sequence on expansion mutagenesis. Nucleic Acids Res. 2000;28:2831-8 pubmed..We suggest alternative models for the production of expansion mutations during lagging strand replication of the [TTCC/AAGG](9) microsatellite. ..
- Agarwal A, Giacchetti G, Lavery G, Nikkila H, Palermo M, Ricketts M, et al. CA-Repeat polymorphism in intron 1 of HSD11B2 : effects on gene expression and salt sensitivity. Hypertension. 2000;36:187-94 pubmed..We conclude that polymorphisms in HSD11B2 and decreased 11-HSD2 activity are associated with sensitivity to sodium loading, but a functional explanation for these associations remains to be elucidated. ..
- Majewski J, Ott J. GT repeats are associated with recombination on human chromosome 22. Genome Res. 2000;10:1108-14 pubmed..We show significant correlation between long tandem GT repeats, which are known to form Z-DNA and interact with several components of the recombination machinery, and recombination hot spots on human chromosome 22. ..
- Gabellini N. A polymorphic GT repeat from the human cardiac Na+Ca2+ exchanger intron 2 activates splicing. Eur J Biochem. 2001;268:1076-83 pubmed
- Katti M, Ranjekar P, Gupta V. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol. 2001;18:1161-7 pubmed..The locations and sequences of all of the repeat loci detected in genome sequences and coding DNA sequences are available at http://www.ncl-india.org/ssr and could be useful for further studies. ..
- Máximo V, Soares P, Seruca R, Rocha A, Castro P, Sobrinho Simoes M. Microsatellite instability, mitochondrial DNA large deletions, and mitochondrial DNA mutations in gastric carcinoma. Genes Chromosomes Cancer. 2001;32:136-43 pubmed..The latter finding--almost no gastric carcinoma with MSI-positive phenotype has large deletions of mtDNA--needs to be confirmed in a larger series and in tumors from other organs. ..
- Neff B, Gross M. Microsatellite evolution in vertebrates: inference from AC dinucleotide repeats. Evolution. 2001;55:1717-33 pubmed..Finally, published microsatellite loci (isolated using conventional hybridization methods) provide a biased estimate of the actual mean repeat length of microsatellites in the genome. ..
- Cuadrado A, Jouve N. Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster. BMC Genomics. 2011;12:205 pubmed publisher..The greater representation of certain SSRs in D. melanogaster heterochromatin suggests that its complexity may be greater than previously thought. ..
- Salih F, Salih B, Kogan S, Trifonov E. Epigenetic nucleosomes: Alu sequences and CG as nucleosome positioning element. J Biomol Struct Dyn. 2008;26:9-16 pubmed..Thus, Alu sequences may harbor special epigenetic nucleosomes with methylation-dependent regulatory functions. Nucleosome DNA sequence probe is suggested to detect locations of such regulatory nucleosomes in the sequences. ..
- Wu Q, Zhou W, Wang J, Yan H. Correlation between the flexibility and periodic dinucleotide patterns in yeast nucleosomal DNA sequences. J Theor Biol. 2011;284:92-8 pubmed publisher..7438 and the lowest correlation is shown by AA/TT with a value of -0.7424. The source codes and data sets are available for downloading on http://www.hy8.com/bioinformatics.htm. ..
- Jiang C, Yuan Y, Liu G, Huang L, Wang X, Yu J, et al. [EST-SSR identification of Lonicera japonica Thunb]. Yao Xue Xue Bao. 2012;47:803-10 pubmed..japonica samples in 13 out of 15 SSR markers tested. The polymorphism in L. japonica, L. japonica var. chinensis and other honeysuckles could be distinguished by three markers (jp.ssr4, jp.ssr64 and jp.ssr65) tested...
- Algire M, Montague M, Vashee S, Lartigue C, Merryman C. A Type III restriction-modification system in Mycoplasma mycoides subsp. capri. Open Biol. 2012;2:120115 pubmed publisher..The coding region of the methyltransferase gene contains 12 consecutive AG dinucleotide repeats that result in a translational termination at a TAA codon immediately beyond the repeat region...
- Pastro L, Smircich P, Pérez Díaz L, Duhagon M, Garat B. Implication of CA repeated tracts on post-transcriptional regulation in Trypanosoma cruzi. Exp Parasitol. 2013;134:511-8 pubmed publisher..Altogether, these results suggest the involvement of polyCA as a signal in gene expression regulation in T. cruzi. ..
- Mandell K, Vallone P, Owczarzy R, Riccelli P, Benight A. Studies of DNA dumbbells VIII. Melting analysis of DNA dumbbells with dinucleotide repeat stem sequences. Biopolymers. 2006;82:199-221 pubmed..These represent the minimal set of 10 possible dinucleotide repeats. To study effects of dinucleotide repeat length, dumbbells with the central sequences (AG)(n), n = 5 and 20,..
- Ashworth J, Smyth J, Pendleton N, Horan M, Payton A, Worthington J, et al. The dinucleotide (CA) repeat polymorphism of estrogen receptor beta but not the dinucleotide (TA) repeat polymorphism of estrogen receptor alpha is associated with venous ulceration. J Steroid Biochem Mol Biol. 2005;97:266-70 pubmed..5, 95% CI = 1.0-2.2, P = 0.03). Our results show that a specific ERbeta variant is associated with impaired healing in the elderly, predisposing individuals to venous ulceration. ..
- Schug M, Regulski E, Pearce A, Smith S. Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae. Genet Res. 2004;83:19-29 pubmed..The dinucleotide repeats we isolated are shorter, on average, than those isolated in many other Drosophila species...
- Lin C, Yang W, Lin S, Chen T, Lee W, Chang C, et al. Length polymorphism in heme oxygenase-1 is associated with arteriovenous fistula patency in hemodialysis patients. Kidney Int. 2006;69:165-72 pubmed..The longer GT repeat in the HO-1 promoter might inhibit gene transcription, and consequently offset the CO-mediated protective effect against vascular injury. ..
- Ferreiro V, Szijan I, Giliberto F. Detection of germline mosaicism in two Duchenne muscular dystrophy families using polymorphic dinucleotide (CA)n repeat loci within the dystrophin gene. Mol Diagn. 2004;8:115-21 pubmed..The results of this study demonstrate the usefulness of the methodology that combine the haplotype analysis with the identification of the mutation in order to detect hidden germline mosaicisms and, thus, improve genetic counseling. ..
- An Z, Zhao Y, Cheng H. [Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg]. Yi Chuan. 2009;31:311-9 pubmed..The results indicated that it is an effective and feasible way to develop EST-SSR markers from H. brasiliensis EST sequences, and the primers designed in this study can be used in genetic study of rubber tree. ..
- Li G, Tolstonog G, Traub P. Interaction in vitro of type III intermediate filament proteins with Z-DNA and B-Z-DNA junctions. DNA Cell Biol. 2003;22:141-69 pubmed
- Seichter D, Krebs S, Forster M. Rapid and accurate characterisation of short tandem repeats by MALDI-TOF analysis of endonuclease cleaved RNA transcripts. Nucleic Acids Res. 2004;32:e16 pubmed
- Hefferon T, Groman J, Yurk C, Cutting G. A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing. Proc Natl Acad Sci U S A. 2004;101:3504-9 pubmedb>Dinucleotide repeats are ubiquitous features of eukaryotic genomes that are not generally considered to have functional roles in gene expression...
- Poetsch M, Petersmann A, Lignitz E, Kleist B. Relationship between mitochondrial DNA instability, mitochondrial DNA large deletions, and nuclear microsatellite instability in head and neck squamous cell carcinomas. Diagn Mol Pathol. 2004;13:26-32 pubmed..were compared with data of an analysis for microsatellite instability at IGFIIR, hMSH3, hMSH6, and 5 dinucleotide repeats. We found mtMSI, low nMSI, and high nMSI in 42%, 36%, and 13% of HNSCC primary tumors, respectively...
- Härkönen P, Kyllönen A, Nordling S, Vihko P. Loss of heterozygosity in chromosomal region 16q24.3 associated with progression of prostate cancer. Prostate. 2005;62:267-74 pubmed..01). Regarding distant metastases, instead, there seemed to be no allelic loss events exclusively typical of metastatic tumors at 16q. The data suggest the location of gene(s) related to prostate cancer progression at 16q24.3. ..
- Smolarz B, Romanowicz Makowska H, Langner E, Kozlowska E, Kulig A, Dziki A. Genetic analysis of microsatellite markers in patients from hereditary nonpolyposis colorectal cancer (HNPCC) families. Exp Oncol. 2004;26:205-9 pubmed..MLH1/MSH2 mutations were only in MSI high samples detected. Genetic alterations seem to be a risk factor of colorectal cancer in subjects belonged to HNPCC families with high incidence of this cancer. ..
- Rozati R, Vanaja M, Nasaruddin K. Genetic contribution of the interferon gamma dinucleotide-repeat polymorphism in South Indian women with endometriosis. J Obstet Gynaecol Res. 2010;36:825-31 pubmed publisher..These results suggest that the IFNG gene CA-repeat polymorphism is associated with susceptibility to endometriosis in South Indian women. ..
- Bhassu S, Bakar Y, Rashid Z. Isolation of dinucleotide microsatellite markers in commercially threatened Malaysian Mahseer, Tor tambroides. Genetika. 2008;44:1145-7 pubmed..The number of alleles per locus ranged from 2 (SYKVJ1-11) to 6 (SYKVJ1-4) while the levels of heterozygosity ranged from 0.0472 (SYKVJ1-11) to 0.7745 (SYKVJ1-2). ..
- Friedrichsen D, Hawley S, Shu J, Humphrey M, Sabacan L, Iwasaki L, et al. IGF-I and IGFBP-3 polymorphisms and risk of prostate cancer. Prostate. 2005;65:44-51 pubmed..Further evaluation of the IGF-I CA-repeat polymorphism and prostate cancer is necessary to determine if the modest risk reduction associated with the 19-CA-repeat homozygous state is observed in other study populations. ..
- Letonja M, Steblovnik K, Peterlin B, Petrovic D. Oestrogen receptor dinucleotide (TA) polymorphism affects total and LDL cholesterol but does not predict premature myocardial infarction in Caucasian men. Acta Cardiol. 2005;60:307-9 pubmed
- McConnell R, Middlemist S, Scala C, Strassmann J, Queller D. An unusually low microsatellite mutation rate in Dictyostelium discoideum, an organism with unusually abundant microsatellites. Genetics. 2007;177:1499-507 pubmed..The causal relation may in fact be reversed, with low mutation rates evolving to protect against deleterious fitness effects of mutation at the numerous microsatellites. ..
- Hong A, Huo D, Kim H, Niu Q, Fackenthal D, Cummings S, et al. UDP-Glucuronosyltransferase 1A1 gene polymorphisms and total bilirubin levels in an ethnically diverse cohort of women. Drug Metab Dispos. 2007;35:1254-61 pubmed..These data have implications for the design of epidemiologic studies of cancer susceptibility and pharmacogenetic studies for adverse drug reactions in populations of African ancestry. ..
- Magaña J, Gomez R, Cisneros B, Casas L, Castorena F, Miranda A, et al. Association of the CT gene (CA) polymorphism with BMD in osteoporotic Mexican women. Clin Genet. 2006;70:402-8 pubmed..77% and -2.51, respectively). Analysis of potential confounder demonstrated that aging has a significant effect on osteoporosis development (odds ratio 1.1; 95% CI; 1.1052-1.152). ..