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Repeat Element (repeat + element)
Selected AbstractsCancer-associated missplicing of exon 4 influences the subnuclear distribution of the DNA replication factor CIZ1,HUMAN MUTATION, Issue 10 2007Faisal Abdel Rahman Abstract Cip1-interacting zinc finger protein 1 (CIZ1, also known as CDKN1A-interacting zinc finger protein 1) stimulates initiation of mammalian DNA replication and is normally tethered to the nuclear matrix within DNA replication foci. Here, we show that an alternatively spliced human CIZ1 variant, lacking exon 4 (, E4), is misexpressed as a consequence of intronic mutation in Ewing tumor (ET) cell lines. In all ET lines tested, exon 4 is skipped and an upstream mononucleotide repeat element is expanded to contain up to 28 thymidines, compared to 16 in controls. In exon-trap experiments, a 24T variant produced three-fold more exon skipping than a 16T variant, demonstrating a direct effect on splicing. In functional assays, , E4 protein retains replication activity, but fails to form subnuclear foci. Furthermore, coexpression of mouse , E4 with Ciz1 prevents Ciz1 from localizing appropriately, having a dominant negative effect on foci formation. The data show that conditional exclusion of exon 4 influences the spatial distribution of the Ciz1 protein within the nucleus, and raise the possibility that CIZ1 alternative splicing could influence organized patterns of DNA replication. Hum Mutat 28(10), 993,1004, 2007. © 2007 Wiley-Liss, Inc. [source] Molecular genetic characterization of Robertsonian translocations in cattleJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2001H. Joerg The chromosome fusion of acrocentric chromosomes, known as Robertsonian translocations, are the most common chromosome rearrangement in Bovidae. Cytogenetic studies revealed differences between the centromeres of Robertsonian translocations: the rob(1; 29) is called monocentric, whereas rob(14; 20) is a dicentric chromosome. To analyse the type of fusion, satellite sequences were hybridised to metaphase chromosomes of carriers of rob(1; 29) from different breeds and rob(14; 20) from the Simmental breed. A repeat element of the bovine 1.715 satellite was located in the centromeric regions of all 29 bovine acrocentric chromosomes. No signals were observed on either the X-,Y- or the rob(1; 29) chromosomes. In contrast, all rob(14; 20) chromosomes gave a distinct hybridisation signal. Microsatellite markers in the linkage group, originating from the fusion, revealed a characteristic allele combination for rob(1; 29) in all carriers and were able to confirm the screening of metaphases of 220 daughters of a heterozygote carrier of the rob(1; 29). The results indicate that rob(1; 29) lost parts of both centromeres and that the 1.715 satellite DNA is not necessary for the functioning of the centromere. Furthermore, rob(1; 29) appears to derive from the same mutation and is transmitted according to Mendelian law. Molekulargenetische Charakterisierung von Robertson'schen Translokationen beim Rind Die Fusion von akrozentrischen Chromosomen, bekannt als Robertson'sche Translokationen, sind die häufigsten Chromosomenveränderungen in der Rindergattung. Zytogenetische Studien zeigten Unterschiede in den Zentromeren von Robertson'schen Translokationen auf. Das Rob(1; 29) Chromosom wird als ein monozentrisches und das Rob(14/20) als ein dizentrisches Chromosom bezeichnet. Um die Fusionsarten zu analysieren, wurden Satellitensequenzen auf Metaphasenchromosomen von Trägern der Rob(1; 29) aus verschiedenen Rassen und von Trägern der Rob(14; 20) aus der Rasse der Simmentaler hybridisiert. Eine Sequenzwiederholung aus dem Rindersatelliten 1.715 wurde in den Zentromerregionen aller 29 akrozentrischer Rinderchromosomen nachgewiesen. Auf dem X, dem Y wie auch auf dem Rob(1; 29) Chromosom konnten jedoch keine Signale beobachtet werden, während alle Rob(14; 20) Chromosomen ein starkes Hybridisierungssignal aufwiesen. Die Mikrosatelliten in der Kopplungsgruppe, welche durch die Fusion entstanden ist, zeigten eine charakteristische Allelkombination für das Rob(1; 29) Chromsom und konnten Untersuchungen an den Metaphasen von 220 Töchtern eines heterozygoten Trägers bestätigen. Die Ergebnisse weisen darauf hin, dass Rob(1; 29) Chromosomen einen Teil beider Zentromere verloren haben und dass die 1.715 Satelliten DNA für ein funktionierendes Chromosom nicht notwendig ist. Die Rob(1; 29) Chromosomen scheinen eine identische Abstammung aufzuweisen und werden nach den Mendel'schen Regeln vererbt. [source] The identification of circular extrachromosomal DNA in the nuclear genome of Trypanosoma bruceiMOLECULAR MICROBIOLOGY, Issue 2 2003N. S. Alsford Summary Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei. [source] Atlantic capelin (Mallotus villosus) tetranucleotide microsatellitesMOLECULAR ECOLOGY RESOURCES, Issue 2 2005K. GORDOS Abstract Twelve microsatellite loci developed for Atlantic capelin (Mallotus villosus) using magnetic bead hybridization enrichment for tetranucleotide microsatellites revealed five loci composed of single repeat elements and six composed of complex repeats. Forty-four beach-spawning females from three different northwestern Atlantic Newfoundland beach-spawning populations were screened at each locus. Loci were polymorphic (two to 59 alleles per locus) and all but two exhibited high heterozygosity (0.86,1). The loci are considered suitable for addressing questions related to fine-scale population structure, spawning fidelity and survivorship/kinship issues. [source] Why repetitive DNA is essential to genome functionBIOLOGICAL REVIEWS, Issue 2 2005James A. Shapiro ABSTRACT There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the ,functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component. [source] First report on autochthonous urease-positive Trichophyton rubrum (T. raubitschekii) from South-east EuropeBRITISH JOURNAL OF DERMATOLOGY, Issue 1 2005M. Arabatzis Summary Background,Trichophyton raubitschekii is a dermatophyte belonging to the T. rubrum complex and is differentiated principally by its positive urease activity and production of profuse macroconidia and microconidia in culture. It is classically isolated from African, South-east Asian and Australian aboriginal patients with tinea corporis or tinea cruris. Objectives, This study was undertaken to screen Greek and Bulgarian clinical isolates identified as T. rubrum for T. raubitschekii and to delineate these strains by two molecular methods used for the first time in T. rubrum epidemiological studies. Methods, Ninety-five Greek and 10 Bulgarian strains, originating from various body sites, initially identified as T. rubrum, were screened for urease activity. The biochemical properties and morphology of the urease-positive strains were determined. Strains were delineated with polymerase chain reaction (PCR)-ribotyping amplifying repeat elements of the intergenic spacer region and by PCR fingerprinting. Results, Five Greek and one Bulgarian T. raubitschekii strains were identified comprising isolates from patients with tinea manuum (one), tinea corporis (one), tinea cruris (one) and tinea unguium (three). Only one strain had the classical T. raubitschekii microscopic morphology, whereas the remaining five presented a dominant arthroconidial phenotype. Both typing methods clustered all T. raubitschekii and T. rubrum isolates together in the same group, indicating strain homogeneity in the genetic regions examined. Conclusions, The reported isolation of T. raubitschekii in the Balkan and South-eastern Mediterranean regions extends the geographical distribution of this species. As the more primitive T. raubitschekii probably represents the parental population of T. rubrum, the Greek and Bulgarian T. raubitschekii strains could represent a remnant of the T. rubrum spread that took place after the First World War, rather than being a recent epidemiological event. [source] | |||||||||||||