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Jörg T. Epplen - One of the best experts on this subject based on the ideXlab platform.

  • on simple Repetitive DNA Sequences and complex diseases
    Electrophoresis, 1997
    Co-Authors: Cornelia Epplen, Winfried Mäueler, Eduardo Jose Melo Dos Santos, Paul D Van Helden, Jörg T. Epplen
    Abstract:

    Simple Repetitive DNA Sequences are abundantly interspersed in eukaryote genomes and therefore useful in genome research and genetic fingerprinting in plants, fungi and animals, including man. Recently, simple repeats were also identified in some prokaryotic genomes. Hence the same probes can be applied for multilocus DNA fingerprinting in medically relevant bacteria. Simple repeats including composite dinucleotide microsatellites are differentially represented in different compartments of eukaryote genomes. Expanded triplet blocks in and around certain genes may, for example, cause so-called trinucleotide diseases in man. As a consequence, simple Repetitive Sequences should also be characterized with respect to their influences on the DNA structure, gene expression, genomic (in)stability and their development on an evolutionary time scale. Here three examples of microsatellites in the human major histocompatibility complex (HLA) are investigated, a (GT)n microsatellite situated 2 kb 5' off the lymphotoxin alpha (LTA) gene, a (GAA)n block in the 5' part of the HLA-F gene and a composite (GT)n(GA)m stretch in the second intron of HLA-DRBl genes. Grossly differing mutation rates are evident in these elements as well as varying linkage disequilibria. The unfolding of these simple repeats in distant human populations is covered including Caucasians, Bushmen and South American Indians. Furthermore, implications of simple repeat neighboring genes are discussed for the multifactorial diseases multiple sclerosis (MS), rheumatoid arthritis (RA) and early onset pauciarticular arthritis (EOPA). Polymorphisms of HLA-DRBl and T cell receptor beta variable (TCRBV) genes confer susceptibility for these autoimmune diseases as demonstrable by intronic simple repeat variability. Microsatellite polymorphisms within the TNF region reveal linkage disequilibria with HLA-DRBl and different promotor alleles of the TNFA gene. Disease associations with TNFA microsatellite alleles are, on the one hand, secondary to associations with HLA-DRBl genes (in MS) or they represent additional risk factors (in RA, EOPA) on the other hand. Evolutionary persistence, various structural conformations and the specific binding of nuclear proteins to several simple repeat Sequences refute the preconceptions of biological insignificance for all of these ubiquitously interspersed elements.

  • Diagnostic applications of Repetitive DNA Sequences.
    Clinica chimica acta; international journal of clinical chemistry, 1992
    Co-Authors: Jörg T. Epplen
    Abstract:

    The potential, the advantages and the different areas of diagnostic applications are discussed for the various categories of Repetitive DNA Sequences. Since all eukaryotes are characterized by genomic redundancy, these sensitive, rapid and comparatively simple techniques are revolutionizing many a field of clinical and experimental diagnostics.

  • Diagnostic applications of Repetitive DNA Sequences.
    Journal of the International Federation of Clinical Chemistry, 1992
    Co-Authors: Jörg T. Epplen
    Abstract:

    Different diagnostic applications are discussed for various categories of Repetitive DNA Sequences. Since all eukaryotes are characterized by genomic redundancy, these sensitive, rapid, and comparatively simple techniques are revolutionizing many fields in clinical and experimental diagnostics. In addition to individuality testing in humans and animals, for example, eukaryotic infectious agents can be identified and tumors classified with respect to genomic changes. The forensic as well as animal and plant breeding sciences have already adopted the DNA technology involving Repetitive sequence tools.

  • A gel retardation assay system for studying protein binding to simple Repetitive DNA Sequences
    Electrophoresis, 1992
    Co-Authors: Winfried Mäueler, Marc Muller, Anja Carola Köhne, Jörg T. Epplen
    Abstract:

    Simple Repetitive DNA Sequences have been regarded as mere "junk" present in all eukaryotic genomes. In fact, mixed simple repeat (gt)n(ga)m Sequences are present in major histocompatibility complex MHC-DRB genes for long evolutionary times, including such distant animals as artiodactyla and man. We describe herein an unsophisticated method which reveals that at least certain simple Repetitive (gt)n(ga)m Sequences bind nuclear proteins and show characteristics of a specific DNA-protein interaction via gel retardation.

Yoichi Matsuda - One of the best experts on this subject based on the ideXlab platform.

  • A novel family of Repetitive DNA Sequences amplified site-specifically on the W chromosomes in Neognathous birds
    Chromosome Research, 2006
    Co-Authors: Kazuhiko Yamada, Chizuko Nishida-umehara, Mami Shibusawa, Masaoki Tsudzuki, Junko Ishijima, Takahiro Murakami, Kimiyuki Tsuchiya, Yoichi Matsuda
    Abstract:

    A novel family of Repetitive DNA Sequences was molecularly cloned from Apa I-digested genomic DNA of two Galliformes species, Japanese quail ( Coturnix japonica ) and guinea fowl ( Numida meleagris ), and characterized by chromosome in-situ hybridization and filter hybridization. Both the repeated sequence elements produced intensely painted signals on the W chromosomes, whereas they weakly hybridized to whole chromosomal regions as interspersed-type Repetitive Sequences. The repeated elements of the two species had high similarity of nucleotide Sequences, and cross-hybridized to chromosomes of two other Galliformes species, chicken ( Gallus gallus ) and blue-breasted quail ( Coturnix chinensis ). The nucleotide Sequences were conserved in three other orders of Neognathous birds, the Strigiformes, Gruiformes and Falconiformes, but not in Palaeognathous birds, the Struthioniformes and Tinamiformes, indicating that the repeated sequence elements were amplified on the W chromosomes in the lineage of Neognathous birds after the common ancestor diverged into the Palaeognathae and Neognathae. They are components of the W heterochromatin in Neognathous birds, and a good molecular cytogenetic marker for estimating the phylogenetic relationships and for clarifying the origin of the sex chromosome heterochromatin and the process of sex chromosome differentiation in birds.

  • New families of site-specific Repetitive DNA Sequences that comprise constitutive heterochromatin of the Syrian hamster (Mesocricetus auratus, Cricetinae, Rodentia)
    Chromosoma, 2006
    Co-Authors: Kazuhiko Yamada, Chizuko Nishida-umehara, Kimiyuki Tsuchiya, Eikichi Kamimura, Mariko Kondo, Yoichi Matsuda
    Abstract:

    We molecularly cloned new families of site-specific Repetitive DNA Sequences from Bgl II- and Eco RI-digested genomic DNA of the Syrian hamster ( Mesocricetus auratus , Cricetrinae, Rodentia) and characterized them by chromosome in situ hybridization and filter hybridization. They were classified into six different types of Repetitive DNA sequence families according to chromosomal distribution and genome organization. The hybridization patterns of the Sequences were consistent with the distribution of C-positive bands and/or Hoechst-stained heterochromatin. The centromeric major satellite DNA and sex chromosome-specific and telomeric region-specific Repetitive Sequences were conserved in the same genus ( Mesocricetus ) but divergent in different genera. The chromosome-2-specific sequence was conserved in two genera, Mesocricetus and Cricetulus , and a low copy number of Repetitive Sequences on the heterochromatic chromosome arms were conserved in the subfamily Cricetinae but not in the subfamily Calomyscinae. By contrast, the other type of Repetitive Sequences on the heterochromatic chromosome arms, which had sequence similarities to a LINE sequence of rodents, was conserved through the three subfamilies, Cricetinae, Calomyscinae and Murinae. The nucleotide divergence of the Repetitive Sequences of heterochromatin was well correlated with the phylogenetic relationships of the Cricetinae species, and each sequence has been independently amplified and diverged in the same genome.

  • Molecular and cytogenetic characterization of site-specific Repetitive DNA Sequences in the Chinese soft-shelled turtle (Pelodiscus sinensis, Trionychidae)
    Chromosome Research, 2005
    Co-Authors: Kazuhiko Yamada, Chizuko Nishida-umehara, Yoichi Matsuda
    Abstract:

    A novel family of Repetitive DNA Sequences that are components of constitutive heterochromatin were cloned from Bgl I-digested genomic DNA of the Chinese soft-shelled turtle ( Pelodiscus sinensis , Trionychidae), and characterized by filter hybridization and chromosome in-situ hybridization. The Bgl I-family of Repetitive Sequences were classified into four types by their genome organization and chromosomal distribution as follows: the repeated Sequences located on (1) two pairs of microchromosomes, (2) four pairs of microchromosomes,(3) about half the number of microchromosomes and (4) the interstitial region of the short arm of chromosome 2. The presence of microchromosome-specific Repetitive Sequences has also been reported in the Struthioniformes and Galliformes, suggesting that turtle chromosomes retain some similarity to the chromosome structure as well as the karyotypes of avian species

  • Molecular cloning and characterization of novel centromeric Repetitive DNA Sequences in the blue-breasted quail (Coturnix chinensis, Galliformes).
    Cytogenetic and genome research, 2002
    Co-Authors: Kazuhiko Yamada, Mami Shibusawa, Masaoki Tsudzuki, Yoichi Matsuda
    Abstract:

    A new family of centromeric highly Repetitive DNA Sequences was isolated from Eco RI-digested genomic DNA of the blue-breasted quail ( Coturnix chinensis , Galliform

Diogo Cavalcanti Cabraldemello - One of the best experts on this subject based on the ideXlab platform.

  • tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA Sequences
    BMC Evolutionary Biology, 2013
    Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti Cabraldemello
    Abstract:

    Background The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive Sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA Sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA Sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems.

  • tracking the evolution of sex chromosome systems in melanoplinae grasshoppers through chromosomal mapping of Repetitive DNA Sequences
    BMC Evolutionary Biology, 2013
    Co-Authors: Octavio M Palaciosgimenez, Elio Rodrigo Daniel Castillo, Dardo A Marti, Diogo Cavalcanti Cabraldemello
    Abstract:

    The accumulation of Repetitive DNA during sex chromosome differentiation is a common feature of many eukaryotes and becomes more evident after recombination has been restricted or abolished. The accumulated Repetitive Sequences include multigene families, microsatellites, satellite DNAs and mobile elements, all of which are important for the structural remodeling of heterochromatin. In grasshoppers, derived sex chromosome systems, such as neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀, are frequently observed in the Melanoplinae subfamily. However, no studies concerning the evolution of sex chromosomes in Melanoplinae have addressed the role of the Repetitive DNA Sequences. To further investigate the evolution of sex chromosomes in grasshoppers, we used classical cytogenetic and FISH analyses to examine the Repetitive DNA Sequences in six phylogenetically related Melanoplinae species with X0♂/XX♀, neo-XY♂/XX♀ and neo-X1X2Y♂/X1X1X2X2♀ sex chromosome systems. Our data indicate a non-spreading of heterochromatic blocks and pool of Repetitive DNAs (C 0 t-1 DNA) in the sex chromosomes; however, the spreading of multigene families among the neo-sex chromosomes of Eurotettix and Dichromatos was remarkable, particularly for 5S rDNA. In autosomes, FISH mapping of multigene families revealed distinct patterns of chromosomal organization at the intra- and intergenomic levels. These results suggest a common origin and subsequent differential accumulation of Repetitive DNAs in the sex chromosomes of Dichromatos and an independent origin of the sex chromosomes of the neo-XY and neo-X1X2Y systems. Our data indicate a possible role for Repetitive DNAs in the diversification of sex chromosome systems in grasshoppers.

Wolfgang Hennig - One of the best experts on this subject based on the ideXlab platform.

  • transcription of Repetitive DNA Sequences in the lampbrush loop pair nooses formed by sterile alleles of fertility gene q on the y chromosome of drosophila hydei
    Molecular Genetics and Genomics, 1994
    Co-Authors: Ron Hochstenbach, Rein Brand, Wolfgang Hennig
    Abstract:

    The Y chromosomal lampbrush loop-forming male fertility genes of Drosophila consist mainly of Repetitive DNA Sequences that do not code for proteins. We investigated whether differences in the transcription of these Sequences can be detected in male-sterile alleles of male fertility gene Q, which forms the loop pair Nooses. The loop consists, for approximately two-thirds, of repeats of the Y-specific ay1 family of Repetitive DNA Sequences. Of the remaining one-third, at least one-half is represented by defective retrotransposons of the gypsy family. Both sequence types are interspersed throughout the loop. Using both ay1 and gypsy Sequences as probes for transcript in situ hybridization, we show that, at the level of the light microscope, transcription of neither sequence is detectably affected in the loops formed by a male-sterile allele of gene Q. We conclude that the transcription of ay1 and gypsy is required, but not sufficient for the function of gene Q.

  • discrimination of related transcribed and non transcribed Repetitive DNA Sequences from the y chromosomes of drosophila hydei and drosophila eohydei
    Molecular Genetics and Genomics, 1994
    Co-Authors: Ron Hochstenbach, Miriam Knops, Wolfgang Hennig
    Abstract:

    The short arm of the Y chromosome of Drosophila hydei carries a single male fertility gene, gene Q, which forms the lampbrush loop pair Nooses. Conflicting observations have been reported concerning the identity of the Repetitive DNA Sequences that are transcribed in this loop pair. It has been claimed by other investigators that the loop transcripts contain repeats of two distinct, but related families of Y-specific Repetitive DNA Sequences, ayl and YsI. We reinvestigated this issue, using as probes single ayl and YsI repeats which, under stringent conditions, hybridize only to members of their own family. Under non-stringent conditions, both repeats hybridize in situ to Nooses transcripts. However, if hybridization conditions are stringent, only the ayl probe hybridizes to loop transcripts. Hybridizations to Northern blots of testis RNA confirm these results. Further, YsI repeats are not found the closely related species D. eohydei. We conclude that the YsI repeats are not relevant for the function of fertility gene Q.

Jiming Jiang - One of the best experts on this subject based on the ideXlab platform.

  • Chromatin-associated transcripts of tandemly Repetitive DNA Sequences revealed by RNA-FISH
    Chromosome Research, 2016
    Co-Authors: Hainan Zhao, Jiming Jiang
    Abstract:

    Tandemly Repetitive DNA Sequences, also named satellite repeats, are major DNA components of heterochromatin and are often organized as long arrays in the pericentromeric, centromeric, and subtelomeric regions of eukaryotic chromosomes. An increasing amount of evidence indicates that transcripts derived from some satellite repeats play important roles in various biological functions. We used a RNA-fluorescence in situ hybridization (RNA-FISH) technique to investigate the transcription of the four well-characterized satellite repeats of maize ( Zea mays ), including the 180-bp knob repeat, the telomeric (TTTAGGG)_n repeat, the 156-bp centromeric repeat CentC, and a 350-bp subtelomeric repeat. Although few transcripts derived from these four repeats were found in the expressed sequence tag and RNA-seq databases, RNA-FISH consistently detected the transcripts from three of the four repeats on interphase nuclei, suggesting that the transcripts from the three repeats are largely integrated into chromatin. The transcripts from the knob and telomeric repeats were mapped to the related DNA loci. In contrast, the transcripts from the CentC repeats were mainly localized to the nucleolus, although nucleoplasmic CentC transcripts were also detectable. The nucleolus and nuclear RNAs appeared to be important for the nuclear localization for at least one centromeric protein, Mis12. We demonstrate that RNA-FISH is a powerful tool to assess the level of transcription as well as to physically map the nuclear locations of the transcripts derived from satellite repeats.