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PubMed1982

Cytological localization of inverted repeated DNA sequences in Vicia faba.

Inverted repeated DNA sequences have been isolated from sheared Vicia faba DNA by hydroxylapatite column chromatography, treated with nuclease S1, tritiated by the nick translation method and hybridized in situ on squashes of Vicia faba root tips. Silver grains appear grouped in a rather limited portion of interphase nuclei and form a sort of band across them. The central regions of metaphase chromosomes are preferentially labeled, labeling being excluded from telomeres, centromeres and secondary constrictions. These results are briefly discussed in relation to those obtained in other species and the functional significance of inverted repeats.

DNA↗
PubMed1993

Clusters of interspersed repeated DNA sequences in the rice genome (Oryza).

We have characterized a repeated DNA sequence (RTL122) from rice (Oryza sativa L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15-20 kb. We characterized three bacteriophage lambda clones that contained the RTL122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.

Bacteriophage lambda↗
PubMed1995

A unique repeated DNA sequence in the cyclosporin-producing strain of Tolypocladium inflatum (ATCC 34921).

Recombinant lambda clones containing repeated DNA sequences were isolated from the cyclosporin A-producing fungus Tolypocladium inflatum (ATCC 34921) by differential hybridization with total fungal DNA and rDNA probes. From this survey 1% of the lambda clones appeared to contain repeated sequences. Subsequent analysis led to the identification of a dispersed repetitive DNA element. It was named CPA element (cyclosporin production associated) and appears to be strain specific, since it is absent from other related strains or fungi. Hybridization with chromosomal restriction fragments indicates an equal distribution of the CPA element in the genome. The copy number was estimated to be between 20 and 30 per haploid genome. Sequence analysis of a 0.9-kb XhoI fragment from three copies of the CPA element revealed strong conservation of this sequence among all copies. A 200-bp region exhibits similarities to a repeated sequence from Zea diploperennis. The use of this DNA sequence as a molecular marker for identification of this cyclosporin-producing strain ATCC 34921 is discussed as is the relevance of repeated DNA sequences for rearrangements of fungal karyotypes.

Base Sequence↗
PubMed1981

Highly repeated DNA sequence limited to knob heterochromatin in maize.

A highly repeated DNA sequence has been isolated from the maize genome as a satellite in actinomycin D/CsCl gradients. By using maize stocks differing in their heterochromatin content we have established that the sequence is a major constituent of one class of heterochromatin, knob heterochromatin, which can occur at 23 locations in the chromosome complement. The repeating unit, of 185 base pairs, has been cloned in plasmid pBR322 and its nucleotide sequence has been determined. The presence of this DNA sequence in knob heterochromatin and its absence from centromeric, nucleolar, and B chromosome heterochromatin parallels the cytogenetic differentiation previously described for these classes of heterochromatin in maize. Because knob heterochromatin has a distinctive cytological appearance and is unique in showing neocentric activity at meiosis, its association with a particular repeated DNA sequence may reflect a functional role for the sequence in the cell cycle.

Journal Article↗
PubMed1989

Analysis of separate isolates of Bordetella pertussis repeated DNA sequences.

Two independent isolates of a Bordetella pertussis repeated DNA unit were sequenced and shown to be an insertion sequence element with five nucleotide differences between the two copies. The sequences were 1053 bp in length with near-perfect terminal inverted repeats of 28 bp, had three open reading frames, and were each flanked by short direct repeats. The two insertion sequences showed considerable homology to two other B. pertussis repeated DNA sequences reported recently: IS481 and a 530 bp repeated DNA unit. The B. pertussis insertion sequence would appear to comprise a group of closely related sequences differing mainly in flanking direct repeats and the terminal inverted repeats. The two isolates reported here, which were from the adenylate cyclase and agglutinogen 2 regions of the genome, were numbered IS48lvl and IS48lv2 respectively.

Base Sequence↗
PubMed1974

Repeated DNA sequences in fungi.

Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10-20% repeated DNA sequences. There are approximately 100-110 copies of repeated DNA sequences of approximately 4 x 10(7) daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5 degrees C difference of T(e)50 (temperature at which 50% duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA.

DNA, Fungal↗
PubMed1993

Comparison of highly repeated DNA sequences in some Lemuridae and taxonomic implications.

Highly repeated DNA sequences of Eulemur fulvus mayottensis, E. coronatus, Lemur catta, and Hapalemur griseus griseus have been identified and compared. Sequence analysis of highly repeated DNA fragments isolated from L. catta and Hapalemur showed a high percentage of similarity (nearly 95%), as did fragments isolated from the two very close Eulemur species, whereas comparison of the DNA fragments isolated from the two Eulemur species and the L. catta/Hapalemur group showed a very low percentage (approximately 40%) of identity, as might be expected for distant species. These results confirm our previous data, obtained by Southern blot hybridization techniques on the same species, and strongly support the existence of a common trunk between L. catta and Hapalemur, but different from the leading to the Eulemur species.

Animals↗
PubMed1989

Cloning and characterization of a tandemly repeated DNA sequence in the crane family (Gruidae).

A tandemly repeated DNA sequence possessing a unique PstI site has been characterized in several species of the crane family. The "Pst family" comprises at least 8800 monomer units 187 base pairs (bp) in length and constitutes 0.14% of the genome of the sarus crane (Grus antigone). The array is located in the centromeric heterochromatin of chromosome 2 in the two species where in situ hybridizations of a cloned monomer to metaphase chromosome spreads were carried out. DNA sequence comparisons between five monomer units from G. antigone revealed a high degree of homology between four of the individual repeats, while the fifth was somewhat divergent. The G + C content deduced from the DNA sequence makes it likely that the Pst family constitutes part of a density satellite seen in profiles of crane DNA centrifuged to equilibrium in CsCl. The common occurrence of tandem arrays such as the Pst family, with repeat lengths close to 200 bp, leads us to an hypothesis implicating nucleosomes in the evolution of such families.

Animals↗
PubMed1990

Functional analysis of a centromere from fission yeast: a role for centromere-specific repeated DNA sequences.

A circular minichromosome carrying functional centromere sequences (cen2) from Schizosaccharomyces pombe chromosome II behaves as a stable, independent genetic linkage group in S. pombe. The cen2 region was found to be organized into four large tandemly repeated sequence units which span over 80 kilobase pairs (kb) of untranscribed DNA. Two of these units occurred in a 31-kb inverted repeat that flanked a 7-kb central core of nonhomology. The inverted repeat region had centromere function, but neither the central core alone nor one arm of the inverted repeat was functional. Deletion of a portion of the repeated sequences that flank the central core had no effect on mitotic segregation functions or on meiotic segregation of a minichromosome to two of the four haploid progeny, but drastically impaired centromere-mediated maintenance of sister chromatid attachment in meiosis I. This requirement for centromere-specific repeated sequences could not be satisfied by introduction of random DNA sequences. These observations suggest a function for the heterochromatic repeated DNA sequences found in the centromere regions of higher eucaryotes.

Base Sequence↗
PubMed1981

A complex repeated DNA sequence within the Drosophila transposable element copia.

A 320 nucleotide repeated DNA sequence within the copia coding element of Drosophila melanogaster has been identified and characterized. This sequence has been localized by DNA-DNA hybridization and electron microscopic analysis of heteroduplexes to the approximate middle of the 5 kb copia coding region. The primary sequence of this repeated DNA has been determined. The sequence is composed of three related subunits, 35-37 nucleotides in length (A, B and C). This 105 nucleotide higher order repeat has apparently been duplicated twice to yield a complex repeated sequence, ABCA'B'C'A"B"C", which exhibits divergence among the individual subunits. This sequence is AT rich, as are the direct terminal repeats which flank the copia coding region, but does not contain any apparent homology with the terminal repeats. This repeated sequence contains three presumptive polyadenylation signals and two 25 nucleotide, imperfectly matched, inverted repeat sequences adjacent to two of the polyadenylation sequences.

Animals↗
PubMed1981

Repeated DNA sequences near the 5'-end of the silk fibroin gene.

Four different repeated sequence elements have been found in cloned silk moth DNA, extending from 5700 base pairs upstream from the silk fibroin gene to 600 base pairs within its intervening sequence. Only 2 of the 12 overlapping restriction fragments examined, ranging from 164 to 1800 base pairs in length, do not contain a repeated sequence. The 830 base pairs adjoining the 5'-end of the fibroin gene hybridize with only one sequence in the Bombyx mori genome. Fibroin gene transcription initiates within this single-copy DNA at least 500 base pairs downstream from any repeated DNA sequence. The data show that repeated sequences comprise a major portion of the DNA flanking this developmentally regulated gene but not the DNA immediately 5' to it; that an intervening sequence can contain a repeated element; and that repeated sequences can be interspersed with one another as well as with single-copy DNA in a typical animal genome. In addition, filter transfer hybridization can be used to quantitate repetition frequency and sequence divergence and to distinguish patterns of repeated sequence organization.

Animals↗
PubMed1993

Restriction fragment length polymorphism analysis of Fusobacterium necrophorum using a novel repeat DNA sequence and a 16S rRNA gene probe.

A repeated DNA sequence was isolated from Fusobacterium necrophorum biotype AB, strain FnS1. The repeated sequence shared considerable homology with the transposase gene from the Pseudomonas syringiae insertion sequence IS801. The repeat sequence was used together with a 16S ribosomal RNA gene probe to type F. necrophorum isolates using restriction fragment length polymorphisms. The probes revealed differences between several clinical isolates and will be useful tools to study the epidemiology of ovine foot abscess and other diseases caused by F. necrophorum.

Amino Acid Sequence↗
PubMed2001

Identification and chromosomal location of tandemly repeated DNA sequences in Allium cepa.

A 314-bp tandemly repeated DNA sequence, named pAc074, was characterized in Allium cepa by fluorescence in situ hybridization (FISH) analyses using random amplified fragment as probe. The nucleotide sequences of the clone pAc074 is partially homologous to the satellite DNA sequences, ACSAT1, ACSAT2, and ACSAT3, of A. cepa with 81%, 81% and 78% similarity, respectively. Our sequential C-banding and FISH with pAc074 probe also clearly showed a close relation between Cheterochromatin at telomeric region and pAc074 sequences on all the chromosomes except on chromosome 6. On the long arm of chromosome 7, pAc074 sequences appeared as interstitial band which did not correspond to C-heterochromatin bands. Instead, the C-heterochromatin bands corresponded with the 5S rDNA signals. This is the first evidence of simultaneous banding of the 5S rDNA and C-band in A. cepa.

Base Sequence↗
PubMed1996

An efficient method for generation and subcloning of tandemly repeated DNA sequences with defined length, orientation and spacing.

Tandemly repeated DNA sequences generated from single synthetic oligonucleotide monomers are useful for many purposes. With conventional ligation procedures low yields and random orientation of oligomers makes cloning of defined repeated sequences difficult. We solved these problems using 2 bp overhangs to direct orientation and random incorporation of linkers containing restriction sites during ligation. Ligation products are amplified by PCR using the linker oligonucleotides as primers. Restriction digestion of the PCR products generate multimer distributions whose length is controlled by the monomer/linker ratio. The concatenated DNA fragments of defined length, orientation and spacing can be directly used for subcloning or other applications without further treatment.

Base Sequence↗
PubMed1996

The molecular structure, chromosomal organization, and interspecies distribution of a family of tandemly repeated DNA sequences of Antirrhinum majus L.

Monomers of a major family of tandemly repeated DNA sequences of Antirrhinum majus have been cloned and characterized. The repeats are 163-167 bp long, contain on average 60% A+T residues, and are organized in head-to-tail orientation. According to site-specific methylation differences two subsets of repeating units can be distinguished. Fluorescent in situ hybridization revealed that the repeats are localized at centromeric regions of six of the eight chromosome pairs of A. majus with substantial differences in array size. The monomeric unit shows no homologies to other plant satellite DNAs. The repeat exists in a similar copy number and conserved size in the genomes of six European species of the genus Antirrhinum. Tandemly repeated DNA sequences with homology to the cloned monomer were also found in the North American section Saerorhinum, indicating that this satellite DNA might be of ancient origin and was probably already present in the ancestral genome of both sections.

Base Sequence↗
PubMed1993

Large arrays of tandemly repeated DNA sequences in the green alga Chlamydomonas reinhardtii.

We describe the characterization of tandemly repeated DNA sequences, which resemble the satellite DNA sequences of multicellular eucaryotes, in the unicellular green alga Chlamydomonas reinhardtii. Restriction enzymes that cleave C. reinhardtii DNA relatively frequently produce a number of high molecular weight DNA fragments in addition to the bulk of low molecular weight DNA fragments. pTANC 1.5 contains a 1.5 kb Sau3A fragment cloned from one of these large bands. pTANC 1.5 hybridized to at least three large arrays (200 to 700 kb) of tandemly repeated DNA sequences in the cell-wall-deficient strain cw1.5. These arrays are composed of repeat units that are each cleaved once by BamHl into bands of 1.5, 1.9, 2.0 and 2.5 kb in size. The copy numbers of the 1.5, 1.9, 2.0 and 2.5 kb BamHl bands vary between different C. reinhardtii strains. Chlamydomonas smithii and a number of C. reinhardtii strains are deficient in all four BamHl bands. Genetic analysis of wild-type strain 137c, which is deficient in the 2.0 kb BamHl band, indicates that the 1.5, 1.9 and 2.5 kb BamHl bands derive from at least five loci. The 1.5, 1.9 and 2.5 kb repeat units are not extensively interspersed with each other in strain 137c. Pulsed-field gel electrophoresis of intact C. reinhardtii chromosomes indicates that TANC arrays are present on more than one chromosome.

Animals↗
PubMed1991

Clustered tRNA genes in Schizosaccharomyces pombe centromeric DNA sequence repeats.

The centromere-associated B' and B DNA sequence repeats of Schizosaccharomyces pombe chromosomes I and II have been found to contain clusters of tRNA genes. The centromere II region (cen2) includes at least 22 tRNA genes distributed among five copies of the B sequence repeat containing genes specifying tRNA(Ile), tRNA(Ala), and tRNA(Val). Individual B repeats are variously associated with other tRNA genes, including those specifying tRNA(Lys), tRNA(Arg), and tRNA(Glu2). The centromere I region (cen1) contains at least six tRNA genes in two copies of the B' repeated element, including genes specifying tRNA(Ile), tRNA(Ala), and tRNA(Glu3). Multiple tandemly arranged clusters of tRNA genes are presumably conserved due to restricted recombination frequencies in the centromere regions.

Base Sequence↗
PubMed2006

Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29.

AIMS: The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. METHODS AND RESULTS: Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. CONCLUSIONS: The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. SIGNIFICANCE AND IMPACT OF THE STUDY: The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic features of deviating E. amylovora strains have to be studied in detail.

Culture Media↗