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PubMed1999

Tandem repeats finder: a program to analyze DNA sequences.

A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human frataxin gene, the human beta T cellreceptor locus sequence and two yeast chromosomes. These sequences range in size from 3 kb up to 700 kb. A World Wide Web server interface atc3.biomath.mssm.edu/trf.html has been established for automated use of the program.

Algorithms↗
PubMed1998

An Assembly Algorithm for DNA Sequence with Repeats.

A program for assembling DNA fragments using a new approach has been developed. In the program, a filter and a sequence alignment are used to identify the true overlap between the two fragments. Then the fragments in repeat copies are put into a repeat contig and the others are put into nonrepeat contigs. The repeat contig is resolved into two contigs and then all contigs are merged into one contig. At last the multiple alignment is obtained by the order of fragments in the contig, thereby forming a consensus sequence.The performance tests of the program for eight fragment libraries have demonstrated the feasibility of the program.

Journal Article↗
PubMed1993

Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli.

Interspersed repeated DNA sequences are characteristic features of both prokaryotic and eukaryotic genomes. REP sequences are defined as conserved repetitive extragenic palindromic sequences and are found in Escherichia coli, Salmonella typhimurium and other closely related enteric bacteria. These REP sequences may participate in the folding of the bacterial chromosome. In this work we describe a unique class of 28 conserved complex REP clusters, about 100bp long, in which two inverted REPs are separated by a singular integration host factor (IHF) recognition sequence. We term these sequences RIP (for repetitive IHF-binding palindromic) elements and demonstrate that IHF binds to them specifically. It is estimated that there are about 70 RIP elements in E. coli. Our analysis shows that the RIP elements are evenly distributed around the bacterial chromosome. The possible function of the RIP element is discussed.

Bacterial Proteins↗
PubMed1999

A family of dispersed repeats in the genome of Vicia faba: structure, chromosomal organization, redundancy modulation, and evolution.

A family of repeated DNA sequences of about 1200 bp in length and bordered by well-conserved, 18 bp inverted repeats (VfB family) was found in the nuclear genome of Vicia faba. The structure, chromosomal organization, redundancy modulation and evolution of these sequences were investigated. They are enriched in A+T base pairs (about 40% G+C) and lack any obvious internally repeated motif. A 64%-73% nucleotide sequence identity was found when pairwise comparisons between VfB sequences were carried out (average 69%). Direct repeats were not found to flank the inverted repeats that border these DNA sequences. The results obtained by hybridizing VfB repeats to Southern blots of V. faba genomic DNA digested with EcoRI indicated that these DNA elements are interspersed in the genome. The appearance of bands in these Southern blots and comparison of the structure of the sequences that flank different VfB elements showed that these repeats might be part of other, longer repeated DNA sequences. A high degree of dispersion throughout the genome was confirmed by cytological hybridization, which showed VfB sequences to be scattered along the length of all chromosomes and to be absent or rare only at heterochromatic chromosomal regions. These sequences contribute to intraspecific alterations of genomic size. Indeed, dot-blot hybridizations proved that their redundancy, which is positively correlated with the overall amount of nuclear DNA in each accession, varies between V. faba land races (27x10(3)-230x10(3) copies per 1C DNA). Southern blot hybridization of VfB repeats to restriction endonuclease-digested genomic DNAs of V. faba, V. narbonensis, V. sativa, Phaseolus coccineus, Populus deltoides, and Triticum durum revealed nucleotide sequence homology of these DNA elements, whatever the stringency conditions, only to the DNAs of Vicia species, and to a reduced extent to the DNAs of V. narbonensis and V. sativa compared with that of V. faba. It is concluded that VfB repeats might be descended from mobile DNA elements and contribute to change genomic size and organization during evolution.

Base Composition↗
PubMed1975

Transcription of repetitive DNA in Neurospora crassa.

Repeated DNA sequences of Neurospora crassa were isolated and characterized. Approximately 10-12% of N. crassa DNA sequence were repeated, of which 7.3% were found to be transcribed in mid-log phase of mycelial growth as measured by DNA:RNA hybridization. It is suggested that part of repetitive DNA transcripts in N. crassa were mitochondrial and part were nuclear DNA. Most of the nuclear repeated DNAs, however, code for rRNA and tRNA in N. crassa.

Cell Nucleus↗
PubMed2002

[Microsatellite markers and applications in the barley genome].

Microsatellites, also called simple sequence repeats (SSR), are simple, tandemly repeated DNA sequences with a repeat length of a few base pairs,and are very ideally used as molecular markers because of their abundance, high level of polymorphism, co-dominance and ease of assay with the polymerase chain reaction (PCR) by selecting primers as the conserved DNA sequences flanking the SSRs,as well as better stability. The experiments showed that SSRs are randomly distributed throughout the barley genome,and there are 3-18 alleles at a single SSR locus,up to 37 alleles/locus. SSR markers have being widely applied in the construction of molecular genetic map, the study of genetic diversity,the identification of germplasm, gene mapping for important traits and molecular marker-assisted selection. Meanwhile,most of markers are strongly clustered around the centromeric regions of all seven linkage groups. As a result of the clustering,genome coverage with SSRs remains incomplete with an obvious lack of markers on the long arms of chromosomes 1H and 5H and short arm of chromosome 6H. Therefore,it is very potential and necessary to further develop SSR markers in barley.

English Abstract↗
PubMed1985

[Characteristics of the distribution of DNA repetitive sequences in the sex chromosomes of 4 species of rodent].

Four rodent species with very large heterochromatic regions on the sex chromosomes have been studied using in situ DNA/DNA hybridization techniques. Repetitious DNA fractions were obtained at C0t 0-0.01. Heterochromatic regions of X and X chromosomes of Cricetulus barabensis and Phodopus sungorus, and the heterochromatic long arm of the Y chromosome of Mesocricetus auratus do not contain disproportionately high amounts of repeated DNA sequences. Heterochromatic regions on sex chromosomes of Microtus subarvalis contain high amounts of repeated DNA sequences. Additional heterochromatic autosomal arms, a heterochromatic arm of the X chromosome, and a short arm of the Y chromosome of Mesocricetus auratus contain high amounts of repeated DNA sequences too.

Animals↗
PubMed1980

Ubiquitous, interspersed repeated sequences in mammalian genomes.

DNA base sequence comparisons demonstrate that the principal family of 300-nucleotide interspersed human DNA sequences, the repetitive double-strand regions of HeLa cell heterogeneous nuclear RNA, and specific RNA polymerase III in vitro transcripts of cloned human DNA sequences are all representatives of a closely related family of sequences. A segment of approximately 30 residues of these sequences is highly conserved in mammalian evolution because it is also present in the interspersed repeated DNA sequences of Chinese hamsters. Further DNA sequence comparisons demonstrate that a portion of this highly conserved segment of repetitive mamalian DNA sequence is similar to a sequence found within a low molecular weight RNA that hydrogen-bonds to poly(A)-terminated RNA molecules of Chinese hamsters and a sequence that forms half of a perfect inverted repeat near the origin of DNA replication in papovaviruses.

Animals↗
PubMed1994

Effect of internal direct and inverted Alu repeat sequences on PCR.

We have studied the effect of repeated DNA sequence, especially Alu repeats, on PCR. Alu repeats are sequences that are approximately 300 bp long and interspersed at a very high copy number throughout the human genome. We amplified part of the human low-density lipoprotein receptor gene containing two Alu repeat sequences in the same orientation, approximately 7.8 kb apart, with unique sequence primers outside these repeats. The major PCR product was a DNA fragment with an in vitro deletion between the Alu repeats. The formation of this product depended on the template concentration and the type of polymerase used. Such a product arose apparently as a result of a "jumping reaction" involving a primer whose extension was terminated prematurely within one Alu repeated followed by annealing of such an incompletely extended primer to the other, distant Alu repeat. No such jumping products were seen when a 0.8-kb region containing two nearby inverted Alu repeats within the human alpha-galactosidase A gene was subject to PCR with unique sequence primers annealing just outside these repeats.

Animals↗
PubMed1989

Genetic deletions between directly repeated sequences in bacteriophage T7.

DNA sequence analysis of genetic deletions in bacteriophage T7 has shown that these chromosomal rearrangements frequently occur between directly repeated DNA sequences. To study this type of spontaneous deletion in more quantitative detail synthetic fragments of DNA, made by hybridizing two complementary oligonucleotides, were introduced into the non-essential T7 gene 1.3 which codes for T7 DNA ligase. This insert blocked synthesis of functional ligase and made the phage that carried an insert unable to form plaques on a host strain deficient in bacterial ligase. The sequence of the insert was designed so that after it is put into the T7 genome the insert is bracketed by direct repeats. Perfect deletion of the insert between the directly repeated sequences results in a wild-type phage. It was found that these deletion events are highly sensitive to the length of the direct repeats at their ends. In the case of 5 bp direct repeats excision from the genome occurred at a frequency of less than 10(-10), while this value for an almost identical insert bracketed by 10 bp direct repeats was approximately 10(-6). The deletion events were independent of a host recA mutation.

Base Sequence↗
PubMed2003

Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA.

BACKGROUND: Simple sequence repeats (SSRs), microsatellites or polymeric sequences are common in DNA and are important biologically. From mononucleotide to trinucleotide repeats and beyond, they can be found in long (> 6 repeating units) tracts and may be characterized by quantifying the frequencies in which they are found and their tract lengths. However, most of the existing computer programs that find SSR tracts do not include these methods. RESULTS: A computer program named Poly has been written not only to find SSR tracts but to analyze the results quantitatively. CONCLUSIONS: Poly is significant in its use of non-standard, quantitative methods of analysis. And, with its flexible object model and data structure, Poly and its generated data can be used for even more sophisticated analyses.

Algorithms↗
PubMed1991

DNA Fingerprinting with a Dispersed Repeated Sequence Resolves Pathotype Diversity in the Rice Blast Fungus.

The poor definition of pathotype variation in the rice blast fungus has historically handicapped strategies for reducing blast disease damage to the world's rice crop. We have employed a probe for a dispersed repeated DNA sequence called MGR [Hamer et al. (1989). Proc. Natl. Acad. Sci. USA 86, 9981-9985] to construct genotype-specific, EcoRl restriction fragment length profiles (MGR-DNA fingerprints) from United States field isolates of this fungus. By using a blind-test design, we demonstrated that MGR-DNA fingerprints distinguished the major pathotypes in the United States, accurately identified the pathotypes of isolates collected over a 30-year period, and defined the organization of clonal lineages within and among pathotype groups. These results resolved a lingering controversy regarding rice blast pathotype stability and illustrated new opportunities for tracking the population dynamics and evolution of this important crop pathogen.

Journal Article↗
PubMed1987

Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup.

Interspecific variation in abundance of highly repeated DNA sequences has been examined in three species of the Aedes scutellaris and three species of the A. albopictus subgroup of the A. scutellaris group. Sequences from a population of A. albopictus were hybridised with whole genomic content from other species and strains. Copy number estimates were determined by dot-blot hybridisation. Variation in sequence abundance between strains of A. albopictus was as great as between it and the other six species. Two clusters were formed by principal components analysis, each of which contains populations of A. albopictus. Copy numbers of highly repeated sequences do not correlate with genome size. The results indicate extensive sequence divergence and rapid evolution. These findings are discussed in relation to the importance of concerted evolution and natural selection in the evolution of the species group.

Aedes↗
PubMed1985

Tandemly repeated nonribosomal DNA sequences in the chloroplast genome of an Acetabularia mediterranea strain.

A purified chloroplast fraction was prepared from caps of the giant unicellular green alga Acetabularia mediterranea (strain 17). High molecular weight DNA obtained from these chloroplasts contains at least five copies of a 10-kilobase-pair (kbp) sequence tandemly arranged. This unique sequence is present in DNA from chloroplasts of all stages of the life cycle examined. A chloroplast rDNA clone from mustard hybridized with some restriction fragments from Acetabularia chloroplast DNA but not with the repeated sequence. An 8-kbp EcoRI-Pst I fragment of the repeated sequence was cloned into pBR322 and used as a hybridization probe. No homology was found between the cloned 8-kbp sequence and chloroplast DNA from related species Acetabularia crenulata or chloroplast DNA from spinach.

Acetabularia↗
PubMed1990

Centromeres of budding and fission yeasts.

Centromeres of the budding yeast Saccharomyces cerevisiae are structurally relatively simple, are specified by only about 125 base pairs of DNA, and contain no repeated DNA sequences. The centromere regions in the fission yeast Schizosaccharomyces pombe span many kilobase pairs of DNA and contain repeated DNA sequences that appear to be necessary for full centromere function. A portion of the repeated sequences is organized into a large inverted repeated structure in the centromere region of each S. pombe chromosome. Fission yeast provides an excellent model system for studying the role of repeated DNA sequences in centromere function.

Base Sequence↗
PubMed2004

Influence of sequence context and length on the structure and stability of triplet repeat DNA oligomers.

Genetic expansion diseases have been linked to the properties of triplet repeat DNA sequences during replication. The most common triplet repeats associated with such diseases are CAG, CCG, CGG, and CTG. It has been suggested that gene expansion occurs as a result of hairpin formation of long stretches of these sequences on the leading daughter strand synthesized during DNA replication [Gellibolian, R., Bacolla, A., and Wells, R. D. (1997) J. Biol. Chem. 272, 16793-7]. To test the biophysical basis for this model, oligonucleotides of general sequence (CNG)(n), where N = A, C, G, or T and n = 4, 5, 10, 15, or 25, were synthesized and characterized by circular dichroism (CD) spectropolarimetry, optical melting studies, and differential scanning calorimetry (DSC). The goal of these studies was to evaluate the influence of sequence context and oligomer length on their secondary structures and stabilities. The results indicate that all single oligomers, even those as short as 12 nucleotides, form stable hairpin structures at 25 degrees C. Such hairpins are characterized by the presence of N:N mismatched base pairs sandwiched between G:C base pairs in the stems and loops of three to four unpaired bases. Thermodynamic analysis of these structures reveals that their stabilities are influenced by both the sequence of the particular oligomer and its length. Specifically, the stability order of CGG > CTG > CAG > CCG was observed. In addition, longer oligomers were found to be more stable than shorter oligomers of the same sequence. However, a stability plateau above 45 nucleotides suggests that the length dependence reaches a maximum value where the stability of the G:C base pairs can no longer compensate the instability of the N:N mismatches in the stems of the hairpins. The results are discussed in terms of the above model proposed for gene expansion.

Base Sequence↗
PubMed1995

Specific stimulation of recA-independent plasmid recombination by a DNA sequence at a distance.

Recombination between directly repeated DNA sequences can occur via both recA-dependent and recA-independent mechanisms. They are differentially affected by the length of the repeat and the distance separating the repeats, respectively. Interestingly, a 623 base-pairs long DNA sequence of the plasmid pBR322 was found to stimulate specifically recA-independent recombination between tandem repeats. Analysis of this stimulating sequence has revealed the following features. (1). It is cis-acting. (2). No specific region of it appears to be essential for the effect. Moreover, a neutral sequence of comparable size was able to substitute for the sequence in influencing recombination. (3). The sequence affects recombination between tandem repeats within the tetA but not the bla gene of pBR322. (4). The sequence exerts its effect in a position-dependent manner. (5). It changes not only the frequency but also the products of recombination. Our results provide an example that recA-independent recombination can be influenced by DNA sequences at a distance.

Antiporters↗
PubMed1993

Brugia malayi and Brugia pahangi: synthetic biotin labeling of oligonucleotide probes for use in species-specific detection assays.

We have developed a novel, high-yield synthetic approach for the incorporation of multiple biotin residues into a series of species-specific oligonucleotide probes for the detection of filarial parasites. The probes are designed to detect species-specific regions of a highly repeated DNA sequence (HhaI repeat) found in all species of Brugia. The synthetic method described in this paper was used to construct oligomer probes tailed on the 5' end with 1 to 46 biotinylated uridine residues. Probes with 46 biotins were found to be more sensitive than probes with 30 or fewer biotins. We also found that alternating the biotinylated uridine residues with nonbiotinylated thymidine residues improved the sensitivity of the probes. Melting temperature studies indicated that the long tails (up to 91 nucleotides) had only a minimal effect on the Tm of the probes. Conditions were found that optimized the sensitivity of the probes while maintaining their species specificity. Using these conditions, the probes were shown to be sensitive enough to detect single parasites in blood using a chemiluminescent detection system. This method of nonradioactively labeling oligonucleotides for the detection of infectious agents will enable the use of such probes in endemic regions in developing countries.

Animals↗