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PubMed2000

Unique chromosome identification and sequence-specific structural analysis with short PNA oligomers.

We have extended our earlier work to show that individual 14-20mer peptide nucleic acid probes directed against interspersed alpha-satellite sequences can specifically identify chromosomes. Peptide nucleic acid (PNA) probes were used to detect chromosomal abnormalities and repeat structure in the human genome by fluorescence in situ hybridization (FISH). The hybridization of a single PNA probe species directed against a highly abundant alpha-satellite DNA repeat sequence was sufficient to absolutely identify a chromosome. Selection of highly repetitive or region-specific DNA repeats involved DNA database analysis. Distribution of a specific repeat sequence in human genome was estimated through two means: a computer program "whole genome" approach based on approximately 400 Mb (12%) human genomic sequence. The other method involved directed search for alpha satellite sequences. In total, approximately 240 unique DNA repeat candidates were found. Forty-two PNA probes were designed for screening chromosome-specific probes. Ten chromosome-specific PNA probes for human Chromosomes (Chrs) 1, 2, 7, 9, 11, 17, 18, X, and Y have been identified. Interphase and metaphase results demonstrate that chromosome-specific PNA probes are capable of detecting simple aneuploidies (trisomies) in human. Another set of PNA probes showed distinct banding-like patterns and could be used as sequence-specific stains for chromosome "bar coding". Potential application of PNA probes for investigating repeat structure and function is also discussed.

Base Sequence↗
PubMed1990

DNA sequence polymorphisms in Alu repeats.

We have developed an efficient method for detection of sequence differences in genomic DNA based on a new principle (M. Orita et al., 1989, Genomics 5: 874-879). Using this method, we show here that approximately half the Alu repeats interspersed in the human genome are significantly polymorphic. Analysis of Alu repeat polymorphism should be useful in construction of a high-resolution map and also in identifying genotypes of individuals for clinical and other purposes because the repeats are ubiquitous and the technique for their detection is simple.

Base Sequence↗
PubMed2002

Nature and evolution of B chromosomes in plants: A non-coding but information-rich part of plant genomes.

This work reviews recent advances providing insights on the origin and evolution of B chromosomes (Bs) in representative plant species. Brachyome dichromosomatica has large and micro Bs. Both carry an inactive ribosomal gene cluster. The large Bs contain the B-specific Bd49 family, mainly located at the centromere. Multiple copies are present in the A chromosomes (As) of related species, whereas only a few copies exist in B. dichromosomatica As. The micro Bs share sequences with the As, the large Bs and have the B-specific repeats Bdm29 and Bdm54. It seems that the large and micro Bs are related in origin. It is very unlikely that the Bs originated by simple excision from the As. Rye Bs are composed of sequences predominantly shared with the As. B-specific sequences are located at the heterochromatic end of the long arm. Probably, they originated from the As after many rearrangements, with a tendency for duplication. The E3900 family derives from a Ty3 gypsy retrotransposon, but the D1100 family shows no evidence of genic origin. The overall composition of maize As and Bs is similar suggesting a common origin. Several B-specific sequences have been found, the most studied being pZmBs, which is located at the B centromere. It shows partial homology to the centromere of chromosome 4 and to the knobs. It is not known whether the B centromere derives from centromere 4, or whether both have a more distant common origin. The dynamics of Bs in populations depends on their non-Mendelian mechanisms of transmission, their effects on carrier fitness and on A genes modulating their parasitic properties. Three representative examples are reviewed. The Bs of Allium schoenoprassum are transmitted at a mean lower than Mendelian and adversely affect vigour and fertility. However, there is a differential selection operating in favour of B-containing seedlings. Rye Bs undergo strong drive, which is counteracted by harmful effects on fertility and instabilities at meiosis. Both nondisjunction and meiotic behaviour, and consequently the establishment of B polymorphisms, mainly depend on the Bs themselves. B nondisjunction in maize is controlled by the B, but the As control preferential fertilisation. Considering the non-equilibrium model, the Bs of Allium seem to have been neutralised by the A genome, the As of maize provide defence against B attack, whereas the Bs of rye are only slightly neutralized.

Biological Evolution↗
PubMed1989

B-G cDNA clones have multiple small repeats and hybridize to both chicken MHC regions.

We used rabbit antisera to the chicken MHC erythrocyte molecule B-G and to the class I alpha chain (B-F) to screen lambda gt11 cDNA expression libraries made with RNA selected by oligo-dT from bone marrow cells of anemic B19 homozygous chickens. Eight clones were found to encode B-G molecules which hybridize with sequences in the chicken MHC as defined by congenic strains; the fusion proteins react with multiple immune but not preimmune sera, they select antibodies from the antisera to B-G, which then react with distinct erythrocyte B-G protein patterns, and they elicit antibodies from mice which in turn react with authentic B-G proteins. None of the clones represent a complete message, some--if not all--bear introns, and none of them match with any sequences presently stored in the data banks. The following new information did, however, emerge. At least two homologous transcripts are present in this homozygous chicken, thereby formally proving the existence of an expressed multigene family. The 3' ends (3'UT) are simple sequences with 80% nucleotide identity between clones, while the 5' ends (either coding or noncoding) are composed of multiple short repeats which are far less similar. These repeats could explain the bewildering variation in size of B-G proteins within and between haplotypes. Southern blots of genomic chicken DNA gave complex patterns for most probes, with many bands in common using different probes, but few bands in common between haplotypes. The sequences detected are all present in the MHC, based on the congenic lines CB and CC. Most of these sequences map into the B-G region, but some map into the B-F/B-L region as defined by the haplotypes B15, B21, and their apparently reciprocal recombinants B21r3 and B15r1.

Animals↗
PubMed2000

Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

Animals↗
PubMed2003

The structure of telomeric DNA.

The telomere is a nucleoprotein complex located at the ends of eukaryotic chromosomes. It is essential for maintaining the integrity of the genome. It is not a linear structure and, for much of the cell cycle, telomeric DNA is maintained in a loop structure, which serves to protect the vulnerable ends of chromosomes. Many of the key proteins in the telomere have been identified, although their interplay is still imperfectly understood and structural data are only available on a few. Telomeric DNA itself comprises simple guanine-rich repeats for most of its length, culminating in a short overhang of single-stranded sequence at the extreme 3' ends. This can, at least in vitro, fold into a wide variety of four-stranded quadruplex structures, many of whose arrangements are being revealed by crystallographic and NMR studies.

DNA↗
PubMed1996

In situ detection of tandem DNA repeat length.

A simple method for scoring short tandem DNA repeats is presented. An oligonucleotide target, containing tandem repeats embedded in a unique sequence, was hybridized to a set of complementary probes, containing tandem repeats known lengths. Single-stranded loops structures formed on duplexes containing a mismatched (different) number of tandem repeats. No loop structure formed on duplexes containing a matched (identical) number of tandem repeats. The matched and mismatched loop structures were enzymatically distinguished and differentially labeled by treatment with S1 nuclease and the Klenow fragment of DNA polymerase.

Base Sequence↗
PubMed1991

Fine mapping of satellite DNA sequences along the Y chromosome of Drosophila melanogaster: relationships between satellite sequences and fertility factors.

The entirely heterochromatic Y chromosome of Drosophila melanogaster contains a series of simple sequence satellite DNAs which together account for about 80% of its length. Molecular cloning of the three simple sequence satellite DNAs of D. melanogaster (1.672, 1.686 and 1.705 g/ml) revealed that each satellite comprises several distinct repeat sequences. Together 11 related sequences were identified and 9 of them were shown to be located on the Y chromosome. In the present study we have finely mapped 8 of these sequences along the Y by in situ hybridization on mitotic chromosome preparations. The hybridization experiments were performed on a series of cytologically determined rearrangements involving the Y chromosome. The breakpoints of these rearrangements provided an array of landmarks along the Y which have been used to localize each sequence on the various heterochromatic blocks defined by Hoechst and N-banding techniques. The results of this analysis indicate a good correlation between the N-banded regions and 1.705 repeats and between the Hoechst-bright regions and the 1.672 repeats. However, the molecular basis for banding does not appear to depend exclusively on DNA content, since heterochromatic blocks showing identical banding patterns often contain different combinations of satellite repeats. The distribution of satellite repeats has also been analyzed with respect to the male fertility factors of the Y chromosome. Both loop-forming (kl-5, kl-3 and ks-1) and non-loop-forming (kl-2 and ks-2) fertility genes contain substantial amounts of satellite DNAs. Moreover, each fertility region is characterized by a specific combination of satellite sequences rather than by an homogeneous array of a single type of repeat.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Patterns of molecular evolution in avian microsatellites.

In order to develop models which appropriately reflect microsatellite evolution, more knowledge is required about the processes by which these simple sequences evolve. In this study, historical mutation events in three avian microsatellite loci belonging to distinct classes of repeat types (one perfect di-, one compound di-, and one perfect tetranucleotide repeat) were examined by sequence analysis of 76 alleles in 39 species spanning the avian phylogeny. The mode and tempo of evolution varied greatly between loci. For the perfect dinucleotide repeat, intraspecific length polymorphism was detected when alleles contained as few as six or seven repeat units, and size expansion over evolutionary timescales was demonstrated for repeats as short as (AG)2. A remarkable level of fragment stability was found for the compound dinucleotide repeat, even in species thought to have diverged over 60 MYA, coinciding with a high level of primer sequence conservation at this locus. In contrast, a hypervariable (AAAG)n locus revealed extraordinary instability and structural heterogeneity in the repeat region, including long arrays of derivative repeat motifs such as (AG)n, (AAGG)n, (AAAAG)n, and even (AAAGAGAG)n. Often, several motifs could be found within the same allele. A large number of cases of allele size homoplasy were detected for all three loci. These findings reinforce the fact that greater attention should be paid to the repeat type and the mutational characteristics of a marker before use in phylogenetic studies.

Alleles↗
PubMed1991

DNA fingerprinting in reptiles: Bkm hybridization patterns in Crocodilia and Chelonia.

The simple tetranucleotide repeat GATA (GACA) occurs in all eukaryotes so far studied. In many species, the arrangement of these sequences varies considerably among individuals. Thus GATA (GACA) type probes produce DNA fingerprints when hybridized with restricted DNA from different individuals within a species. Banded krait minor (Bkm) satellite DNA (related to sequences originally recovered from the W chromosome of the banded krait and consisting essentially of a series of GATA repeats) is found in a wide spectrum of vertebrates and invertebrates. We used the Bkm 2(8) clone to evaluate the occurrence of this satellite in DNA from five species of Crocodilia and six species of Chelonia, including the sea turtles Chelonia mydas and Lepidochelys kempi. Well-resolved DNA fingerprints were obtained. Among the crocodilians, fewer restriction fragments were generated and fewer of the fragments were polymorphic, than among the chelonians, consistent with the view that the crocodilians are less divergent within species. The Bkm 2(8) clone can accordingly be used to advantage in individual, familial, and population studies, and perhaps in the evaluation of taxonomic relationships in these animals. This is of potential value in endangered species such as C. mydas and L. kempi.

Alligators and Crocodiles↗
PubMed2002

tacg--a grep for DNA.

BACKGROUND: Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple motifs with IUPAC degeneracies, regular expressions, patterns allowing mismatches, and probability matrices. RESULTS: I describe a small application which allows searching for all the above pattern types individually, which further allows these atomic motifs to be assembled into logical rules for more sophisticated analysis. CONCLUSION: tacg is small, portable, faster and more capable than most alternatives, relatively easy to modify, and freely available in source code.

Algorithms↗
PubMed1989

Vowel quality changes produced by surrounding tone sequences.

In three experiments, we examined whether energy at the same frequency as one of a vowel's harmonics in the F1 region can be captured by a preceding or following sequence of tones. The position of the /I/-/E/ phoneme boundary along an F1 continuum was used to assess the extent of capture. The first two experiments showed that a sequence of tones at 500 Hz (56-msec duration at 10/sec) can perceptually remove added energy at 500 Hz from a steady vowel (F0 = 125 Hz) that forms part of the sequence. The effect is detectable with one preceding tone, asymptotes with four, and is greater when two tones follow the vowel than when none do. Rising and falling sequences of tones (at 62.5-Hz intervals or at whole-tone intervals) differ in their effect. Falling sequences behave much like constant tones at 500 Hz but with less effect, whereas rising sequences show no evidence of removing the added tone. The second experiment replicated the first and also showed that when the vowel is embedded in a rising or a falling sequence of tones that continue after it, the following tones have no effect. The third experiment suggested that the different effects found with rising versus falling sequences are qualitatively predictable on the basis of the additive effects of their constituent tones rather than by virtue of their contour. The experiments indicated that sequences of repeating tones are much more effective at capturing a harmonic from a vowel than are sequences that follow a simple pattern. This result may reflect the operation of a principle of least commitment in auditory grouping.

Attention↗
PubMed1976

Electron microscopy of analysis of circular repetitive mitochondrial DNA molecules from genetically characterized rho- mutants of Saccharomyces cerevisiae.

1. We have studied mtDNA purified from nine p- petite mutants in which most of the wild type sequence has been deleted but the genetic markers conferring resistance to erythromycin of oligomycin or paromomycin have been retained. 2. All mtDNA contained numerous circular molecules. The size distribution of the circles conformed to a multimeric series which was characteristic for each mutant. We conclude that any one region of the wild type mtDNA molecule, when maintained in a p- clone, while other regions are deleted, can give rise to a multimeric series of circles. 3. In tandem straight repetitive mtDNAs the circles contain odd and even number of unit sequence repeats. In palindrome repetitive mtDNAs the circles contain mostly even number of unit sequence repeats. Thus, one straight or two inverted repeats constitute the monomeric unit of circularization. 4. We found that the frequency distribution of circles follows on a number basis a simple rule: frequency of numeric circles = 1/n frequency of monomeric circles, for n = 2, 3 and 4. Thus, on a mass basis each class represents the same fraction of total mtDNA and the mitochondrial genome has the same probability to constitute one monomeric circle or to be a part of n-meric circle. We interpret this finding that in vivo all molecules are circular. 5. Four mutants displayed a single multimeric series of circles ranging from 0.3 mum to 2.4 mum monomer circle length. Five mutants displayed multiple different multimeric series. In the latter case, the longest unit sequence repeat length was equal to the sum of the two shorter unit sequence repeat lengths. Sorting out, recombination and internal deletions of circular repetitive p- mtDNA molecules are discussed.

Centrifugation, Density Gradient↗
PubMed1981

Base substitutions, length differences and DNA strand asymmetries in the human G gamma and A gamma fetal globin gene region.

We have studied differences arising subsequent to the 5 kilobase pair (kb) duplication that led to the human G gamma and A gamma fetal globin genes. The local occurrence of base substitutions in the duplicated 5 kb region correlates positively with the local AT base pair content. This correlation also occurs in two mouse beta-globin genes and in two mouse immunoglobulin genes. The relationship is valid for transcribed or nontranscribed DNA and for DNA that contains only coding sequences. Length differences in the fetal globin duplicated regions correlate positively with the occurrence of short direct repeats of greater than or equal 5 base pairs. Path analysis of the interrelationships of base composition, base substitutions, repeats and length differences provides an integrated view of the relative effects on chromosomal changes of these variables and of selection. The distributions along the chromosome of simple sequences and of base compositions show highly significant local asymmetries between the transcribed and nontranscribed strands of the DNA, which permit us to divide the fetal globin gene region into chromosomal domains. Comparable domains are present in DNA from other sources, including the mammalian viruses SV40 and polyoma virus strain A-2 in which some of the domains appear related to discrete functions.

Animals↗
PubMed1996

[A detection for replication error (RER) and LOH by microsatellite analysis in human lung cancer].

Recently, it has been considered that the pleomorphic changes in the microsatellite areas, which are said to exist at 50 to 100 thousand places on the human chromosome, are the results of abnormality in the repairing mechanism in cancer cells, and active attempts are now being made to detect such changes using PCR. In the DNA of cancer tissue where the repairing function has decreased, sequence repeat different in length from that of the DNA of normal tissue is observed. Such abnormal repeat shows itself as replication error (RER). As method of detecting RER, PCR was hitherto performed using RI-labeled primer, and after electrophoresis, detection was made by autoradiography. In order to obtain a reproducible result in a simple way, we attempted to detect by RER with auto-sequencer in 60 patients with lung cancer. As a result, we obtained data with a high sensitivity and objectivity. Therefore, a report is made on this study of ours.

Base Sequence↗