Cytological localization and organization of dispersed middle repetitive DNA sequences of Drosophila subobscura

To study the middle repetitive fraction of the Drosophila subobscura genome, 26 phage clones containing repetitive sequences were examined by Southern DNA blot analysis and by in situ hybridization to polytene chromosomes. These results led to a classification of the clones according to five different types of hybridization patterns. Two types, each containing seven clones, are characterized by hybridization at 100 to 300 sites dispersed over the euchromatic parts of the chromosomes, and in addition by one prominently labelled chromosome band. One of these two classes also showed strong labelling of the chromocentre. The remaining types of hybridization pattern lacked a prominent band but showed hybridization either to the euchromatic regions or to the chromocentre or both. Chromosome A (=X) was the preferred location of prominently labelled bands and it also showed an excess of labelling by some clones. Some of the cloned dispersed sequences were localized cytologically on chromosomes of larvae from crosses between different strains of D. subobscura and between two closely related species, in order to detect heterozygosity at hybridization sites. Comparisons of the chromosomal distribution of labelling sites showed differences in number and location, indicating the possibility of transposition events.     

Patterns of polytene-chromosome replication in Simulium ornatipes (Diptera: Simuliidae)

Double labelling of Simulium ornatipes polytene chromosomes with H³- and C¹⁴-thymidine shows that chromosome synthesis follows three distinct phases viz. a short phase of initiation in puffs and interbands spreading to more condensed regions; a long continuous labelling phase, then a discontinuously labelled end phase as bands complete their replication in temporal sequence. Analysis of H³ labelling patterns indicates that while heterochromatic bands replicate there is no clear correlation between heterochromatic or C-banding regions and band replication time. The major characteristic governing band replication time appears to be band size and density. However, in some bands this relationship is modified, perhaps it is suggested, by DNA organisation influencing the efficiency of replicons. The existence of great variability in homologous band replication times, even within a chromosome pair, indicates that the control of band replication is highly autonomous. It is suggested that polymorphisms at the molecular level determine this variation. Replication time of active nucleolar organisers is very long in contrast to the short replication of condensed inactive organisers. This may reflect differential polytenisation of ribosomal DNA as a result of a developmental polymorphism, or the amplification of ribosomal DNA by active nucleolar organisers.     

Polytene chromosome structure at the submicroscopic level

Electron microscopic observations on sections of squashed glutar-aldehyde-fixed salivary gland X-chromosomes ofDrosophila melanogaster provided an ultrastructural map of the band sequence of region 1A1 to 4E3. Comparison of this map with the map of Bridges (1938) revealed a significantly lower number of bands. Only 67% of the bands depicted in Bridges' map could be identified. This discrepancy seems to be a consequence mainly of the absence of doublet characters of bands on Bridges' map. — A possible relationship between bands and genes is discussed for some regions, including the white-Notch region. It appears that a one to one relationship between bands and genes does exist for two regions, whereas in region 3C1–3C7 more genes than bands are present. In this respect the structural organization of bands at the submicroscopic level is discussed. — The average DNA content of a band at the haploid level is calculated on the basis of the reduction in band number to be 4.5 × 10^?5 picogram.     

Localisation of foldback DNA sequences in nuclei chromosomes of Scilla, Secale, and of mouse.

Foldback DNA, prepared from mouse and Scilla sibirica main band DNA, and from rye (Secale cereale) total DNA, was characterised by denaturation, renaturation, and electron microscopy. 3H-cRNA of this DNA was hybridised in situ to nuclei and chromosomes of the respective species. There is no universal labelling pattern among the three species. In mouse, highly repetitive foldback DNA is present in the whole chromatin including the satellite DNA-containing regions. In Scilla sibirica, on the contrary, the highly repetitive foldback sequences are excluded form the satellite DNA loci and are arranged in clusters in the remaining chromatin. In rye, there is a clear preferential labelling of the chromocenters in the interphase nuclei as well as metaphase chromosomes, indicating that highly repetitive foldback DNA is preferentially located among other highly repetitive sequences.     

Comparative cytogenetic analysis of Cestrum (Solanaceae) reveals different trends in heterochromatin and rDNA sites distribution

Species of Cestrum L. (Solanaceae) exhibit large variability in the accumulation of repetitive DNA, although their species possess a stable diploid number with 2n = 16. In this study, we used chromosome banding and fluorescence in situ hybridization (FISH) to characterize the karyotypes and populations of two species, Cestrum nocturnum L. and C. mariquitense Kunth. We also performed a karyotype comparison using 16 idiograms, of which 4 were developed in this study and 12 were obtained from the literature. Cestrum nocturnum displayed more bands than C. mariquitense, but the latter exhibited greater interpopulational variation in the band patterns. There was a tendency for large bands to be located at intercalary/terminal regions and for small bands to be located at intermediate/proximal regions. The idiogram comparison revealed a large variation in the amount, distribution, and size of heterochromatic bands. FISH with rDNA probes revealed stability in the number and location of 5S sites, while 45S was more variable in size and number of sites. Although 45S rDNA always appeared in the subterminal regions, this DNA family exhibited a mobility among chromosome pairs. These data highlight the dynamic of repetitive DNA families in these genomes, as well as the contribution for intra- and interspecific karyotype differentiation in Cestrum.     

自身基因组原位杂交揭示植物基因组重复DNA沿染色体的分布

重复DNA沿染色体的分布是认识植物基因组的组织和进化的要素之一。本研究采用一种改良的基因组原位杂交程序,对基因组大小和重复DNA数量不同的6种植物进行了自身基因组原位杂交(self-genomic in situ hybridization,self-GISH)。在所有供试物种的染色体都观察到荧光标记探针DNA的不均匀分布。杂交信号图型在物种间有明显的差异,并与基因组的大小相关。小基因组拟南芥的染色体几乎只有近着丝粒区和核仁组织区被标记。基因组相对较小的水稻、高粱、甘蓝的杂交信号分散分布在染色体的全长,但在近着丝粒区或近端区以及某些异染色质臂的分布明显占优势。大基因组的玉米和大麦的所有染色体都被密集地标记,并在染色体全长显示出强标记区与弱标记或不标记区的交替排列。此外,甘蓝染色体的所有近着丝粒区和核仁组织区、大麦染色体的所有近着丝粒区和某些臂中间区还显示了增强的信号带。大麦增强的信号带带型与其N-带带型一致。水稻自身基因组原位杂交图型与水稻Cot-1DNA在水稻染色体上的荧光原位杂交图型基本一致。研究结果表明,自身基因组原位杂交信号实际上反映了基因组重复DNA序列对染色体的杂交,因而自身基因组原位杂交技术是显示植物基因组中重复DNA聚集区在染色体上的分布以及与重复DNA相关联的染色质分化的有效方法。     

Cloning of DNA sequences localized on proximal fluorescent chromosome bands by microdissection in Pinus densiflora Sieb. & Zucc.

Japanese red pine, Pinus densiflora, has 2n=24 chromosomes, of which most carry chromomycin A3 (CMA) and 4',6-diamidino-2-phenylindole (DAPI) bands at their centromere-proximal regions. It was proposed that these regions contain highly repetitive DNA. The DNA localized in the proximal fluorescent bands was isolated and characterized. In P. densiflora, centromeric and neighboring segments of the somatic chromosomes were dissected with a manual micromanipulator. The centromeric DNA was amplified from the DNA contained in dissected centromeric segments by degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) and a cloned DNA library was constructed. Thirty-one clones carrying highly repetitive DNA were selected by colony hybridization using Cot-1 DNA from this species as a probe, and their chromosomal localization was determined by fluorescent in situ hybridization (FISH). Clone PDCD501 was localized to the proximal CMA band of 20 chromosomes. This clone contained tandem repeats, comprising a 27 bp repeat unit, which was sufficient to provide the proximal FISH signal, with a 52.3% GC content. The repetitive sequence was named PCSR (proximal CMA band-specific repeat). Clone PDCD159 was 1700 bp in length, with a 61.7% AT content, and produced FISH signals at the proximal DAPI band of the remaining four chromosomes. Four clones hybridized strongly to the secondary constriction and gave weak signals at the centromeric region of several chromosomes. Clone PDCD537, one of the four clones, was homologous to the 26S rRNA gene. A PCR experiment using microdissected centromeric regions suggested that the centromeric region contains 18S and 26S rDNA. Another 24 clones hybridized to whole chromosome arms, with varying intensities and might represent dispersed repetitive DNA.     

Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.

Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.     

Cytological differentiation of constitutive heterochromatin

The constitutive heterochromatin, as demonstrated by the C band technique, may be subdivided into a number of categories when other characteristics are considered. The responses to fluorochromes QM and 33258 Hoechst, the behavior following G band staining, the repetitive DNA content, and many other criteria are useful for the classification of heterochromatin. The heterochromatin patterns of three mammalian species are presented to demonstrate that within each karyotype there may be several different types of C bands. In general, a correlation may also be made between GC-rich satellite DNA and dull (or negative) Q fluorescence, and between AT-rich satellite DNA and bright Q, fluorescence.On Sabbatical leave from Department of Biology, University of North Dakota, Grand Forks, North Dakota.     

Characterization of a human alphoid satellite DNA sequence: Potential use in assessing genetic diversity in Indian populations

Sequence analysis of a human repetitive DNA sequence (pTRF5.6) revealed considerable homology (76%) to the alphoid consensus sequence. Genomic blots of StuI-digested human DNA, hybridized to pTRF5.6, generated a ladder of bands with each band corresponding to oligodeoxyribonucleotide of an approx. 170-bp repeat, indicating a tandemly arrayed organization of this repeat element within the genome. Genomic hybridization analyses of unrelated individuals belonging to various geographical regions of India, using this alphoid satellite probe, revealed polymorphic bands ranging between 2 and 9 kb. Along with an individual-specific band pattern, several isomorphic bands below 2 kb were also evident. There was very little of genetic variability between populations, suggestive of low polymorphism at the inter-population level. Our result suggest that alphoid satellite sequence probe can be used in assessing the genetic diversity of various ethnic groups/populations belonging to different geographical regions.     

Distribution of Mitomycin C-induced damage in human chromosomes with special reference to regions of repetitive DNA

The distribution of gaps, breaks, exchanges and other effects induced by Mitomycin C on human chromosomes was analysed to examine the possibility of a correlation between chromosome lesions and regions of repetitive DNA. Homologous and non-homologous exchanges between chromosomes Nos. 1, 9 and 16, and also between and with the acrocentric chromosomes were more frequent than expected, but breaks and gaps appeared to be located randomly with regard to chromosome light and dark bands.     

Characterization of extrachromosomal DNA in the flesh fly Sarcophaga bullata

The polytene pupal foot pad cells of the flesh fly Sarcophaga bullata contain numerous extrachromosomal DNA containing granules. We have determined both the origin and the nature of the DNA sequences present in these granules. Studies done with quinacrine staining of seven day old pupal foot-pad polytene nuclei showed that the granules fluoresced very brightly while the chromosomal bands to which the granules were attached did not. The only other highly fluroescent regions of the polytene karyotype were the centromeric heterochromatin of chromosomes C and E and several bands associated with the nucleolus of Chromosome A. When polytene nuclei were hybridized in situ with cRNA made from highly repetitive DNA, many of the granules positively labeled. Most of the label on these slides was concentrated on the centromeric heterochromatin of chromosomes C and E. Quinacrine staining of the foot-pad cells at very early stages of pupal development showed that when granules were present, they were always closely associated with the same two centromeric regions, those of chromosomes C and E. Since the highly repetitive DNA located in these centromeric regions is underreplicated, we conclude that the granules result from an extrusion process which takes place early during the polytenization of these cells. The chromosomal integrity of the centromeric heterochromatin of chromosomes C and E is apparently disrupted and repetitive sequences are dissociated from the chromosomes as DNA granules which then secondarily become associated with chromosomal bands throughout the nucleus.     

An alternative view of mammalian DNA sequence organization: I. Repetitive sequence interspersion in Syrian hamster DNA: A model system

The biochemical and biophysical techniques originally introduced by Davidson et al. (1973) and Graham et al. (1974) for the determination of the general organization and length of repetitive and non-repetitive sequences in eukaryotic DNA have been extended and modified. Improvements in the experimental methods employed in these pioneering works have led to novel interpretations and conclusions about mammalian DNA sequence organization. In what is commonly referred to as an interspersion experiment, the average spacing of repetitive DNA regions is inferred from the length dependence of hydroxyapatite binding of radio-labeled tracer DNAs reassociated with an excess of short 200 nucleotide repetitive sequence driver DNA. Studies on Syrian hamster DNA, using an improved procedure for conducting interspersion experiments, suggest that either a frequent cluster in the distribution of non-repetitive DNA sequence lengths occurs at 7200 (±2000) nucleotides or that repetitive sequences are randomly spaced on a number average basis. In contrast, measurements obtained using the traditional methods suggest that a frequent cluster in the distribution of non-repetitive DNA sequence lengths occurs at approximately 1000 nucleotides. When reassociations were conducted at elevated temperatures, to allow only well-matched repetitive sequences to hybridize, the amount of DNA operationally observed as “repetitive” was reduced. Interspersion experiments conducted with Syrian hamster DNA at a reassociation temperature of 75 °C yielded data similar to those obtained by Manning et al. (1975) for Drosophila melanogaster DNA reassociated at 60 °C.     

Satellite DNA associated with heterochromatin in Rhynchosciara

The DNA of Rhynchosciara hollaenderi was examined using isopycnic centrifugation in neutral CsCl. Two low density minor bands (collectively termed satellite DNA) were detected in addition to the main band DNA. Main band DNA has a buoyant density of 1.695 g/cm³. The larger of the two minor bands has a buoyant density of 1.680 g/cm³ while the smaller of the two minor bands has a buoyant density of about 1.675 g/cm³. Thermal denaturation studies have confirmed the presence of the two minor classes of DNA.—The satellite and main band DNAs were isolated in relatively pure form and were transcribed in vitro using DNA-dependent RNA polymerase from Escherichia coli. Annealing of the two complementary RNAs (cRNAs) with main band and satellite DNA was examined using filter hybridization techniques.—The chromosomal distribution of the satellite DNA was determined by in situ molecular hybridization of satellite-cRNA with Rhynchosciara salivary gland chromosomes. Satellite-cRNA hybridized with the centromeric heterochromatin of each of the four chromosomes (A, B, C, and X) and with certain densely staining bands in the telomere regions of the A and C chromosomes. Main band-cRNA annealed with many loci scattered throughout the chromosomes including areas containing satellite DNA.     

Hot spots of DNA instability revealed through the study of somaclonal variation in rye

RAPD analysis was performed to assess DNA variation among rye plants regenerated from immature embryos and inflorescences. From the studied plants, 40% showed at least one variation, and the number of mutations per plant was quite high, ranging from 1 up to 12. On some occasions (2.9% of the scored bands) the modified band was observed in only one plant or in several but originated from the same callus (variable band). In other cases (5.25%) the same band varied in several plants obtained from different calli. We call these hypervariable bands and they could vary between plants belonging to different cultivars and/or with different origins, inflorescences or embryos. Thus, they must originate through independent mutational events. We assume that these bands represent hypervariable regions of the rye genome and so detect hot spots of DNA instability. Some of these bands proved to be unique sequences, others were present in a low copy number while the remaining ones were moderately or highly repetitive. Received: 10 May 1999 / Accepted: 17 June 1999 Communicated by R. Hagemann     

Two Types of Alpha Satellite DNA in Distinct Chromosomal Locations in Azara's Owl Monkey

Alpha satellite DNA is a repetitive sequence known to be a major DNA component of centromeres in primates (order Primates). New World monkeys form one major taxon (parvorder Platyrrhini) of primates, and their alpha satellite DNA is known to comprise repeat units of around 340 bp. In one species (Azara''s owl monkey Aotus azarae) of this taxon, we identified two types of alpha satellite DNA consisting of 185- and 344-bp repeat units that we designated as OwlAlp1 and OwlAlp2, respectively. OwlAlp2 exhibits similarity throughout its entire sequence to the alpha satellite DNA of other New World monkeys. The chromosomal locations of the two types of sequence are markedly distinct: OwlAlp1 was observed at the centromeric constrictions, whereas OwlAlp2 was found in the pericentric regions. From these results, we inferred that OwlAlp1 was derived from OwlAlp2 and rapidly replaced OwlAlp2 as the principal alpha satellite DNA on a short time scale at the speciation level. A less likely alternative explanation is also discussed.     

Sequence organization in Xenopus DNA studied by the electron microscope.

Xenopus laevis DNA was extracted from red blood cells and sheared to a mean length of 2780 nucleotides. The DNA was stripped of foldback-containing fragments and incubated to C₀t 10 (mol · s · l⁻¹), allowing most repetitive sequences to form duplex structures. Duplex-containing fragments were eluted from an hydroxylapatite column and visualized for electron microscopy by spreading from 57% formamide according to the modified Kleinschmidt technique of Davis et al. (1971). The mean length of the fragments observed was 2445 nucleotides. A total of 1700 DNA strands were photographed and studied. Less than 5% of the total strand length was in uninterpretable structures. Every molecule falling within the confines of the plates was included in the sample. Over 50% of the total strand length in the sample was found in structures bearing at least one interspersed repetitive sequence duplex terminated by four single-strand regions. The fraction of DNA present in duplex regions was almost exactly that predicted if the duplex regions represent all the interspersed middle repetitive sequence in the Xenopus genome. Direct measurement of visualized duplexes shows that the mean length of interspersed repetitive sequence elements in this genome is 345 nucleotides. Duplex length was shown to be independent of the length of the strands bearing the duplexes. These observations provide direct confirmation of the length of approximately 300 nucleotides indicated for interspersed repetitive sequences by earlier physical-chemical studies 011 Xenopus DNA. In strands carrying two duplexes terminated by single-strand regions the interduplex, or single-copy sequence element length could be measured. Sequence interspersion curves generated from these data are roughly consistent with those derived earlier from measurements of hydroxylapatite binding as a function of fragment length.