Human satellite-III DNA: an example of a "macrosatellite" polymorphism

Identification of homogeneously staining regions by G-banding and chromosome microdissection, and FISH marker selection using human Alu sequence primers in a scleractinian coral Coelastrea aspera Verrill, 1866 (Cnidaria)

Karyotype analysis was performed on the scleractinian coral Coelastrea aspera Verrill, 1866, commonly found along temperate coasts in Japan (30-35°N) and in coastal waters in the Indian and Pacific oceans. G-banding of Coelastrea aspera was successfully performed, although the banding pattern was not as clear as that in mammals. The karyogram clearly revealed that this coral had a homogeneously staining region (hsr) in chromosome 11. This hsr consisted of ribosomal RNA (rRNA) related genes, which was demonstrated by fluorescence in situ hybridization (FISH) with probes generated using 28S ribosomal DNA (rDNA) primers and those generated through chromosome microdissection. In addition, we conducted silver-stained nucleolus organizer region (Ag-NOR) analysis and found Ag depositions in the interphase nuclei but not on rRNA gene loci and hsr(s) in the mitotic stage. The hsr of this coral was observed in approximately 50% of the metaphase spreads analyzed. This may explain the diversity of coral rDNA based on the molecular study of sequence analysis. Furthermore, it was discovered that human telomere and Alu repeated sequences were present in this Coelastrea aspera. Probes derived from human Alu sequences are expected to play an important role in the classification of corals. Overall, our data can be of great value in discriminating among scleractinian coral species and understanding their genetics, including chromosomal evolution.

Counterstained enhancement of TaqI resistant sites after distamycin A/diamidinophenylindole treatment

Numerous selective and differential staining techniques have been used to investigate the hierarchical organisation of the human genome. This investigation demonstrates the unique characteristics that are produced on fixed human chromosomes when sequential procedures involving restriction endonuclease TaqI. distamycin A (DA) and 4',6-diamidino-2-phenylindole (DAPI) are employed. TaqI produces extensive gaps in the heterochromatic regions associated with satellite II and III DNAs of human chromosomes 1, 9, 15, 16 and Y. DA/DAPI selectively highlights, as brightly fluorescent C-bands, the heterochromatin associated with the alpha, beta, satellite II and III DNAs of these chromosomes. When DA and DAPI are used on chromosomes before TaqI digestion, and then stained with Giemsa, the centromeric regions appear to be more resistant, producing a distinct C-banding pattern and gaps in the heterochromatin regions. Sequential use of the DA/DAPI technique after TaqI treatment produces a bright fluorescence on the remaining pericentromeric regions of chromosomes 1, 9, 16 and Y, which also displayed a cytochemically unique banding pattern. This approach has produced specific enhanced chromosomal bands, which may serve as tools to characterize genomic heterochromatin at a fundamental level.

Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes

Classical satellites I, II and III are composed of a mixture of repeated sequences. However, each of them contains a simple family of repeated sequences as a major component. Satellites 2 and 3 are simple families of repeated sequences that form the bulk of human classical satellites II and III, respectively, and are composed of closely related sequences based on tandem repeats of the pentamer ATTCC. For this reason, extensive cross-hybridizations are probably responsible for the similar in situ hybridization patterns obtained for satellites II and III. We have used a fluorescent in situ hybridization method with highly specific oligonucleotides for satellites 2 and 3, respectively, as probes. Our results show that satellite 2 is mainly located on chromosomes 1, 2, 10 and 16, whereas the major domain of satellite 3 is on chromosome 9. Furthermore, minor sites of satellites 2 and 3 are shown. Two-colour in situ hybridizations have enabled us to define the spatial relationships existing between the major domains of both satellites and centromeric alpha satellite sequences. These experiments indicate that the heterochromatin regions of chromosomes 1, 9 and 16 have different molecular organizations.

Organization of the variant domains of alpha satellite DNA on human chromosome 21

The de novo creation of long, homogeneous, satellite DNA domains was postulated previously to occur by saltatory amplification. In this paper, pulsed field gel electrophoresis analysis of the alpha satellite DNA block organization of the human chromosome 21 supports this hypothesis. Double-dimension electrophoresis indicated that the variant copies of the basic alpha satellite repeat of chromosome 21 are organized in a single 3,150 Kb-long domain. It was also established that the other satellite DNAs found in man (beta, II, and III) are organized independently of the alpha satellite DNA block of the same chromosome.

Demonstration of somatic rearrangements and genomic heterogeneity in human ovarian cancer by DNA fingerprinting

A detailed study was performed in 14 patients with epithelial ovarian tumours using the satellite probes 33.15, 228S and 216S to investigate the nature of somatic changes and frequency with which clonal changes could be demonstrated during metastasis and progression. Somatic changes were evident in approximately 70% of ovarian tumours, the most common being a deletion or reduction in intensity of a band suggesting loss of heterozygosity. Additional changes that were observed included increased intensification of single bands and the appearance of novel DNA fragments. Somatic alterations were seen following digestion of DNA with methylation resistant restriction endonucleases indicating that methylation differences alone could not account for all of the somatic changes. Using DNA fingerprint analysis ovarian tumours were shown to be heterogeneous with different DNA patterns observed in different sites in five of eight patients. Generally, within an individual patient the primary and metastases appeared to share a DNA fingerprint pattern with minor variations occurring in different sites suggesting that different populations have derived from a common stem line. This study clearly demonstrates that DNA fingerprint analysis is a sensitive method to detect somatic changes in tumour DNA and for investigating the development of clonal heterogeneity in ovarian tumours.

Human satellite III DNA: genomic location and sequence homogeneity of the TaqI-deficient polymorphic sequences

Human Satellite III DNA is a major tandem repeat in the human genome and presents a TaqI-specific hypervariable restriction fragment length polymorphism when a Satellite III related sequence (228S) is used as a probe. In situ examination shows this sequence to be near specific for the region 9qh on chromosome 9 when it is used at low probe concentrations. However the region 9qh does not appear to be the only or even the primary source of the TaqI-deficient polymorphic sequences (TDPS). Rather, such sequences appear to be mostly present in chromosomes 20, 21, and 22, and these represent the largest regions of homogeneous Satellite III in the genome; they are also resistant to digestion with a range of other restriction endonucleases. The TDPS do not arise from either of the two currently recognized Satellite III-enriched genomic regions, namely autosomal 'K-domains', which form part of 15p in chromosome 15 or the heterochromatin of chromosome Y.

Very low rate Y-chromosome mosaicism (1:5,400) detectable by a novel probe enzyme combination

DYZ1 is a repetitive DNA family located on the long arm of the Y chromosome and is the major component of the Q-positive region. DYZ1 consists of about 3,000 copies of a 3.4 kb repeat unit which mainly consists of a tandem array of pentanucleotides, TTCCA. Because of this large number of repeats, DYZ1 has been used as a probe in Southern hybridization for sensitive and rapid detection of the Y chromosome. In cases of XX/XY mosaicism, however, autosomal sequences having homology to DYZ1 hinder the detection of the Y chromosome, especially when the ratio of the Y-bearing cells is low. To solve this problem and improve the detection limit, we have sought the optimum hybridization condition by changing several variables. These variables include the length of probes, the methods of probe labeling, the endonucleases used to digest the genomic DNA and the hybridization buffer. Here we show that the StuI digestion of genomic DNA in combination with the nick translated DYZ1 probe significantly improves the detection limit of the Y-chromosome bearing cells. The presence of Y-chromosome bearing cells was detectable against a background of 5,400-fold female DNA.

Hypervariable polymorphism of autosomal origin detected by the Y-chromosome derived probe, pHY10

A recombinant DNA probe (pHY10) hybridizing specifically to human DNA family DYZ1, 3,000 copies of which are present on the long arm of the Y chromosome, was used for probing human genome DNA digested with various restriction enzymes. To our surprise, the probe detected a hypervariable polymorphism of autosomal origin in human DNA when digested with TaqI. None of other 12 restriction enzymes revealed polymorphic patterns. Codominant segregation of the polymorphism was established in family studies. This probe has been widely used in the detection of the Y chromosome. Its ease of availability as well as highly discriminating polymorphic pattern makes it potentially very useful for forensic and human genetic purposes.