Conservation of repeated DNA sequences in aneuploid human tumor cells

Rapid interphase and metaphase assessment of specific chromosomal changes in neuroectodermal tumor cells by in situ hybridization with chemically modified DNA probes

Repeated DNAs from the constitutive heterochromatin of human chromosomes 1 and 18 were used as probes in nonradioactive in situ hybridization experiments to define specific numerical and structural chromosome aberrations in three human glioma cell lines and one neuroblastoma cell line. The number of spots detected in interphase nuclei of these tumor cell lines and in normal diploid nuclei correlated well with metaphase counts of chromosomes specifically labeled by in situ hybridization. Rapid and reliable assessments of aneuploid chromosome numbers in tumor lines in double hybridization experiments were achieved, and rare cells with bizarre phenotype and chromosome constitution could be evaluated in a given tumor cell population. Even with suboptimal or rare chromosome spreads specific chromosome aberrations were delineated. As more extensive probe sets become available this approach will become increasingly powerful for uncovering various genetic alterations and their progression in tumor cells.

Genomic representation of the Hind II 1.9 kb repeated DNA

The genomic representation and organization of sequences homologous to a cloned Hind III 1.9 kb repeated DNA fragment were studied. Approximately 80% of homologous repeated DNA was contained in a genomic Hind III cleavage band of 1.9 kb. Double digestion studies indicated that the genomic family, in the majority, followed the arrangement of the sequenced clone, with minor restriction cleavage variations compatible with a few base changes. Common restriction sites external to the 1.9 kb sequence were mapped, and hybridization of segments of the cloned sequence indicated the 1.9 kb DNA was itself not tandemly repeated. Kpn I bands which were homologous to the sequence contained specific regions of the repeat, and the molecular weight of these larger fragments could be simply explained. Mapping of common external restriction sites indicated that in some but not all cases the repeat could be organized in larger defined blocks of greater than or equal to 5.5 kb. In some instances, flanking regions adjacent to the repeat may contain common DNA elements such as other repeated DNA sequences, or possibly rearranged segments of the 1.9 kb sequence. It is suggested that although the 1.9 kb sequence is not strictly contiguous, at least some of these repeated sequences in the human genome are arranged in clustered or intercalary arrays. A region of the 1.9 kb sequence hybridized to a mouse repeated DNA, indicating homology beyond the primates.

Novel classes of mouse repeated DNAs

Mouse DNA cleaved with Eco R11 (bst NI) displays two prominent restriction bands of 1.5 and 1.7 kb in agarose gels stained with ethidium bromide. These constitute novel subsets of repeated DNA in the mouse. Sequential Hoechst 33258-CsCl gradient fractionation of mouse DNA, yielding more GC rich main band DNA, and AT rich satellite DNA, revealed that both these fragments copurified with GC rich main band DNA. They were not detected in purified satellite preparations. Together these restriction bands constituted larger than or equal to 0.2% of main band DNAs. Hybridization of 32p labelled satellite DNA to blots of Eco R11 restricted mouse DNA showed positive hybridization only to smaller satellite restriction fragments, indicating satellite DNA had little or no homology with either the 1.5 or 1.7 kb fragments. The 1.5 and 1.7 kb fragments were isolated from gels and labelled with 32p by nick translation. Using a series of restriction endonucleases each of these two fragments showed different cleavage patterns. Filter hybridization confirmed that these two fragments were distinct subsets as they did not cross hybridize with each other. They also did not hybridize to other more minor repeated non-satellite DNA bands noted in ethidium bromide stained gels. Neither of them could be assigned to ribosomal genes as they did not hybridize to 32p kinase labelled 18S and 28S RNA. Isolation of DNA from male and female mice showed comparable amounts of both the 1.5 and 1.7 kb fragments. Thus neither was Y chromosome specific. From restriction patterns, and preliminary chromosome hybridization studies, these fragments are thought to represent "interspersed" repeated sequences rather than very long tandem (satellite like) centromeric arrays. The relationship between these repeated sequence subsets, their evolution and detailed organization, and their representation in different mouse species, remain to be determined.

Soft x-ray lithographic studies of interphase chromosomes

Soft x-ray absorption lithograph patterns of purified interphase human nuclei and chromosome arrays, imaged on PMMA resists, were examined by scanning EM. The patterns obtained were compared to those utilizing more conventional sources, including transmission EM, scanning EM, high voltage EM, and various light microscopic techniques. The x-ray resist images revealed orderly arrays of absorption profiles in the 3-dimensional specimen with both mild and more extensive developments of the resist. Dense chromatin at the edge of interphase nuclei revealed aligned periodic peaks on the order of 2200 A diameter, with substructure. The periodicity and alignment of interphase chromosomes were entirely consistent with birefringent data on nuclei indicating a high degree of 3-dimensional order. This degree of 3-dimensional order was observed in nuclei containing essentially DNA and histones with only very few other minor (probably structural) proteins. Sonication and nuclease treatment to disperse interphase chromosomes revealed similar absorption periodicities in individual chromosome fibers. Analysis of x-ray absorption profiles thus appears to offer significant new insights into the ordered structure of these defined biological specimens.