We examined Barr bodies formed by isodicentric human X chromosomes in cultured human cells and in mouse-human hybrids using confocal microscopy and DNA probes for centromere and subtelomere regions. At interphase, the two ends of these chromosomes are only a micron apart, indicating that these inactive X chromosomes are in a nonlinear configuration. Additional studies of normal X chromosomes reveal the same telomere association for the inactive X but not for the active X chromosome. This nonlinear configuration is maintained during mitosis and in a murine environment. (4) or in situ hybridization (2) places the Barr body adjacent to the nuclear envelope in 75-80% of interphase cells. Comings (5) suggested that inactive X chromosomes attach randomly to the nuclear membrane, and the multiple Barr bodies in aneuploid cells are widely distributed (6, 7). Nuclear matrix attachment sites are similar for the active and inactive X chromosomes (8). Yet, the configuration of the Barr body has been relatively unexplored. DNA hybridization, in situ (9), has provided a powerful method to examine chromosomes during interphase, revealing an orderly arrangement of chromosomes in the interphase nucleus (10-13) and tissue-specific variation (14, 15). Using such methods to explore the human inactive X chromosome, we find that the Barr body consists of a condensed X chromosome in a nonlinear configuration, with telomeres in close proximity.We examined the Barr body in interphase and mitotic cells using fluorescent probes for centromere and telomere regions of human X chromosomes. In addition to normal X chromosomes, we studied isodicentric X chromosomes (16), which form bipartite Barr bodies (16). Always inactive, they are mirror image duplications with two centromeres (one nonfunctional) and with two identical telomeres (see Fig. 1). The duplicate centromeres as well as common telomeres and their longer length facilitate structural analysis. To compare distance between hybridization signals with relative physical length we examined three isodicentrics, two joined by their long arms (3935 and 7213) and the third attached at the short arms (411). We isolated these dicentric chromosomes from their normal homologue in hybrid cells so that all signals would come from the dicentric X chromosome and to examine the human Barr body in a mouse cell environ. Finally, we simultaneously hybridized centromere and subtelomere probes using differential labels and confocal microscopy. MATERIALS AND METHODSCell Lines. These are characterized in Table 1. The hybrids derived from A9 mouse fibroblasts were selected in hypoxanthine/aminopterin/thymidine medium, back selected in 6-thioguanine to eliminate the active X; to retain the inactive X, the silent HPRT locus was reactivated by 5-azacytidine. Inactive X hybrids derived from tsA1S9T mouse cells were selected directly at 390C for activity of the AJS9T locus at Xpll (17).Preparation of Slides. Interphase cells. Confluent cells in LabTek slide chambers were fixed in methanol/acetic acid (3:1...

We have generated a nested series of interstitial deletions in a fragment of human X chromosome-derived DNA cloned into a yeast artificial chromosome (YAC) vector. A yeast strain carrying the YAC was transformed with a linear recombination substrate containing at one end a sequence that is uniquely represented on the YAC and at the other end a truncated long interspersed repetitive element (LINE 1, or Li). Homologous recombination between the YAC and the input DNA resulted in a nested series of interstitial deletions, the largest of which was 500 kilobases. In combination with terminal deletions that can be generated through homologous recombination, the interstitial deletions are useful for mapping and studying gene structure-function relationships.The ability to clone large fragments of DNA into yeast artificial chromosomes (YACs) is providing a new method for the analysis of complex genomes (1). Large fragments of DNA (as long as 1 megabase) can be introduced into YAC vectors to yield artificial chromosomes.The open-ended size capacity of YAC cloning technology suggests that virtually any mammalian gene or gene complex can be isolated as a single contiguous segment of DNA. Because of the large insert size, methods to facilitate the mapping and functional analysis of genes within the YACs are needed. In addition, the development of methods for targeted modification and transfer of the modified YACs back into cultured cells and experimental organisms will provide powerful tools for the study of gene structure and function.The long-range structure-function relationships of genes can be studied by introducing a large YAC that contains a gene of interest into mammalian cells and eliciting regulated gene expression. If deletions of variable portions of DNA in and around the gene (interstitial deletions) can be obtained, YACs bearing such deletions could be introduced into cells to study the effects of the modifications. Recent successes in introducing YACs into mammalian cells (2-4) provide encouragement for the feasibility of these types of studies. The ability to make interstitial deletions would also be helpful in generating restriction maps of YACs and in assigning genetic markers to precise regions within a YAC.Homologous recombination (HR) in yeast has been used to generate terminal deletions in normal as well as artificial chromosomes in yeast (5, 6). Pavan et al. (6) constructed a vector that contains a yeast telomeric sequence, a yeast selectable marker, and a polylinker into which a human highly repetitive sequence (Alu repeat) was added. When a linearized version of this plasmid was introduced into yeast cells carrying human DNA in a YAC, the input plasmid was able to recombine with each of several homologous regions in the YAC, yielding different-size terminal deletions. The generation of these deletions requires a single crossover event between the target and the input DNA.We have used a modification of the terminal deletion strategy to generate interstitial deletions in a YAC carrying a 650-kb...

The N syndrome is characterized by mental retardation, malformations, chromosome breakage, and development of T-cell leukemia (Opitz et al.: Proceedings of the II International Congress IASSMD pp 115-119, 1971; Hess et al.: Clinical Genetics 6:237-246, 1974b, American Journal of Medical Genetics [supplement] 3:383-388, 1987). N syndrome fibroblasts were studied to see if the high chromosome breakage rate associated with this apparently X-linked syndrome could be related to a deficiency of DNA polymerase alpha, a product of a gene localized to the X chromosome. Bleomycin, which is known to break double-stranded DNA, produced increased chromosome breakage in normal control, Fanconi anemia, and N syndrome fibroblasts. When aphidicolin was used to inhibit repair mediated by DNA polymerase alpha, both normal control and Fanconi anemia fibroblasts showed significantly more chromosome breakage than was produced by bleomycin alone, but there was no increase in the amount of breakage seen in the N syndrome fibroblasts over that seen with bleomycin alone. This suggests that the N syndrome is due to a mutation affecting the region of the X chromosome on which the gene for DNA polymerase alpha is located, and that the high risk of T-cell leukemia observed in the hemizygote is due to this DNA repair defect.