G. van den Engh

Studies of Metaphase and Interphase Chromosomes Using Fluorescence In Situ Hybridization

Our measurements have bearing on the resolution with which maps can be constructed and abnormalities can be detected by studying the proximity of DNA sequences in metaphase and interphase chromosomes. The results of our analyses are summarized in Figure 8. Metaphase chromosomes are compacted sufficiently that it is impractical to order sequences separated by less than approximately 1 Mbp. In contrast, 100-kbp resolution can be obtained in interphase chromosomes. Distance measurements reveal that interphase chromatin behaves as a random polymer over distances up to 1-2 Mbp. At greater distances, higher order constraints, perhaps the dimensions of the individual chromosome domains, come into play. A caveat remains: Because the effect of the FISH procedure on native chromosome organization is not well understood, these conclusions may not be applicable to native chromatin. We have illustrated that FISH, with appropriately chosen probes, can supplement conventional cytogenetics in the study of chromosome abnormalities. The technique is increasingly being applied in research laboratories to detect and characterize chromosome abnormalities and point the way to the location of genes involved in human disease.

Physical mapping studies on the human X chromosome in the region Xq27-Xqter.

We have characterized three terminal deletions of the long arm of the X chromosome. Southern analysis using Xq27/q28 probes suggests that two of the deletions have breakpoints near the fragile site at Xq27.3. Flow karyotype analysis provides an estimate of 12 X 10(6) bp for the size of the deleted region. We have not detected the deletion breakpoints by pulsed-field gel electrophoresis (PFGE) using the closet DNA probes, proximal to the fragile site. The physical distance between the breakpoints and the probes may therefore be several hundred kilobases. The use of the deletion patients has allowed a preliminary physical map of Xq27/28 to be constructed. Our data suggest that the closest probes to the fragile site on the proximal side are 4D-8 (DXS98), cX55.7 (DXS105), and cX33.2 (DXS152). PFGE studies provide evidence for the physical linkage of 4D-8, cX55.7, and cX33.2. We have also found evidence for the physical linkage of F8C, G6PD, and 767 (DXS115), distal to the fragile site.

The binding kinetics and interaction of DNA fluorochromes used in the analysis of nuclei and chromosomes by flow cytometry

SummaryThe interactions and binding characteristics of DNA dyes used in the flow cytometric analysis of chromatin were studied using human chromosomes and mouse thymocyte nuclei. The kinetics of dye binding and the relationship between fluorescence intensity and dye concentration are presented. Under the conditions used, Hoechst 33258, propidium iodide and chromomycin A3 reach an equilibrium with thymocyte nuclei after approximately 5 min, 20 min and more than 1 h, respectively. The same binding kinetics are observed with Hoechst 33258 and chromomycin when nuclei are stained with a mixture of the two dyes. Sodium citrate, which improves the resolution of flow karyotypes, causes a rapid increase in Hoechst and propidium iodide fluorescence, but a decrease in the fluorescence of chromomycin. The relative peak positions of chromosomes in a flow karyotype are unaffected by sodium citrate addition. The spectral interaction between Hoechst and chromomycin is quantified. There is variation among the human chromosome types in the amount of energy transferred from Hoechst to chromomycin. By measuring the Hoechst and chromomycin fluorescence of each chromosome after Hoechst excitation, it is shown that the amount of energy transferred is correlated to the ratio of the amount of Hoechst to chromomycin bound. Although the energy transfer between the two dyes is considerable, this has little effect on the reproducibility of flow karyotype measurements. The relative peak positions of all human chromosomes in a 64×64 channel flow karyotype, except for the 13 and Y chromosomes, vary in the order of 0.5 channel over a 16-fold change in either Hoechst or chromomycin concentration. This implies that, with the present flow cytometers, variation in staining conditions will have minimal effects on the reproducibility of the relative peak positions in flow karyotypes.

Flow Karyotyping and Sorting of Human Chromosomes

Flow cytometry and sorting are becoming increasingly useful as tools for chromosome classfication and for the detection of numerical and structural chromosome aberrations. Chromosomes of a single type can be purified with these tools to facilitate gene mapping or production of chromosome specific recombinant DNA libraries. For analysis of chromosomes with flow cytometry, the chromosomes are extracted from mitotic cells, stained with one or more fluorescent dyes and classified one-by-one according to their dye content(s). Thus, the flow approach is fundamentally different than conventional karyotyping where chromosomes are classified within the context of a metaphase spread. Flow sorting allows purification of chromosomes that can be distinguished flow cytometrically. The authors describe the basic principles of flow cytometric chromosome classification i.e. flow karyotyping, and chromosome sorting and describe several applications. 30 refs., 8 figs.