Supercoils in human DNA

Higher order structure of chromosomes

Isolated Chinese hamster metaphase chromosomes were resuspended in 4 M ammonium acetate and spread on a surface of distilled water or 0.15 to 0.5 M ammonium acetate. The DNA was released in the form of a regular series of rosettes connected by interrossette DNA. The mean length of the rosette DNA was 14 micron, similar to the mean length of 10 micron for chromomere DNA of Drosophila polytene chromosomes. The mean interrosette DNA was 4.2 micron. SDS gel electrophoresis of the chromosomal nonhistone proteins showed them to be very similar to nuclear nonhistone proteins except for the presence of more actin and tubulin. Nuclear matrix proteins were present in the chromosomes and may play a role in forming the rosettes. Evidence that the rosette pattern is artifactual versus the possibility that it represents a real organizational substructure of the chromosomes is reviewed.

A probe into nuclear events during the cell cycle of Saccharomyces cerevisiae: studies of folded chromosomes in cdc mutants which arrest in G1

The sedimentation behavior of folded chromosomes from cell-division-cycle (cdc) mutants which arrest in G1 was examined. At the restrictive temperature the folded genome of cdc 7, which arrests after spindle pole body (SPB) separation and spindle formation, cosediments with a standard g1 structure, indicating that by the cdc 7 step the g1 form of the folded genome has been assembled. In the mutant, cdc 4, which arrests before SPB separation but after SPB duplication, a standard g1 structure is not formed. cdc 4 cells, however, are able to enter G0 at the restrictive temperature, and the corresponding go structure is stable. These results indicate that the cdc 4 gene product may be involved in the development of folded genome conformation which leads to the g1 structure. Since the cdc 4 gene product is required for SPB separation, the g1 structure may be defined by an association between chromosomes and spindle components. The folded chromosomes of the "start" mutants cdc 25 and cdc 28 are unstable at the restrictive temperature. In contrast to cdc 4, neither cdc 25 nor cdc 28 are able to enter the G0 stage in a normal manner, i.e., the g0 structure is unstable at the restrictive temperature. The inference is that both the cdc 25 and cdc 28 gene products are required for the functional integrity of the folded genome at both a stage early in G1 and in the pathway to G0.

Absence of anthracycline-induced degradation of nuclear DNA in Ehrlich ascites tumour cells

The in vivo effects of anthracycline antibiotics on the integrity of Ehrlich ascites tumour cell DNA have been studied by sedimentation analysis of nuclear structures containing superhelical DNA in neutral sucrose gradients. These fast-sedimenting protein-DNA complexes may be released by gently lysing cells in solution containing non-ionic detergents and high NaCl concentrations (1.95 M). The supercoiled structure of DNA in these protein-DNA complexes is suggested by the characteristic sedimentation in the presence of intercalating agents. Apparently, no DNA damage could be detected in Ehrlich cells from 7-day-old tumours within 3 h after various doses of daunomycin (0.5--10 mg/kg of body wt.) were administered i.p. to mice. Sedimentation anomalies could not be observed even 15 or 30 h after administration of rtherapeutic doses of daunomycin or adriamycin. In contrast, at 30 min after administration to mice, therapeutic doses of bleomycin (2--8 mg/kg) caused extensive fragmentation of tumour cell DNA, which could be monitored as slowly sedimenting DNA structures (compared with the the control). Similarly, DNA damage could be induced by procarbazine at therapeutic doses. Exposure to bleomycin or procarbazine abolished the characteristic biphasic response to ethidium bromide. The absence of anthracycline-induced degradation of Ehrlich ascites tumour cell DNA is apparently in contrast with the DNA damage observed in L1210 tumour cells. These observations suggest that DNA damage is not a necessary condition for antitumour activity.

Effect of salt-treatment on manually isolated polytene chromosomes from Chironomus tentans

A method for the rapid manual isolation of polytene chromosomes and nuclear membranes from salivary glands of Chironomus tentans is presented and the analysis of some of their RNA and protein components before and after treatment with 2 M salt solutions is summarized.--After salt-incubation the chromosomes still display a considerable number of bands which stain with ethidium bromide and which are sensitive to treatment with DNase, RNase, trypsin, and proteinase K, to a lesser extent with pronase and papain. Analysis of the iodinated residual proteins on SDS gels yield three major and two minor bands (MW between 50,000 and 70,000 dalton) which were also shown to be present in interphase chromosomes of Ehrlich ascites cells which had been treated similarly and are also tightly bound constituents of DNA prepared according to Gross-Bellard et al. (1973). This result indicates the existence of a general class of non-histone proteins involved in keeping the DNA in a supercoiled state. Furthermore their presence in salt-treated nuclear membranes of Chironomus salivary gland cells (and Xenopus oocytes, unpubl.) will be of interest with respect to functional aspects of the nuclear matrix.

Folded chromosomes in non-cycling yeast cells: evidence for a characteristic g0 form

Folded chromosomes from stationary phase or ammonia-starved yeast (Saccharomyces cerevisiae) cells can be isolated as compact structures, distinct and separable by sedimentation from the folded chromosomes of pre-replicative (G1) and post-replicative (G2) nuclei. Such cells are in a dormant or non-cycling (G0) stage. The folded genome from such cells is referred to as the g0 form and has a sedimentation velocity of about 1700S. Sedimentation analysis of mixed G0 and G1 and G2 lysates indicates that the g0 structure is not an artifactual breakdown product of the g1 or g2 structures. A comparison of the proteins from g0 versus g1 and g2 structures by gel electrophoresis has revealed differences in about 10--11 non-histone and perhaps 2 histone proteins. Entry into the G0 stage, and emergence into G1 after G0 arrest, are accompanied by an ordered transition from g2 to g1 to g0, and from g0 to g1 to g2 forms, respectively. Hence, entry into G0 and re-emergence from G0 can be considered as differentiative processes, not normally part of the cell cycle, and accompanied by specific changes in the tertiary organization of the genome.

Spectrofluorometric measurement of the binding of ethidium to superhelical DNA from cell nuclei

Structures retaining many of the morphological features of nuclei may be released by lysing HeLa cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids contain few chromatin proteins. We have shown that the DNA of nucleoids is quasicircular and supercoiled by measure spectrofluorometrically the amount of the intercalating dye, ethidium, bound to unirradiated and gamma-irradiated nucleoids. Ethidium binds to nucleoids in the manner characteristic of the binding to superhelical DNA: at low concentrations more ethidium binds to unirradiated nucleoids than to their gamma-irradiated counterparts with broken DNA, and at higher concentrations less ethidium binds to the unirradiated nucleoids. The quasi-circles in nucleoids are 22 times less sensitive to gamma-irradiation than are circles of pure PM2 DNA: they must contain about 2.2 X 10(5) base pairs. The constraints that maintain the quasi-circularity of nucleoid DNA are very resistant to extremes of temperature and alkali; some remain under conditions in which the duplex is denatured. The constraints are destabilised by ethidium suggesting that they are stabilised by free energy of supercoiling. Proteolytic enzymes, but not ribonucleases, remove the constraints. Possible structures for the constraining mechanism are discussed.

The influence of some prostaglandins on DNA synthesis and DNA excision repair in mouse spleen cells in vitro

In vitro experiments were performed on mouse spleen cells to establish possible influences of some naturally occurring prostaglandins on DNA synthesis and DNA excision repair. The prostaglandins A1, B1, E1, E2 and F2alpha were tested in concentrations of lopg, 5ng and 2.5microgram per ml cell suspension. DNA synthesis was significantly increased by PgF2alpha in all the three concentrations tested, while the other tested prostaglandins were essentially ineffective. DNA excision repair was significantly inhibited by PgE1 and PgE2 at 5ng/ml and at 2.5microgram/ml but increased by PgF2alpha in the two lower concentrations. The rejoining of DNA-strand breaks after gamma-irradiation was slightly reduced by PgE1, PgE2 and PgF2alpha at 2.5microgram/ml.

Interactions stabilizing DNA tertiary structure in the Escherichia coli chromosome investigated with ionizing radiation

The structure of the bacterial chromosome was investigated after introducing breaks in the DNA with gamma irradiation. It is demonstrated that irradiation of the chromosome in the cell prior to isolation results in partial unfolding of the isolated condensed DNA, while irradiation of the chromosome after it is released from the cell has no demonstrable effect on DNA folding. The results indicate that RNA/DNA interactions which stabilize DNA folds are unstable when breaks are introduced in the DNA prior to isolation of the chromosome. It is suggested that the supercoiled state of the DNA is required for the initial stabilization of some of the critical RNA/DNA interaction in the isolated nucleoid. However, some of these interactions are not affected by irradiation of the cells. Remnant supercoiling in partially relaxed chromosomes containing a limited number of DNA breaks has the same superhelical density as the unirradiated chromosome. This suggests that restraints on rotation of the packaged DNA are formed prior to the physical unwinding which occurs at the sites of the radiation induced DNA breads. - Analysis of the in vitro irradiated chromosomes shows that there are 100 +/- 30 domains of supercoiling per genome equivalent of DNA. The introduction of up to 50 double-strand breaks per nucleoid does not influence rotor speed effects of the sedimentation coefficient of the chromosome.

The superhelical density of nuclear DNA from human cells

Structures resembling nuclei may be released by gently lysing human cells in solutions containing non-ionic detergents and high concentrations of salt. These structures, which we call nucleoids, sediment in sucrose gradients containing the intercalating agent, actinomycin D, in the manner characteristic of superhelical DNA. We have determined the concentration of actinomycin that minimises the rate of sedimentation of nucleoids. At this concentration, we have determined the amount of drug bound per base pair of DNA by means of a double-labelling procedure. Assuming that each molecule of actinomycin bound to nucleoid DNA unwinds the double helix by 26 degrees, we calculate that there is one supercoil every 90-180 base pairs in nucleoid DNA. These values lie within the range found for the circular DNA molecules of plasmids and viruses.

Investigations on supercoiled DNA in various rat cells

The effect of radiation induced single-strand breaks in nuclear DNA and the repair of this damages on the sedimentation properties of nucleoids obtained from rat spleen, rat thymus and rat Yoshida tumour cells was studied. A dose dependent effect of ethidium bromide intercalation on the behaviour of supercoiled DNA could be demonstrated. The repair process of radiation induced single-strand breaks in the DNA of Yoshida tumour cells was delayed in the presence of prostaglandin E2 in the incubation medium. Additionally some in vivo repair experiments were carried out on cells of whole body irradiated rats.