Binding of actinomycin D to calf thymus chromatin

Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection

BACKGROUND

Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-free DNA (cfDNA) molecules have jagged ends.

METHODS

Jagged ends of cfDNA were detected by incorporating unmethylated cytosines during a DNA end-repair process, followed by bisulfite sequencing. Incorporation of unmethylated cytosines during the repair of the jagged ends lowered the apparent methylation levels measured by bisulfite sequencing and were used to calculate a jagged end index. This approach is called jagged end analysis by sequencing.

RESULTS

The jagged end index of urinary cfDNA was higher than that of plasma DNA. The jagged end index profile of plasma DNA displayed several strongly oscillating major peaks at intervals of approximately 165 bp (i.e., nucleosome size) and weakly oscillating minor peaks with periodicities of approximately 10 bp. In contrast, the urinary DNA jagged end index profile showed weakly oscillating major peaks but strongly oscillating minor peaks. The jagged end index was generally higher in nucleosomal linker DNA regions. Patients with bladder cancer (n = 46) had lower jagged end indexed of urinary DNA than participants without bladder cancer (n = 39). The area under the curve for differentiating between patients with and without bladder cancer was 0.83.

CONCLUSIONS

Jagged ends represent a property of urinary cfDNA. The generation of jagged ends might be related to nucleosomal structures, with enrichment in linker DNA regions. Jagged ends of urinary DNA could potentially serve as a new biomarker for bladder cancer detection.

Comparative evaluation of several DNA binding dyes in the detection of apoptosis-associated chromatin degradation by flow cytometry

Mouse thymocytes readily undergo apoptosis-associated DNA degradation upon exposure to glucocorticoids or ionizing radiation. It has been previously shown that flow cytometric cell cycle analysis of propidium iodide-stained apoptotic thymocytes results in the appearance of a distinct cell cycle region (the A0 region) below the G0/G1 region. Cells in this region were shown to be undergoing apoptosis, and determination of apoptosis by flow cytometric analysis was proposed as a superior method for evaluating thymocyte apoptosis. In this study, a variety of DNA binding dyes with diverse primary binding mechanisms were evaluated for their ability to detect glucocorticoid and ionizing radiation-induced apoptosis in mouse thymocytes. Apoptotic thymocytes stained with DNA binding dyes from the phenanthridinium, acridine, actinomycin, chromomycinone, anthracycline, and bisbenzimidazole groups all demonstrated clearly defined A0 regions with percentages comparable to those obtained for propidium iodide. These results indicate that the appearance of the A0 region is not dependent on a particular dye binding characteristic and may be the consequence of extensive changes in chromatin structure resulting in a significant degree of dye exclusion.

Chromosome preparation and high resolution banding techniques. A review

High resolution banding techniques enable detection of chromosome rearrangements even within major bands. Banded chromosomes prepared for light microscopic studies of intact metaphase plates are, however, highly modified structures compared with native chromosomes, and the high resolution banding techniques only seem possible because the following methods were standardized and combined. The use of colcemid, which prevents formation of the spindle and thereby collects cells at the metaphase-anaphase border, is routinely used for chromosome preparations. For high resolution banding studies, short exposure time and concentrations near the threshold value have been recommended by several authors. Several agents interfere with chromosome contraction processes, but only a few have had a lasting influence on high resolution banding studies. The most used agents are ethidium bromide, actinomycin D, and Hoechst 33258, which all partially inhibit chromosome contraction. Treatment with hypotonic solutions induces swelling of animal cells, and the methanol in the fixative denatures and precipitates protein by dehydration. The acetic acid coagulates nucleoproteins and causes swelling of the cells. The fixative penetrates the cells rapidly and preserves the chromosome structure. To obtain long segmented chromosomes suitable for high resolution banding hypotonic treatment with .075 M KCl, frequent changes of fixative and overnight fixation at 4 degrees C have been recommended. The use of cell synchronization, 5-bromodeoxyuridine incorporation into DNA, and fluorochrome-photolysis Giemsa (FPG)-staining have improved the quality of high resolution banding. Synchronization techniques, which select for lymphocyte populations in early divisions, provide excellent materials for chromosome preparations and induction of high resolution banding. The banding techniques seem to enhance differences already present in the chromosomes, and the differential Giemsa staining has recently been explained by interactions between the hydrophobic dye complex, the supercoiled DNA helix, and the denaturated histone core of the nucleosomes.

Characterization of DNA binding proteins released from sarcoma-180 chromatin during brief digestion with DNase-I

Brief digestion of sarcoma-180 chromatin (less than or equal to 5%) by pancreatic DNase-I releases six non-histone proteins with Mol. wt. 21.5K, 26K, 72.5K, 77K, 90K and 120K dalton and pI values ranging from 4.7 to 12.4. The protein of Mol. wt. 77K dalton was obtained at high alkaline range of pH = 12.4. The antibodies against these proteins induce dose dependent inhibition in transcription of native chromatin. Results suggest a role of these proteins in positive control of gene transcription in sarcoma-180 cells.

Analysis of the effects of antibiotics on the structure of nucleosome core particles determined by DNAase I cleavage

Patterns of sensitivity to DNAase I cleavage have been analysed in order to investigate the effects of anti-tumour antibiotics and related drugs on nucleosome core particles containing different DNA restriction fragments. In this article, we review the experimental results which show that after controlled digestion of defined-sequence core particles, new cleavage products appear in the enzyme digestion patterns which lie approximately mid-way between the strong bands characteristic of native nucleosome core particles. The effects of the antibiotics, which include bis-intercalators as well as minor groove-binding ligands (but not monofunctional intercalators), are explained in terms of an induced change in rotational setting (phasing) of the core DNA. The new rotational positioning of DNA induced by antibiotic binding appears to be almost independent of DNA sequence, although some differences can be observed with the various pieces of DNA, most likely reflecting the exact number and disposition of antibiotic binding sites.

Antibiotics which can alter the rotational orientation of nucleosome core DNA

Four well-characterised DNA-binding ligands have been tested for effects on reconstituted nucleosome core particles containing the 160 bp tyrT DNA fragment. Two, netropsin and berenil, were found to change the rotational orientation of the DNA on the surface of the protein as judged by marked alterations in the pattern of fragments produced by exposure to DNAase I. Qualitatively their effects were very similar to those previously reported for the related antibiotic distamycin, suggesting that the phenomenon of induced rotation may be a characteristic property of ligands which bind in the narrow groove of the DNA helix. Two intercalators did not produce the effect but, at high concentrations, caused gross disruption of the nucleoprotein structure with apparent release of DNA from the histone octamer. At moderate concentrations little or no effect was detectable with nogalamycin, suggestive of failure to bind as a result of constraints on local opening of the DNA helix. With moderate concentrations of actinomycin, protection of GpC sequences was clearly visible together with some evidence of increase in helix pitch, but no sign of altered phasing of DNA within the nucleosome core particles.

Preferential binding of adriamycin and nogalamycin to DNase-I hypersensitive sites of Sarcoma-180 chromatin

Binding of nogalamycin and adriamycin with Sarcoma-180 ascites tumor cell chromatin was studied by a spectrofluorometric method. There was significant reduction in the number of available drug binding sites per nucleotide when the chromatin was digested with DNase I for a period which releases only 7% of the chromosomal DNA. Results indicate preferential binding of these drugs with DNase I hypersensitive sites of chromatin. The DNase-I hypersensitive sites of chromatin were shown to correlate to the sequences required for gene expression. Further digestion with DNase I increases availability of drug binding sites, probably due to relaxation of the compact chromatin.

Alterations of [3H]actinomycin D binding to axotomized dorsal root ganglion cell nuclei: an autoradiographic method to detect changes in chromatin structure and RNA synthesis

An autoradiographic method was developed to quantify on a comparative basis the binding of [3H]actinomycin D (Act D) to the cell nuclei of frozen, unfixed sections of spinal sensory ganglia in rats. After a crush lesion of the sciatic nerve, alterations of [3H]Act D binding were found in L5 and L6 dorsal root ganglia which corresponded to changes in RNA synthesis observed in other studies. An increase in Act D binding was seen at 1 to 3 days postoperation, followed by a decrease at 5 to 7 days. By 9 to 11 days a second increase in binding occurred, followed by a decrease at 14 days. Contralateral ganglia exhibited an increase in Act D binding only at 5 days compared with unoperated controls. The timing of the response in axotomized ganglia differed with the distance of the lesion from the cell body. The observed patterns of Act D binding confirm that changes of chromatin structure are closely associated with the alterations of RNA and protein synthesis occurring after axon injury. The method may be useful as an indicator for alterations in RNA synthesis related to changes in chromatin structure in complex tissues.

Interaction of doxorubicin with nuclei isolated from rat liver and kidney

The interaction of doxorubicin with nuclei isolated from rat liver and kidney was studied by fluorospectrometry . The nuclei had at least two different types of binding sites for the drug. Both Mg2+ and Ca2+ competitively inhibited the binding of doxorubicin to the nuclei, which showed a remarkable temperature dependency. No significant difference was observed between the numbers of binding sites (n = 6.70 X 10(-2) mol/mol of DNA for liver; 6.41 X 10(-2) mol/mol of DNA for kidney) or the affinity constants (Ka = 4.85 X 10(5) M-1 for liver; 5.41 X 10(5) M-1 for kidney) under quasi-physiological conditions. These results obtained from in vitro binding experiments support previous suggestions that the differences in the in vivo distribution of doxorubicin among tissues are not due to differences in the nuclear binding of the drug. The amount of nuclei per gram of tissue is the primary determinant of the characteristic tissue distribution of doxorubicin.

Interaction of nogalamycin with chromatin

Number of available nogalamycin binding sites in Sarcoma-180 chromatin is less than that present in Sarcoma-180 DNA. Gradual removal of proteins from chromatin by salt leads to increase in available drug binding sites, without appreciable alteration in binding affinity. Histones restrict the accessibility of nogalamycin to chromosomal DNA, whereas high mobility group (HMG) proteins have no effect. Association of histone H1 with chromosomal DNA has a more marked inhibitory effect on nogalamycin binding than other types of histones. Chromosomal protein induced conformational change in DNA appears to be the main factor in determining the availability of strong binding sites.

Retinoblastoma and its association with a deletion in chromosome #13: a survey using high-resolution chromosome techniques

To our knowledge, 20 cases of retinoblastoma associated with a chromosome #13 aberration have been reported. The present study utilized high-resolution prophase banding analysis of 12 additional retinoblastoma patients to determine the occurrence of chromosome aberrations and identify consistently associated clinical abnormalities. Six male and six female patients were studied representing seven cases of bilateral and five cases of unilateral retinoblastoma. One case of unilateral and two cases of bilateral retinoblastoma and detectable cytogenetic abnormalities, all involving an interstitial deletion of 13q14 on the long arm of one chromosome #13. In all five unilateral cases the tumor manifested in the left orbit, and in all seven bilateral cases the left eye was at a more malignantly advanced stage than the right eye. All three cases with a chromosome abnormality had varying degrees of developmental and/or mental retardation, along with at least one other congenital abnormality. In addition to the 12 cases of retinoblastoma, a patient with severe ophthalmologic abnormalities and mild congenital anomalies was studied by the prophase banding technique and found to be partially trisomic for the 13q14 region with gene loci for optic development and indicate that cytogenetic abnormalities may occur even more frequently in retinoblastoma than indicated by the small number of cases reported in the literature.

Observations on the structure of mechanically stretched chromatin fibrils

During the spreading of human chromosomes prepared from cultured human lymphocytes, the peripheral fibers attaching the chromosome to the support film are mechanically stretched. The stretching reveals structural elements of the fibers; some of these features have been described earlier, for extracted chromatin. The molecule of DNA is bared through stretching and binds labeled actinomycin D in consequence. One of the prominent features of stretched fibers is the irregularity of resulting structures. This paper further demonstrates the excellent resolution obtainable by electron impact evaporation of tungsten.

Microfluorometric investigations of chromatin structure. I. Evaluation of nine DNA-specific fluorochromes as probes of chromatin organization

The ability of the highly condensed chromatin of small thymocyte nuclei and the more loosely organized chromatin of hepatocyte nuclei to interact with nine DNA-specific fluorochromes was assessed by microfluorometry. Although the results obtained with five of the fluorochromes - mithramycin, 7-aminoactinomycin D, Hoechst 33258, DAPI, and propidium iodide - were found to be virtually unaffected by differences in the degree of condensation of the chromatin, the values obtained with the remaining fluorochromes - proflavine, quinacrine mustard, berberine sulfate, and pyronin Y - appeared to be affected significantly by organizational differences of the chromatin. All of the latter "structural probes," except quinacrine mustard, produced fluorescence values which were higher in the 2c nuclei of hepatocytes than in the nuclei of small thymocytes. Quinacrine mustard yielded higher values in thymocyte nuclei; and in the hepatocyte polyploid series (2, 4, and 8c), it did not produce the expected multiples of the 2c value. Pretreatment of the two types of nuclei with RNase affected their total fluorescence in unpredictable ways. While RNase extraction lessened the differences between thymocyte and 2c hepatocyte nuclei stained with propidium iodide, Hoechst 33258, proflavine, and berberine sulfate, it increased the differences between nuclei stained with mithramycin, quinacrine mustard, pyronin Y, and 7-aminoactinomycin D. The ability of RNA-depleted chromatin to interact with various types of fluorochromes might be a useful parameter in subsequent studies of chromatin organization.

In vitro decondensation of human sperm chromatin

The swelling of human sperm head and the decondensation of the sperm chromatin were investigated using a microscopic observation and the increased binding of AMD as the probes. Incubation of the human spermatozoa with 1 mM DTT produced sperm head swelling within 30 min. Addition of soybean trypsin inhibitor or PMSF blocked the swelling induced by 1 mM DTT. The DTT induced a large increase in the binding of AMD to the spermatozoa, to the sperm head and to the triton X-100 treated spermatozoa. This increase in AMD binding was completely abolished by the presence of PMSF. These results suggested the participation of a sulfhydryl reducing agent and a proteolytic enzyme in the sperm head swelling and the chromatin decondensation. The simplicity of probing the chromatin decondensation with AMD binding offers a means to study kinetic and quantitative aspects of the process.

Studies on corneal endothelial growth and repair. II. increased transcription as detected by incorporation of 3H-uridine and 3H-actinomycin D

Endothelial cells from injured frog corneas undergo increased 3H-uridine and 3H-actinomycin D (3H-AMD) incorporation as judged by autoradiography. The increase in 3H-AMD binding occurs when living endothelium is labeled in vitro or when fixed preparations are exposed to the drug. The changes in 3H-AMD incorporation detected by the two methods are comparable (55 and 62% for living and pre-fixed tissue respectively). However, when fixed endothelium is also de-histonized with 2 N HCl, differential binding of 3H-AMD is eliminated. This result suggests that the enhanced incorporation of 3H-AMD into nuclei is at least partly due to a modification in the association of chromosomal proteins with DNA and not entirely to cell permeability changes that may accompany wound repair. This contrasts with observations of cells that are killed outright by the injury. Such cells bind very large amounts of 3H-AMD compared with their living neighbors. Here the difference in incorporation is eliminated by prefixation. Thus, in the dead cells increased binding may be due to a reduction of cell surface permeability barriers which accompanies cell morbidity.

The interaction of chromatin with alkylating agents. The monofunctional action of bis(2-chloroethyl)methylamine

The reaction of L5178Y lymphoblast cell chromatin with the alkylating agent bis(2-chloroethyl)methylamine has been studied as a function of time, pH and reagent concentration. The reaction with DNA of chromatin from which the proteins were dissociated, as well as with purified calf thymus DNA, was studied in parallel. The extent of alkylation of DNA in intact chromatin was 4--5 times as much as in parallel free DNA samples; up to 4% of nucleotide base pairs were substituted. The extent of monofunctional substitution of the proteins was similar, on a weight basis, to that of DNA. Chromatographic analysis of the depurinated products showed that in chromatin, as in DNA, position N-7 of guanine is the major site of reaction. Up to 25% of the reaction products were guanines cross-linked as bis(2-guanin-7-yl-ethyl)methylamine, indicating a considerable degree of DNA-DNA cross linking. Column analysis shows that up to 40% of the nuclear proteins are cross-linked to DNA at 10 mM bis(2-chloroethyl)methylamine. The increased reactivity of intact chromatin is interpreted in terms of a conformational change in the position of the DNA bases when in the organized nucleohistone complex.

Changes of nucleosome frequency in nucleolar and non-nucleolar chromatin as a function of transcription: an electron microscopic study

The morphology of nucleolar and non-nucleolar (lampbrush chromosome loops) chromatin was studied in the electron microscope during states of reduced transcriptional activity in amphibian oocytes (Xenopus laevis, Triturus alpestris, T. cristatus). Reduced transcriptional activity was observed in maturing stages of oocyte development and after treatment with an inhibitor, actinomycin D. Strands of nucleolar chromatin appear smooth and thin, and contain only few, if any, nucleosomal particles in the transcribed units. This is true whether they are densely or only sparsely covered with lateral ribonucleoprotein fibrils. This smooth and non-nucleosomal character is also predominant in the interspersed, apparently nontranscribed rDNA spacer regions. During inactivation, however, nucleolar chromatin frequently and progressively assumes a beaded appearance in extended fibril-free--that is, apparently nontranscribed--regions. In either full-grown oocytes or late after drug treatment, most of the nucleolar chromatin is no longer smooth and thin, but rather shows a beaded configuration indistinguishable from inactive non-nucleolar chromatin. In many chromatin strands, transitions of fibril-associated regions of smooth character into beaded regions without lateral fibrils are seen. Similarly, in the non-nucleolar chromatin of the retracting lampbrush chromosome loops, reduced transcriptional activity is correlated with a change from smooth to beaded morphology. Here, however, beaded regions are also commonly found interspersed between the more or less distant bases of the lateral fibrils, the putative transcriptional complexes. In both sorts of chromatin, detergents (in particular Sarkosyl) that remove most of the chromatin proteins including histones from the DNA axis but leave the RNA polymerases of the transcriptional complexes attached were used to discriminate between polymerases and nucleosomal particles. The results suggest that nucleosomes are absent in heavily transcribed chromatin regions but are reformed after inactivation. In contrast to the findings with inactivated nucleolar genes, in lampbrush chromosome loops the beaded nucleosomal configuration appears to be assumed also in regions within transcriptional units that, perhaps temporarily, are not involved in transcription.

Studies on the action of the nuclear factor promoting actinomycin D-binding capacity of chromatin

It is well known that actinomycin D binds to C-G pairs of DNA. The amount of actinomycin D bound to chromatin thus depends directly on the demasked sites of chromatin DNA. The actinomycin D binding of rat liver chromatin, obtained by the method of Dingman and Sporn, was studied in the presence and absence of liver and kidney nuclear extracts (NE). The actinomycin D binding of liver chromatin increases greatly under the action of liver nuclear extract. No changes occur in liver chromatin actinomycin D binding capacity after the action of kidney NE. The removal of protein or RNA from liver NE removes its ability to change the actinomycin D binding capacity of the liver chromatin. According to the obtained results it may be assumed that the nuclear extract contains the factor which plays a role in controlling cell differentiation.

Binding of polylysine to chromatin subunits and cleavage by micrococcal nuclease. A comparison of accessible sites

Native chromatin and chromatin subunits (nucleosomes) were titrated with polylysine and digested with micrococcal nuclease and deoxyribonuclease I at individual lysine/nucleotide ratios. In contrast to earlier reports, which had been obtained using mechanically sheared chromatin, a comparison of the sites accessible for micrococcal nuclease and polylysine reveals that polylysine does not preferentially protect the micrococcal-nuclease-susceptible sites in chromatin. Similar results were obtained in digestion experiments with DNase I. From the experimental data presented we conclude that polylysine does not preferentially bind to the internucleosomal DNA, which is the prime target site for micrococcal nuclease, but rather to the total nucleosomal DNA moiety.

Buoyant density fractionation of Drosophila melanogaster chromatin

Buoyant density fractionation of Drosophila melanogaster chromatin utilizing low molecular weight molecules such as actinomycin-D to induce changes in buoyant density has been investigated. Fractions of chromatin containing identifiable repeated DNA sequences could be isolated using actinomycin-D as the selective agent. Protein displacement from the chromatin complex was found to be a prerequisite for the observed buoyant density changes.

Ion binding and chromatin condensation

1. The binding of 45Ca2+ to hen erythrocyte chromatin has been studied to help elucidate how cations induce a reversible condensation of this chromatin. 2. As the unbound Ca2+ of the medium rises from 0.5 to 4 mM, Ca2+ is bound to the chromatin with a stability constant of approx. 3.1 and a saturation value of 0.25 Ca2+ per DNA phosphate, or one-half the value for pure DNA. Condensation of the chromatin is half complete when this binding of calcium is roughly half complete. Hence the transition from the uncondensed to the condensed state occurs as repulsion between the free DNA phosphates of erythrocyte chromatin is neutralised by bound cations. Genetically active chromatin may be maintained in an uncondensed state in living cells by the presence of different negative groups that remain unneutralised at the unbound cation concentrations of the cell. 3. That only one-half of the calcium binding sites of DNA are masked in erythrocyte chromatin supports recent models of chromatin structure in which the DNA double helix is wound round a core of histones. 4. Competition for calcium binding sites in the chromatin by other cations was also studied.

Antiestrogen action: differential nuclear retention and extractability of the estrogen receptor

Since there is a much longer uterine nuclear retention of the U-11, 100A (antiestrogen) receptor complex (UARC) than of the estradiol receptor complex (ERC) at 4-12 hrs after injection, experiments were designed to determine if there is a difference between the relative nuclear affinities for the two RCs as determined by extraction with various ionic strength mediums. Although the UARC was retained longer in the nuclear fraction in vivo, the UARC was completely extractable with 0.3M KCl or 50mM spermine, whereas the ERC demonstrates a salt-resistant form. This suggests that the ERC is more tightly bound to nuclear components through this salt-resistant form of the receptor. In addition, various intercalating agents were used to distinguish the different nuclear chromatin DNA sites where the UARC and ERC may be binding. With actinomycin D (50 uM) more ERC than UARC was retained in the nuclear fraction. However, with ethidium bromide (100uM) less ERC than UARC was retained. Also, the ERC selectively released by ethidium bromide is precisely that fraction not released by salt. These results indicate that the UARC and ERC bind to different chromatin loci.

Distribution of intercalative dye binding sites in chromatin

Actinomycin D (AMD) and ethidium bromide (EB) were found to bind to chromatin isolated from a variety of gander tissues according to a strong and weak process analogous to that found for deproteinized DNA. Distribution of the dye intercalation sites in chromatin and DNA were evaluated at low r-values (dye bound per nucleotide) by following the appearance of free dye released from chromatin and DNA during thermal denaturation. The AMD dissociation profiles closely resembled the DNA or chromatin-DNA denaturation profiles; whereas the EB derivative dissociation profiles, indicated 3 major transitions for transcriptionally active chromatin with the main component corresponding to the single component which characterizes DNA. The DNA-like component was greatly reduced for mature erythrocyte chromatin but could be generated by removal of histone I and V. Removal of residual non acid-soluble proteins from dehistonized chromatin, urea treatment or dissociation and reconstitution of chromatin favoured conversion to the DNA-like component with loss of the other two. This study indicates that more than one type of binding exists generally in chromatin.

Changes in template activity and structure of nuclei from WI-38 cells in the prereplicative phase

Quiescent confluent monolayers of WI-38 fibroblasts were stimulated to proliferate by either adding 10% fetal calf serum or by trypsinization and replating at lower density. The length of the prereplicative phase was 12 hr after serum stimulation and 18 hr after trypsinization and replating at lower density. Nuclei were isolated from WI-38 cells at different time intervals after either type of stimulation and their template activity, circular dichroism spectra, and ability to bind ethidium bromide were investigated. All these parameters were similarly increased after either type of stimulation. However, these changes, like the onset of DNA synthesis, were delayed 6 hr in cells trypsinized and replated at lower density. While there were no detectable changes in nuclear protein content after serum stimulation, at least 40% of nuclear protein, mostly nonhistone chromosomal proteins, were lost after trypsinization. The amount of nuclear proteins returned to prestimulation levels only 6-8 hr after replating. These data seem to suggest that nonhistone chromosomal proteins lost by trypsinization are essential for the entrance of WI-38 cells into the "prereplicative phase".