Effects of sex difference and dietary protein level on the binding of aflatoxin B1 to rat liver chromatin proteins in vivo

The risk of aflatoxin-induced hepatocarcinoma is greater in males than in females and is similarly higher in animals fed 20% casein diets than in those fed 5%. In this study, groups of male and female F344 rats were fed either a 5 or 20% casein diet for 6 weeks. Two hr after a 1-mg/kg i.p. dose of [3H]aflatoxin B1, animals were killed and four protein fractions were sequentially extracted from the liver chromatin of each. Within each treatment group, aflatoxin binding to nonhistones was greater than to histones, both before and after dialysis. Comparing treatments, the higher-risk factors were associated with a greater liver content of aflatoxin as well as with increased binding of both nondialyzable and dialyzable aflatoxin to the various fractions. The high degree of correlation between total liver content and adduct formation implicates the former as a major determinant of the latter. Also associated with the higher-risk factors was a shift in the distribution of dialyzable aflatoxin toward greater adduct formation with one of the nonhistone fractions, suggesting the possibility of a role for noncovalent aflatoxin:protein adducts in hepatocarcinogenesis.

In vitro recognition of DNA base pairs by histones in histone-DNA complexes and reconstituted core particles: an ultraviolet resonance Raman study

Resonance Raman spectra of complexes between DNA and the four core histones, alone or associated, have been investigated in vitro using excitations at 300 and 257 nm, which give complementary informations about the DNA bases. H2A and H2B fractions recognize the G-C base pairs, while H3 and H4 (arginine rich fractions) recognize the A-T base pairs. The associated fractions form complexes with DNA which yield about the same DNA spectral modifications as the DNA-H4 complexes. This reveals the important role of the arginine rich fractions in the core particle formation and confirms the preferential in vitro assembly of nucleosome cores on A-T rich regions of DNA (25).

[Deoxyribonucleoprotein and nucleic acid changes in the tissues of rats after a flight on the Kosmos-1129 biosatellite]

The concentration of polydeoxyribonucleotides and nucleic acids was measured in the spleen, thymus, liver, bone marrow and blood of rats flown for 18.5 days on Cosmos-1129. The exposure led to an increase in the polydeoxyribonucleotide content in the thymus and a decrease of the DNA and RNA concentration in the spleen and thymus. These changes returned to normal at R+6.

Replicative conformation of parental nucleosomes: salt sensitivity of deoxyribonucleic acid-histone interaction and alteration of histone H1 binding

The transiently altered DNA-histone interaction of parental chromatin during replication was studied by micrococcal nuclease digestion. A large amount of nuclease-resistant pulse-labeled DNA and a small fraction of nonreplicating DNA are released from chromatin fragments by treatment with 0.5 M NaCl and appear as protein-free DNA. As shown by reconstitution experiments, the salt sensitivity of digested nascent chromatin is most probably a consequence of the shorter DNA fragment size (55 +/- 15 base pairs) in these complexes. This new DNA is associated with parental chromatin fragments which are structurally changed in such a way that parts of nucleosomal DNA were more susceptible to nuclease attack. The core histones of these particles are probably not distinct from those of salt-stable nucleosomes. However, histone H1 and probably high-mobility group proteins appear to be more weakly bound during replication as shown by electrophoresis under nondenaturing conditions. The results agree with the assumption that the transient alteration of nucleosomal conformation describes a state in which DNA could be replicated without leaving the associated core histone complexes. A possible attachment of pulse-labeled chromatin with nuclear matrix is discussed.

Repair of trans-Pt(II) diamminedichloride DNA-protein crosslinks in normal and excision-deficient human cells

In this investigation the persistence of DNA-protein crosslinks (DPC) induced by trans-Pt was determined in normal and excision-deficient xeroderma pigmentosum (XP) group A fibroblasts. After exposure to 50 microM trans-Pt for 2 h, the level of DPC increased in both cell types for several hours but by 12 h it was significantly less in normal cells. By 18 h it was approximately half the maximal value in normal cells but had decreased little in XP cells. When cells were incubated with trans-Pt and polymerase inhibitor, DNA single-strand breaks accumulated in normal but to a much lower level in XP cells. These single-strand breaks were presumably produced during excision repair and were roughly comparable in frequency to the number of DPC removed in normal cells during the same interval. By colony survival, trans-Pt was more toxic to XP cells. These results indicate that DPC were recognized in normal cells and repaired by the excision repair pathway.

[Proteins and the functional properties of the chromatin fractions from the nuclei of the normal liver and of experimental hepatomas]

Chromatin fragments generated in normal liver and solid hepatoma nuclei due to the action of endogenous nucleases and in ascites hepatomas nuclei treated with micrococcal nuclease differ in the ability to be released from the nuclei into a medium of low ionic strength. It is suggested that such a fractionation is based on different solubility of DNP fragments attached to the nuclear skeleton and of those that are not bound with it. DNP fragments extracted in a low-salt buffer contain all five histones with a negligible admixture of nonhistone proteins having the protein/DNA ratio about 1.1. No endogenous RNA-polymerase activity could be detected in these DNP fragments. The bulk of the RNA-polymerase activity is found in the matrix-associated DNP fragments that appear to be enriched in nonhistone proteins (their protein/DNA ratio amounted to 2.5). The possibility that transcribable DNP fragments are associated with the matrix through low-salt-stable linkages like those in the DNA-(RNA-polymerase-RNA or RNP)-matrix seems to be confirmed by the data obtained.

Mechanism of replication of bacteriophage phi X174 XX. Sensitivity of nascent DNA to single-strand-specific nucleases

We reported earlier that dephosphorylated nascent phi X174 viral strand DNA molecules were less extensively degraded from the 5' end by spleen exonuclease than were non-nascent molecules. Experiments described here revealed that the insensitivity to the 5'-OH end-specific nuclease was more evident among the longer molecules in the population than among the shorter, all of the molecules being less than unit length in size. The smallest molecules in the population were about as sensitive to the enzyme as the control molecules and hence must possess unblocked 5'-terminal nucleotides. Degradation of the nascent DNA with the 3' end-specific snake venom phosphodiesterase revealed only a small enrichment for [3H]thymidine near the 3' end, seemingly insufficient to account completely for the apparent insensitivity of the longer molecules to spleen exonuclease. When the nascent molecules were isolated without the use of proteolytic enzymes, some pronase-sensitive material was found associated with the DNA, particularly the longer molecules. We suggest that the resistance of the longer nascent (pronase-treated) molecules to spleen exonuclease occurs because they have remnants of the viral gene A or A* protein covalently bound to the 5' end.

The Croonian Lecture, 1981. Lampbrush chromosomes

Lampbrush chromosomes were first observed nearly 100 years ago, and this lecture attempts a historical survey of what has been learnt from their study, particularly that over the past 30 years. There have been many controversies concerning the structure and functional significance of lampbrush chromosomes, and although their general structural layout has now, after several misconceptions, been firmly established their functional significance remains controversial. Research on lampbrush chromosomes played a significant part in establishing that chromatids in the germ lines of eukaryotic organisms are unineme in regard to DNA, and thereby exposed the C-value paradox. It also helped to establish that a DNA duplex is continuous throughout the length of a chromatid, but that the DNA/histone complex is at intervals reflected back on itself to form lateral loops. This organization, at one time thought to be a special feature of lampbrush chromosomes, now appears to be widespread in chromosomes undergoing compaction. However, despite attempts to determine the sequence organization of those portions of the DNA that are transcribed by lampbrush chromosomes, the function of these transcripts remains an open question, and the C-value paradox is still unresolved.

[UV-light-tested protein--DNA interactions in the nuclei during the cell cycle in Physarum polycephalum]

The release of DNAs from nuclear preparations isolated at different steps of the cell cycle of the synchronous culture of Physarum polycephalum and irradiated with UV-light for 5 min (lambda 253.7 A, i = 1.8 . 10(2) j . m-2 . min-1) into 1% Na-DS - 1.5 M NaCl solution was studied. The value obtained correlated well with the degree of binding of interacting proteins with DNA in chromatin and was identical for all the preparations tested with the only exception of the nuclei isolated at the end of the S-phase, when a slight but significant (15 +/- 10%) increase in DNA release was observed. The results obtained are discussed in terms of structural transitions and function of chromatin during the cell cycle of the myxomycete Physarum polycephalum.

Site-specific cleavage/packaging of herpes simplex virus DNA and the selective maturation of nucleocapsids containing full-length viral DNA

Defective genomes present in serially passaged herpes simplex virus (HSV) stocks have been shown to consist of tandemly arranged repeat units containing limited sets of the standard virus DNA sequences. Invariably, the HSV defective genomes terminate with the right (S component) terminus of HSV DNA. Because the oligomeric forms can arise from a single repeat unit, it has been concluded that the defective genomes arise by a rolling circle mechanism of replication. We now report on our studies of defective genomes packaged in viral capsids accumulating in the nuclei and in mature virions (enveloped capsids) translocated into the cytoplasm of cells infected with serially passaged virus. These studies have revealed that, upon electrophoresis in agarose gels, the defective genomes prepared from cytoplasmic virions comigrated with nondefective standard virus DNA (M(r) 100 x 10(6)). In contrast, DNA prepared from capsids accumulating in nuclei consisted of both full-length defective virus DNA molecules and smaller DNA molecules of discrete sizes, ranging in M(r) from 5.5 to 100 x 10(6). These smaller DNA species were shown to consist of different integral numbers (from 1 to approximately 18) of defective genome repeat units and to terminate with sequences corresponding to the right terminal sequences of HSV DNA. We conclude on the basis of these studies that (i) sequences from the right end of standard virus DNA contain a recognition signal for the cleavage and packaging of concatemeric viral DNA, (ii) the sequence-specific cleavage is either a prerequisite for or occurs during the entry of viral DNA into capsid structures, and (iii) DNA molecules significantly shorter than full-length standard viral DNA can become encapsidated within nuclear capsids provided they contain the cleavage/packaging signal. However, capsids containing DNA molecules significantly shorter than standard virus DNA are not translocated into the cytoplasm.

In vitro reassembly of vesicular stomatitis virus skeletons

Vesicular stomatitis virus (VSV) has been disrupted with nonionic detergent plus 0.5 M NaCl under conditions which result in solubilization of the viral glycoprotein (G), matrix protein (M), and lipids, leaving the nucleocapsid in a highly extended state. Dialysis of these suspensions to remove NaCl was found to result in reassociation of nucleocapsids with M protein. Reassociated structures were highly condensed and similar in appearance to "native" VSV skeletons produced by extraction of virions with detergent at low ionic strength. For instance, electron microscopic analysis revealed that, like "native" skeletons, "reassembled" skeletons were cylindrical in shape, with diameters in the range of 51.0 to 55.0 nm and cross-striations spaced approximately 6.0 nm apart along the length of the structure. Like native skeletons, reassembled skeletons were found by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to contain the viral N and M proteins, but they lacked the glycoprotein entirely. Both native and reassembled skeletons were found to be capable of in vitro RNA-dependent RNA synthesis (transcription). In vivo skeleton assembly required the presence of M protein and nucleocapsids. No skeleton-like structures were formed by dialysis of nucleocapsids in the absence of M protein or of M protein in the absence of nucleocapsids. These results provide strong support for the view that the VSV M protein plays a functional role in condensing the viral nucleocapsid in vitro and raise the possibility that it may play a similar role in vivo.

Microfluorometric assessment of sperm maturation in testicular biopsies from men with histologically normal or reduced spermatogenesis

Spermatogenesis has been studied in testicular biopsies by means of microfluorometric assessment of the DNA-DNP complex using ethidium bromide in 10 men with histologically normal spermatogenesis and in 10 men with histologically reduced spermatogenesis. The expected haploid DNA value was found in the round spermatids, whereas only 70% of the haploid fluorescence value was found in the elongated spermatids and around 60% in the testicular spermatozoa. No difference was found in the mean fluorescence values between the pathological group and the controls. it is suggested that structural changes or an increase in basic nuclear proteins gradually exclude the ethidium bromide from the binding to the DNA molecule and that this phenomenon occurs concomitantly with a decrease in double-stranded RNA. The difference in fluorescence intensity before and after RNAase treatment was regarded as an approximate estimate of the RNA content. There was a significant decrease of these values during spermatogenesis.

Characterization of a rat liver mitochondrial DNA-protein complex. Replicative intermediates are protected against branch migrational loss

A stable DNA-protein complex was released from rat liver mitochondria by sodium dodecyl sulfate-lysis and isolated by sedimentation velocity in sucrose density gradients. The mtDNA-protein complex was washed with 0.5 M NaCl and any unbound contaminants were removed by hydroxyapatite column chromatography. The only detectable polypeptide in the complex was a single low molecular weight species (Mr = 16,000) having a slightly basic isoelectric point of 7.6-7.8. Complete digestion of the mtDNA-protein complex with restriction endonuclease HindIII revealed in agarose gels an "extra" band consisting of a subset of the largest fragment population. The fragments in this subset were shown to contain the replicative intermediates which were retarded in electrophoretic migration due to the parental strand separation in the region of the replication loops. No loss of nascent strands due to branch migration of the parental strands was observed upon HindIII cleavage of the covalently closed circular DNA in the mtDNA-protein complex. However, HindIII digestion of completely deproteinized mtDNA resulted in quantitative loss of nascent strands from replicating molecules. These results are interpreted as evidence that the single low molecular weight polypeptide present in the complex plays a major role in maintaining the integrity of replication loops during parental strand scission.

Protein-associated deoxyribonucleic acid strand breaks in L1210 cells treated with the deoxyribonucleic acid intercalating agents 4'-(9-acridinylamino) methanesulfon-m-anisidide and adriamycin

The DNA intercalating agents 4'-(9-acridinyl-amino) methanesulfon-m-anisidide (m-AMSA) and adriamycin were studied by using filter elution methods to measure DNA single-strand breaks (SSB's), DNA-protein cross-links (DPC's), and double-stranded breaks (DSB's) in mouse leukemia L1210 cells. Both compounds produced SSB's and DPC's at nearly 1:1 ratios. The SSB's and DPC's were shown to be localized with respect to each other; this was inferred from the finding that filter assays based on protein adsorption completely prevented the elution of the DNA single-strand segments between SSB's. In the case of m-AMSA, which produces relatively high frequencies of DNA lesions, the possibility that a protein bridges across the SSB was excluded by alkaline sedimentation studies. Both compounds also produced DSB's, but the SSB/DSB ratios differed; the SSB/DSB ratios increase in the following order: ellipticine greater than adriamycin greater than m-AMSA greater than X-ray [results of this paper combined with those of Ross, W. E., & Bradley, M. O. (1981) Biochim. Biophys. Acta (in press)]. The o-AMSA isomer is much less cytotoxic than m-AMSA and did not produce protein-associated strand breaks. The simplest model to explain the results is that a protein becomes covalently bound to either the 3' or the 5' termini of the intercalator-induced strand breaks. At moderately cytotoxic doses, m-AMSA yielded much larger frequencies of protein-associated SSB's than did adriamycin. m-AMSA-induced protein-associated SSB's saturated at approximately 60000 per cell over a concentration range in which m-AMSA uptake by the cells was proportional to the drug concentration. m-AMSA was found to enter and exit from cells very rapidly at 37 degrees C; protein-associated SSB's and DSB's also appeared and disappeared rapidly. At reduced temperature, however, the appearance and disappearance of protein-associated SSB's could be blocked while m-AMSA entry and exit still occurred. The saturation behavior and temperature dependence suggest that the formation and disappearance of protein-associated strand breaks is enzymatic. The simplest hypothesis is that the linked protein is a nuclease, such as a topoisomerase, which becomes bound to one terminus of the strand break it produces. It is proposed that topoisomerases producing SSB's and DSB's are stimulated to different degrees by different intercalators.

Studies on structure and function of chromatin

This article covers research work in this laboratory on the structure and function of chromatin. Early studies have led to discovery of skeletal fibrils (nucleonemas) within the nuclei and showed the specific role of histone H1 in chromatin condensation and in restriction of transcription. More recently with the aid of a novel DNP electrophoresis technique the relation of histone H1 and non-histone proteins to nucleosomes was studied. Three types of mononucleosomes and a number of subnucleosomes were identified in chromatin digests. The complexes of certain HMG proteins with short DNA segments were isolated and found to originate frm transcriptionally active chromatin. Different forms of SV40 minichromosome were characterized. A method for the analysis of nucleosome distribution along the DNA sequence was elaborated and used to show non-random (phased) location of nucleosomes on SV40 DNA. The attachment of DNA to skeletal elements of interphase nuclei and metaphase chromosomes was shown to be a non-random, probably sequence-specific process.

Changes in chromatin structure at the replication fork. II The DNPs containing nascent DNA and a transient chromatin modification detected by DNAase I

Discrete deoxyribonucleoproteins (DNPs) containing nascent and/or bulk DNA, were obtained by fractionating micrococcal nuclease digests of nuclei form 3H-thymidine pulse (15-20 sec) and 14C-thymidine long (16 h) labeled sea urchin embryos in polyacrylamide gels. One of these DNPs was shown to contain the micrococcal nuclease resistant 300 bp "large nascent DNA" described in Cell 14, 259-267, 1978. The bulk and nascent mononucleosome fractions provided evidence for the preferential digestion by micrococcal nuclease of nascent over bulk linker regions to yield mononucleosome cores with nascent DNA. DNAase I was used to probe whether any nascent DNA is in nucleosomes. Nascent as well as bulk single-stranded DNA fragments occurred in multiples of 10.4 bases with higher than random frequencies of certain fragment sizes (for instance 83 bases) as expected from a nucleosome structure. However, a striking background of nascent DNA between nascent DNA peaks was observed. This was eliminated by a pulse-chase treatment or by digestion of pulse-labeled nuclei with micrococcal nuclease together with DNAase I. One of several possible interpretations of these results suggests that a transient change in nucleosome structure may have created additional sites for the nicking of nascent DNA by DNAase I; the micrococcal nuclease sensitivity of the interpeak radioactivity suggest its origin from the linker region. Endogenous nuclease of sea urchin embryos cleaves chromatin DNA in a manner similar to that of DNAase I.

Cessation of reentry of simian virus 40 DNA into replication and its simultaneous appearance in nucleoprotein complexes of the maturation pathway

Newly synthesized SV40 DNA is used as a template for further DNA synthesis (reenters replication) or as a substrate in the assembly of virions (maturation pathway). The time courses of reentry into replication and progression along the maturation pathway were both determined on identical samples. DNA, synthesized during a 20-min pulse, reentered replication over a period of several hours and then was removed from the pool of molecules available for replication. The cessation of reentry coincided with the maturation of this DNA from the chromatin form to previrion and virion forms. More reentry and less maturation was observed at 24 h postinfection than at 42 h postinfection. The data are consistent with the hypothesis that the factor(s) responsible for cessation of reentry is also responsible for initiation of the maturation pathway.

A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins

It is proposed that a general function of noncoding DNA and RNA sequences in higher organisms (intergenic and intervening sequences) is to provide multiple binding sites over long stretches of polynucleotide for certain types of regulatory proteins. Through the building up or abolishing of high-order structures, these proteins either sequester sites for the control of, e.g., transcription or make the sites available to local molecular signals. If this is to take place, the existence of a 'c-value paradox' becomes a requirement. Multiple binding sites for a given protein may recur in the form of a sequence 'motif' that is variable within certain limits. Noncoding sequences of the chickens ovalbumin gene furnish an appropriate example of a sequence motif. GAAAATT. Its improbably high frequency and significant periodicity are both absent from the coding sequences of the same gene and from the noncoding sequences of a differently controlled gene in the same organisms, the preproinsulin gene. This distribution of a sequence motif is in keeping with the concepts outlined. Low specificity of sequences that bind protein is likely to be compatible with highly specific conformational changes.