Subunit structure of simian-virus-40 minichromosome

Cytotoxic effect of Drosophila deoxynucleoside kinase gene on replicating plasmid in HeLa cells

To enhance the levels of transgene expression from plasmid-based nonviral vectors, replicating plasmids containing the SV40 origin and the SV40 large T antigen gene, as a model replicating unit, were constructed. The replicating luciferase plasmid DNA produced the luciferase protein more efficiently than the non-replicating luciferase plasmid DNA, as expected. Surprisingly, the introduction of the replicating plasmid DNA containing the Drosophila melanogaster deoxyribonucleoside kinase (Dm-dNK) gene was highly cytotoxic and caused cell death without nucleoside analogs. Our results confirm that transgenes on a replicating plasmid represent an excellent tool for effective protein production and suggest that efficient production of the Dm-dNK protein in tumor cells could be an attractive cancer therapy.

During lytic infections, herpes simplex virus type 1 DNA is in complexes with the properties of unstable nucleosomes

The genomes of herpes simplex virus type 1 (HSV-1) are regularly chromatinized during latency such that their digestion with micrococcal nuclease (MCN) releases nucleosome-sized DNA fragments. In lytically infected cells, in contrast, MCN releases HSV-1 DNA in primarily heterogeneously sized fragments. Consistently, only a small percentage of this HSV-1 DNA coimmunoprecipitates with histones. Most current models propose that histones associate with HSV-1 DNA during lytic infections at low occupancy. However, histone modification or occupation is also proposed to regulate HSV-1 transcription. It remains unclear how the histones associated with a small percentage of HSV-1 DNA may regulate transcription globally. Moreover, the physical properties of the complexes containing histones and HSV-1 DNA are unknown. We evaluated the HSV-1 DNA-containing complexes at 5 h after (lytic) infection by biochemical fractionations. Nuclear HSV-1 DNA did not fractionate as protein-free HSV-1 DNA but as DNA in cellular nucleosomes. Moreover, MCN released HSV-1 DNA in complexes that fractionate as cellular mono- and dinucleosomes by centrifugation followed by sucrose gradients and size-exclusion chromatography. The HSV-1 DNA in such complexes was protected to heterogeneous sizes and was more accessible to MCN than DNA in most cellular chromatin. Using a modified MCN digestion to trap unstable digestion intermediates, HSV-1 DNA was quantitatively recovered in discrete mono- to polynucleosome sizes in complexes fractionating as cellular mono- to polynucleosomes. The HSV-1 DNAs in complexes fractionating as mono- to dinucleosomes were stabilized by cross-linking. Therefore, most HSV-1 DNA forms particularly unstable nucleosome-like complexes at 5 h of lytic infection.

Small DNA tumour viruses and their contributions to our understanding of transcription control

The study of small DNA tumour viruses like SV40 and polyoma was one of the major entry points for the study of eukaryotes. It opened fields like gene structure, transcription or replication control, chromatin structure and cell transformation. This review outlines the breakthroughs that occurred at the end of the 1970s and during the 1980s in our understanding of gene structure and the basic processes involved in control of gene expression starting with DNA tumour viruses and reaching their cellular hosts. These developments were made possible by concomitant advances in the isolation of restriction enzymes, developing DNA sequencing protocols, DNA cloning, DNA transfections, in vitro transcription systems and isolation of sequence specific DNA binding protein among others. The conceptual and methodological advances that resulted from the studies of small DNA tumour viruses opened the era for the study of host genomes far more complex, culminating with the establishment of the sequence and a functional map of the human genome.

Adeno-associated virus vector genomes persist as episomal chromatin in primate muscle

Recombinant adeno-associated virus (rAAV) vectors are capable of mediating long-term gene expression following administration to skeletal muscle. In rodent muscle, the vector genomes persist in the nucleus in concatemeric episomal forms. Here, we demonstrate with nonhuman primates that rAAV vectors integrate inefficiently into the chromosomes of myocytes and reside predominantly as episomal monomeric and concatemeric circles. The episomal rAAV genomes assimilate into chromatin with a typical nucleosomal pattern. The persistence of the vector genomes and gene expression for years in quiescent tissues suggests that a bona fide chromatin structure is important for episomal maintenance and transgene expression. These findings were obtained from primate muscles transduced with rAAV1 and rAAV8 vectors for up to 22 months after intramuscular delivery of 5 x 10(12) viral genomes/kg. Because of this unique context, our data, which provide important insight into in situ vector biology, are highly relevant from a clinical standpoint.

Glial cell-specific regulation of the JC virus early promoter by histone deacetylase inhibitors

The human polyomavirus JC virus is the etiologic agent of the fatal disease demyelinating progressive multifocal leukoencephalopathy. Although multiple transcription factors have been shown to interact with the JC virus promoter and regulate transcriptional activity, their relevance to cell specificity remains elusive. To investigate whether chromatin structure controls glial cell-specific expression of JC virus early genes, glial and nonglial cells were transfected with a reporter plasmid containing the JC virus early promoter and then treated with the histone deacetylase (HDAC) inhibitors trichostatin A (TSA) and sodium butyrate. TSA and butyrate induced 20- to 30-fold activation of the JC virus promoter in nonglial cells, whereas less than 2-fold induction was observed in glial cells. These results indicate that the JC virus early promoter might be highly suppressed in nonglial cells by hypoacetylated chromatin and activated by hyperacetylation. In support of this, chromatin immunoprecipitation assays demonstrated acetylation of the JC virus promoter region in U87MG cells but no acetylation in HeLa cells. In addition, treatment of HeLa cells with TSA induced hyperacetylation of the JC virus promoter, whereas minimal induction was seen in U87MG cells. Deletional and site-directed mutational analyses revealed that the enhancer region and Sp1 binding site upstream of the TATA box were important for TSA-mediated activation. We confirmed TSA-mediated activation of the JC virus promoter in the context of natural chromatin structure in stable cell lines. Thus, it appears that chromatin structure may control JC virus transcription in a cell-specific manner.

Abutilon mosaic geminivirus double-stranded DNA is packed into minichromosomes

An intermediate form of Abutilon mosaic geminivirus, a complex of viral double-stranded DNA (dsDNA) and protein, was characterized by two different techniques. Cesium sulphate gradient centrifugation was used to show that the majority of this form comigrates with host chromatin. Micrococcus nuclease digestion experiments with isolated nuclei demonstrated that the viral dsDNA is organized in a manner comparable to that of host nucleosomes. Results from a previous electron microscopical work (Abouzid, A. M., Frischmuth, T., and H. Jeske, 1988, Mol. Gen. Genet. 212, 252-258) suggested to us that a part of the viral dsDNA must be free of nucleosomes. Whether this nucleosome-free space corresponds to the intergenic region which contains most of the promotor sequences and the putative origin of replication is discussed.

Location of nucleosomes in simian virus 40 chromatin

Over the past decade, the results of numerous indirect mappings analyses have not clarified whether or not nucleosomes occupy preferred positions in simian virus 40 (SV40) chromatin. To address this question more directly, we followed a shotgun cloning approach and determined the nucleotide sequences of over 400 cloned nucleosomal DNA fragments obtained from digestion of SV40 chromatin with micrococcal nuclease. Our results demonstrate and establish that nucleosomes do not occupy unique positions in SV40 minichromosomes and thus indicate the existence of at least several types of chromatin molecules having different nucleosome organization patterns. We developed two types of statistical analysis in order to examine the cloning data in greater detail. One type, overlap analysis, revealed the distribution of the cloned fragments with respect to SV40 DNA. The distribution exhibits an oscillating pattern, dividing the genome into regions of weak or strong nucleosome density. The other analysis determined the distribution of the midpoints of the cloned fragments and revealed potential strong and weak nucleosome location sites, and an early versus late distinction in organization of nucleosomes in SV40 chromatin. The late region appears to contain more strong nucleosome location sites (8) than the early region (4). The strongest nucleosome abuts the late side of the nuclease-hypersensitive region and includes the major transcription initiation site of the late genes. Another strong site precedes this nucleosome and includes sequences implicated in controlling the expression of the SV40 early and late genes. A strong or weak nucleosome location site is not apparent near the early side of the nucleosome-hypersensitive region. Only weak and overlapping nucleosome location sites are found in the region where replication terminates in the SV40 minichromosomes.

The SV40 nucleosome-free region is detected throughout the virus life cycle

The structures of SV40 intracellular chromatin complexes and of extracellular virus particles were examined by photolabeling with a radioactive psoralen derivative in order to determine the fate of the exposed origin region during the virus life cycle. We have previously shown that the origin region of intracellular SV40 chromatin is preferentially accessible to psoralen derivatives in vivo, whereas psoralen adducts are uniformly distributed when purified virus particles are photoreacted. We demonstrate here that when virion is photoreacted prior to a freeze-thaw cycle, the exposed regulatory region detected in intracellular nucleoprotein complexes is also found in mature virus particles. In contrast, if the virion is frozen and thawed prior to the photoreaction, the origin is not preferentially exposed to photoaddition. Virus particles that have not been subjected to a freeze-thaw cycle were found to exhibit preferential labeling in the origin region whether they were irradiated intracellularly, in culture medium, or following purification. Banding the virus in CsCl had no significant effect on the relative accessibility of the origin region to psorealen. Our findings indicate that the open regulatory region found on intracellular SV40 chromatin persists throughout the virus life cycle.

Occurrence of bovine herpesvirus-1 DNA in nucleosomes and chromatin of bovine herpesvirus-1-infected cells: identification of a virion-associated protein in chromatin of infected cells

During virus replication a fraction of the intranuclear DNA of bovine herpesvirus-1 (BHV-1) was present in the nucleosomal structure of infected eukaryotic cells, and virion proteins were associated with the chromatin of virus infected cells. Synthesis of BHV-1 DNA in bovine embryonic lung (BEL) cells was found to begin four to six hours post-infection (p.i.) and to continue until at least 24 hours p.i. Chromatin isolated from infected cell nuclei at ten hours p.i. contained both BHV-1 viral and cell DNA. No BHV-1 DNA was found in mock-infected cell chromatin. Micrococcal nuclease cleavage products of both mock-infected and BHV-1-infected BEL cell nuclei produced monomers and multimers of unit fragment size which were indistinguishable from each other and displayed a typical nucleosome pattern on agarose gels. Southern analyses of micrococcal nuclease digests of infected cell nuclei indicated that some of the intranuclear BHV-1 DNA was present in a nucleosomal form. Three new proteins (with approximate molecular weights: 125,000, 42,000, and 17,000) were identified in chromatin isolated from BHV-1-infected BEL cells at ten hours p.i. These proteins were not present in mock-infected BEL cell chromatin. The 17,000 molecular weight protein was recognized by BHV-1 virion specific antisera. Neither of the two larger proteins appear to bind DNA from BHV-1. The smallest protein co-migrates with cellular histones, but no DNA binding proteins with the same molecular weight were found in the virion.

Curvature of mouse satellite DNA and condensation of heterochromatin

Cloned, sequenced mouse satellite DNA exhibits properties characteristic of molecules that possess a stable curvature. Circularly permuted fragments containing the region predicted to bend were used to map the curvature relative to DNA sequence. The altered mobility of these fragments in polyacrylamide gels is reversed when gels are run in the presence of distamycin A, a drug that binds preferentially to AT-rich DNA. Treatment of living mouse cells with this drug dramatically reduces the condensation of centromeric heterochromatin, the exclusive location of satellite sequences. In situ hybridization of satellite probes to extended chromosomes at the electron microscope level shows that satellite does not comprise a single block but is distributed throughout the centromere region. Based on these experiments, we hypothesize that the structure of mouse satellite DNA is an important feature of centromeric heterochromatin condensation.

Deletion mutants which affect the nuclease-sensitive site in simian virus 40 chromatin

A short segment of simian virus 40 (SV40) chromatin on the late side of the origin of replication is hypersensitive to nuclease cleavage. The role of DNA sequence information in this nuclease-sensitive feature was examined by constructing deletion mutations in this region. Deletions were introduced into the inserted segment of in(Or)-1411 (a viable, partially duplicated variant of SV40), and nuclease sensitivity of the inserted segment was compared with that of the unaltered sequences in their normal location in the viral genome. Extended deletions (118 to 161 base pairs) essentially abolished nuclease sensitivity within the inserted segment. Shorter deletions (21 to 52 base pairs) at separate locations retained the nuclease-sensitive feature. In some short-deletion mutants nuclease susceptibility was substantially reduced. We conclude that more than one genetic element in this region contributes to the organization of the nuclease-sensitive feature and that the SV40 72-base repeat is not, in itself, sufficient signal for this feature.

Characterization of SV40 chromatin by mass determination on STEM

Direct mass determination of purified SV40 minichromosomes was obtained by scanning transmission electron microscopy. Twenty to thirty percent of the minichromosomes were found with an Mr of 6.9 +/- 0.4 X 10(6). The rest of the molecules formed a spread Mr distribution ranging from 7.3 X 10(6) to 9.5 X 10(6) due possibly to different contents of the virus-coded proteins, mainly VP1. The apparent mass histogram of individual SV40 nucleosomes presents three maxima at Mr 2.1 X 10(5), 2.6 X 10(5) and 3.1 X 10(5) that could correspond to partially unravelled nucleosomes, complete nucleosomes and complete nucleosomes with the addition of VP1. Beaded structures with a higher mass were also measured; some were found at either side of the open nucleosome-free region.

Chromatin assembly during SV40 DNA replication in vitro

A cytosol extract from human 293 cells supports efficient replication of SV40 origin-containing plasmid DNA in the presence of the SV40 T antigen. Addition of a nuclear extract from the same cells promotes negative supercoiling of the replicated DNA but not the bulk of the unreplicated DNA. The level of superhelicity is affected by the concentrations of T antigen and nuclear extract factors and by the time of addition of the nuclear extract. The replicated DNA in isolated DNA-protein complexes resists relaxation by purified HeLa cell topoisomerase I. Micrococcal nuclease digestion, sucrose gradient sedimentation, and electron microscopy demonstrate that the negative supercoils result from assembly of the replicating DNA into a chromatin structure. These results suggest that, during DNA replication, the core histones can be assembled on both sides of the replication fork by an active, replication-linked mechanism that does not require a template of preexisting nucleosomes.

Structure of replicating simian virus 40 minichromosomes. The replication fork, core histone segregation and terminal structures

The structure of replicating simian virus 40 (SV40) minichromosomes was studied by DNA crosslinking with trimethyl-psoralen. The procedure was used both in vitro with extracted SV40 minichromosomes as well as in vivo with SV40-infected cells. Both procedures gave essentially the same results. Mature SV40 minichromosomes are estimated to contain about 27 nucleosomes (error +/- 2), except for those molecules with a nucleosome-free gap, which are interpreted to contain 25 nucleosomes (error +/- 2). In replicative intermediates, nucleosomes are present in the unreplicated parental stem with the replication fork possibly penetrating into the nucleosomal DNA before the histone octamer is removed. Nucleosomes reassociate on the newly replicated DNA branches at distances from the branch point of 225 ( +/- 145) nucleotides on the leading strand and of 285( +/- 120) nucleotides on the lagging strand. In the presence of cycloheximide, daughter duplexes contained unequal numbers of nucleosomes, supporting dispersive and random segregation of parental nucleosomes. These were arranged in clusters with normal nucleosome spacing. We detected a novel type of interlocked dimer comprising two fully replicated molecules connected by a single-stranded DNA bridge. We cannot decide whether these dimers represent hemicatenanes or whether the two circles are joined by a Holliday-type structure. The joining site maps within the replication terminus. We propose that these dimers represent molecules engaged in strand segregation.

Transcriptionally active SV40 minichromosomes are restriction enzyme sensitive and contain a nucleosome-free origin region

A nucleosome-free region or gap containing the origin of replication and the transcriptional promoter elements is observed on 20 to 25% of the SV40 minichromosomes isolated at physiological ionic strength late in infection. We used the preferential sensitivity of the gapped minichromosomes to restriction enzymes to obtain sucrose gradient fractions containing 50 to 80% of gapped molecules. The same fractions are also enriched in RNA polymerase B (II) molecules engaged in transcription. Using electron microscopy, we demonstrate here that the transcriptional complexes are preferentially sensitive to restriction enzyme digestion, which indicate that they represent a subpopulation of the gapped minichromosomes.

T-antigen is the only detectable protein on the nucleosome-free origin region of isolated simian virus 40 minichromosomes

A nucleosome-free region or nucleosome gap, containing the origin of replication and the transcriptional promoter elements, is observed on 20%-25% of the SV40 minichromosomes isolated at physiological ionic strength at late time during the infectious cycle. We found that this subpopulation of gapped minichromosomes was more sensitive to digestion with a variety of single-cut restriction enzymes than the rest of the minichromosomes. This increased digestibility of gapped minichromosomes allowed us to excise the gap region by concomitant digestion with Bgl I and Msp I. T-antigen was the only detectable protein bound to this isolated chromatin fragment. In particular no histones could be detected. The presence of T-antigen on the gap region was confirmed by immunoelectron microscopy. Most of the T-antigen appeared to be located on the late side of the Bgl I restriction enzyme site.

S1-sensitive sites in the supercoiled double-stranded form of tomato golden mosaic virus DNA component B: identification of regions of potential alternative secondary structure and regulatory function

The sensitivity of the supercoiled double-stranded form of the DNA of tomato golden mosaic virus (TGMV), a geminivirus, to the single-strand specific enzyme S1 nuclease has been demonstrated. Specific S1 cleavage sites were identified in TGMV DNA component B by cloning into the single-strand bacteriophage vector M13 mp8 and sequencing of the inserted DNA. Analysis of the DNA sequence at the sites of S1 sensitivity in TGMV DNA component B revealed several possible regions of alternative secondary structure which were clustered in an intergenic region upstream of the starts of the two major open reading frames which are in opposite orientations. This region contains putative transcriptional promoter and modulatory sequences and a possible replication origin. The extreme S1 sensitivity of the supercoiled form of TGMV DNA component A precluded its cloning under the conditions employed for selective cleavage of DNA component B.

Structural organization and polypeptide composition of the avian adenovirus core

CELO virus (fowl adenovirus 1) contained three core polypeptides of molecular weights 20,000, 12,000, and 9,500. The core was similar to that of human adenoviruses, with some evidence of compact subcore domains. Micrococcal nuclease digestion of CELO virus cores produced a smear of DNA fragments of gradually decreasing size, with no nucleosome subunit or repeat pattern. Moreover, when digested cores were analyzed without protease treatment, there was again no evidence of a nucleosome substructure; neither DNA fragments nor core proteins entered a 4% polyacrylamide gel. The organization of the core is thus quite unlike that of chromatin. Restriction endonuclease analysis of the DNA from digested cores showed that the right end was on the outside of the core. We suggest that adenovirus DNA is condensed into the core by cross-linking and neutralization by the core proteins, beginning with the packaging sequence at the center of the core and ending with the right end of the DNA on the outside.

Unwinding of the DNA helix in simian virus 40 chromosome templates by RNA polymerase

We measured the distortion of the DNA helix by RNA polymerase transcribing simian virus 40 (SV40) chromosome templates and compared it with the distortion caused by the enzymes as it transcribes naked SV40 DNA, using RNA polymerase from Escherichia coli. Purified DNA topoisomerase I was added to the transcription reactions and the number of supercoil turns in DNA, after deproteinising and removal of RNA, was determined by gel electrophoresis and band-counting. The number of polymerase molecules bound per naked DNA molecule was determined by electron microscopy. Each bound RNA polymerase distorted the template in such a way as to lead to on apparent average of 0.6-0.7 negative superhelical turn in the extracted DNA. Thus only few base-pairs are melted per RNA polymerase molecule. When SV40 chromosomes were transcribed the extracted DNA had a higher number of supercoil turns than DNA extracted from the initial chromosomes. We conclude that the polymerase deforms the DNA in chromatin in the same way as it deforms pure DNA. From control experiments with inhibitors of initiation we estimated that on average 9-10 RNA polymerase molecules were bound per SV40 chromosome. This suggests that transcription can proceed while the majority or all the nucleosomal structures are intact on an SV40 DNA molecule. We discuss the implications of these findings for the mechanism of transcription of chromatin.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.

Configurational changes in rat liver nuclear chromatin caused by azo dyes

The effects of azo dyes on the chromatin configuration of isolated rat-liver nuclei were examined by electron microscopy for elucidation of the mechanism of dye-stimulated in vitro RNA synthesis. Sunset Yellow FCF had no effect on the incorporation of [3H]UTP into RNA but amaranth and Ponceau 3R stimulated incorporation approximately two- and 3.5-fold, respectively. Sunset Yellow FCF did not produce any major alteration in liver nuclei. Isolated liver nuclei treated with amaranth or Ponceau 3R showed dissociation of heterochromatin and the nucleoli lost their fine-granular structure acquiring a coarse-granular configuration. The dense structure of heterochromatin in liver nuclei treated with Ponceau 3R was completely dissociated and appeared as a lace-like configuration. These results suggest that both Ponceau 3R and amaranth stimulate in vitro RNA synthesis by causing the dissociation of heterochromatin in isolated rat-liver nuclei.

Barriers to nuclease Bal31 digestion across specific sites in simian virus 40 chromatin

A portion of the nucleoprotein containing viral DNA extracted from cells infected by simian virus (SV40) is preferentially cleaved by endonucleases in a region of the genome encompassing the origin of replication and early and late promoters. To explore this nuclease-sensitive structure, we cleaved SV40 chromatin molecules with restriction enzymes and digested the exposed termini with nuclease Bal31. Digestion proceeded only a short distance in the late direction from the MspI site, but some molecules were degraded 400 to 500 base pairs in the early direction. By comparison, BglI-cleaved chromatin was digested for only a short distance in the early direction, but some molecules were degraded 400 to 450 base pairs in the late direction. These barriers to Bal31 digestion (bracketing the BglI and the MspI sites) define the borders of the same open region in SV40 chromatin that is preferentially digested by DNase I and other endonucleases. In a portion of the SV40 chromatin, Bal31 could not digest through the nuclease-sensitive region and reached barriers after digesting only 50 to 100 base pairs from one end or the other. Chromatin molecules that contain barriers in the BglI to MspI region are physically distinct from molecules that are open in this region as evidenced by partial separation of the two populations on sucrose density gradients.

Negatively supercoiled DNA from plants infected with a single-stranded DNA virus

A method for isolating covalently closed circular double-stranded DNA from plants infected with the geminivirus, tomato golden mosaic virus, is described. Ethidium bromide titration showed this DNA to be negatively supercoiled with a superhelical density of -0.062. The presence of S1 nuclease-sensitive secondary structure in the supercoiled DNA was demonstrated by its conversion to the open circular and linear DNA forms on treatment with this enzyme.

SV40 virus particles lack a psoralen-accessible origin and contain an altered nucleoprotein structure

The nucleoprotein structure of SV40 virions was examined by photolabeling purified virus with the radioactive psoralen derivative hydroxymethyltrimethylpsoralen (HMT). Unlike SV40 chromatin in situ, the viral origin region is not preferentially accessible to drug addition. The ratio of the distribution of radioactivity in the DNA restriction fragments of virion DNA to that of purified SV40 DNA demonstrates that the photoadducts are positioned similarly on the circular molecule in both samples. Virion purified from infected cells was also analyzed for the presence of an open region and found to exhibit the same pattern of [3H]HMT addition as mature extracellular virion. The nucleosome-free region detected at the SV40 replication origin in intracellular minichromosomes is not present in either population of intact virus particles. We also examined the level of drug addition obtained when purified virion or SV40-infected cells were treated with saturating doses of [3H]HMT. Marked differences in the plateau levels of bound drug indicate that an altered nucleoprotein structure exists in SV40 virions that does not protect the DNA from photoaddition to the same extent as do the nucleosomes of intracellular SV40 DNA.

Visualization of anti-histone antibodies on SV40 minichromosomes by scanning transmission electron microscopy (STEM)

The unique capabilities of the scanning transmission electron microscope (STEM) have been used for a high resolution study of antibody binding to individual SV40 minichromosomes. A method of sample preparation has been developed which allows direct visualization of the antibody molecules in a clearly recognizable form. Using this technique, we have studied the binding of anti-H2B and anti-H3 immunoglobulins to SV40 minichromosomes. The results indicate that histones H2B and H3 are located only in the nucleosomes and are absent in the linker regions.

The simian-virus-40 large-tumor antigen in replicating viral chromatin. A salt-resistant protein-DNA interaction

The large tumor antigen (T antigen) is a genome regulation protein, coded by simian virus 40, that binds with high affinity to specific binding sites on viral DNA. The specifically bound T antigen is released from these sites in 0.2-0.3 M NaCl. Immunoprecipitation techniques were used to show that T antigen also dissociates in 0.2-0.3 M NaCl from mature viral chromatin but not from replicating viral chromatin. In fact, a considerable fraction of T antigen remains associated with replicating chromatin at NaCl concentrations as high as 1.2 M NaCl when most chromatin proteins, including histones, dissociate. However, T antigen binding to both replicating DNA and mature DNA is sensitive to intercalating drugs such as caffeine and ethidium bromide. We consider the possibility that the unexpectedly tight binding of T antigen to replicating DNA is related to the function that T antigen performs during viral DNA replication.

Intracellular forms of simian virus 40 nucleoprotein complexes. IV. Micrococcal nuclease digestion

The structures of DNAs present in various intracellular forms of simian virus 40 (SV40) nucleoprotein complexes were analyzed by micrococcal nuclease digestion. The results showed that the 70S SV40 chromatin was completely sensitive to nuclease digestion, whereas CsCl gradient-purified mature virion was completely resistant. Virion assembly intermediates with different degrees of virion maturation showed intermediate resistance, and three products were found: nucleosomal DNA fragments, representing the fraction of intermediates that were sensitive to nuclease; linear SV40 genome-sized DNA, representing the more mature intermediates that contained one or limited defects in the capsid shell; and supercoiled SV40, which was derived from mature virions. These digestion products, however, remained associated with capsid shells after nuclease digestion. These results were consistent with the model in which maturation of the SV40 virion is achieved through the organization of capsid proteins that accumulate around SV40 chromatin. Mild digestion of SV40 nucleoprotein complexes with micrococcal nuclease revealed the difference in nucleosome repeat length between SV40 chromatin and virion assembly intermediates. A novel DNA fragment of about 75 nucleotides was observed early in nuclease digestion.

Simian virus 40 encapsidation: characterization of early intermediates

Simian virus 40 chromosomes were separated into various species by a two-step purification consisting of low-ionic-strength glycerol gradient sedimentation followed by low-ionic-strength agarose gel electrophoresis. For each species of simian virus 40 chromosome purified, the comigrating DNA and proteins were identified by agarose or polyacrylamide gel electrophoresis, respectively. Two species of chromosomes were identified which contained form I and form II DNA and large amounts of viral protein; they migrated more slowly than most of the free simian virus 40 chromosomes, which contained very little viral protein. The nuclease susceptibility of these chromosomes suggests to us that they are intermediates in encapsidation, and we describe an encapsidation model.

Absence of nucleosomes in a histone-containing nucleoprotein complex obtained by dissociation of purified SV40 virions

Reduction of disulfide bonds involving the major capsid protein with dithiothreitol and removal of the calcium ions by EGTA disrupts the simian virus 40 virions. This process yields normal circular viral minichromosomes containing the four core histones and traces of the capsid proteins at pH values higher than 8.5. However, when carried out at pH 7.5, this procedure yields nucleoprotein complexes that contain both histones and the viral structural proteins. These pH 7.5 complexes appear as circular structures with a mean of 93 +/- 17 beads with a diameter of 7 nm and no visible nucleosomes when observed by electron microscopy. In contrast to the compaction of the viral DNA in minichromosomes, the length of these beaded structures is roughly the same as free DNA. We suggest that VP1, the major capsid protein, can act as a nucleosome unfolding agent in neutral pH and low ionic strength.

Deletion mutants which affect the nuclease-sensitive site in simian virus 40 chromatin

A short segment of simian virus 40 (SV40) chromatin on the late side of the origin of replication is hypersensitive to nuclease cleavage. The role of DNA sequence information in this nuclease-sensitive feature was examined by constructing deletion mutations in this region. Deletions were introduced into the inserted segment of in(Or)-1411 (a viable, partially duplicated variant of SV40), and nuclease sensitivity of the inserted segment was compared with that of the unaltered sequences in their normal location in the viral genome. Extended deletions (118 to 161 base pairs) essentially abolished nuclease sensitivity within the inserted segment. Shorter deletions (21 to 52 base pairs) at separate locations retained the nuclease-sensitive feature. In some short-deletion mutants nuclease susceptibility was substantially reduced. We conclude that more than one genetic element in this region contributes to the organization of the nuclease-sensitive feature and that the SV40 72-base repeat is not, in itself, sufficient signal for this feature.

A transcriptionally active, covalently closed minichromosome of cauliflower mosaic virus DNA isolated from infected turnip leaves

Purified nuclei from turnip leaves infected by cauliflower mosaic virus (CaMV) have been shown to contain a fraction of CaMV DNA that consists of covalently closed circular molecules; possesses a nucleosome structure, based on sensitivity to micrococcal nuclease; and contains nuclear RNA polymerase II that selectively transcribes the coding strand of CaMV DNA in vitro. Our results suggest that the transcriptionally active CaMV DNA is in the form of a minichromosome and that this DNA does not contain the site-specific discontinuities characteristic of the virion.

Changes in endonuclease activity and in chromatin structure of rat hepatocytes during fetal and neonatal life

A developmental study of rat hepatic endonuclease has been performed. Nuclei, from different stages of hepatocyte maturation, were analyzed for endogenous endonuclease activity. The chromatin extracted from these nuclei does not show any fragmentation during the first 17 days of fetal development. On the 18th day of fetal life there is a massive increase in specific endonuclease activity. At birth this activity reaches a maximum level (3.5 units/mg DNA); thereafter it undergoes a gradual decrease. The size of the basic DNA repeats produced by the endonuclease action is 218.9 +/- 1.6 in 18-day-old fetuses and decreases to 204.9 +/- 2.5 in 19-day-old fetuses, a value which remains constant in the following fetal and postnatal life. This difference in monomer size is due to changes in the chromatin structure. Micrococcal nuclease digests show that the "nucleosome core" does not change during hepatocyte development. Therefore, the difference in size of the endonuclease DNA fragments must be due to the linker regions.

New procedure using a psoralen derivative for analysis of nucleosome associated DNA sequences in chromatin of living cells

Sites for restriction endonuclease cleavage in double helical DNA are blocked from cleavage when the photoaffinity drug trimethylpsoralen is photobound at or near the site. In general, Hind III sites are about 15 fold more sensitive to inactivation than the other restriction sites which were tested, although sensitivity of different Hind III sites seems to vary somewhat depending on base sequences adjacent to the site. Hind III sites can be inactivated in two ways; one which completely blocks action of the specific restriction endonuclease and one permitting the introduction of a swivel which relaxes DNA supercoiling without producing a double strand break. Nucleosomes and perhaps other protein-DNA complexes can protect the underlying DNA sequence from trimethylpsoralen photobinding and thus protect restriction sites from inactivation. This property can be exploited to determine if specific sites are accessible to the psoralon probe in vivo and thus to establish if specific nucleotide sequences are nucleosome associated. Using this procedure evidence is obtained that nucleosomes on SV40 DNA in living infected cells are either distributed randomly or at many discrete alternate sites that approach a random distribution.

Cytophotometric determinations of DNA, histone, arginine, lysine, and their concentrations in eu- and heterochromatin of the cell nucleus of dysplasias, carcinoma in situ, and carcinoma of the human cervix uteri

In the cell nuclei of dysplasias, carcinoma in situ, and carcinoma the amount of DNA, histone, arginine, lysine, and their condensed areas were determined by cytophotometry. Moreover their concentrations in the euchromatic and heterochromatic areas of the nuclei were measured. Statistical analysis showed that the quantitative relations between parameters did not change during carcinogenesis. The significantly increased amount of lysine underlines the role of the lysine-rich histones in producing denser coiling of the chromatin fibril in heterochromatin.

Structure of adenovirus chromatin

The structure of adenovirus type 2 chromatin isolated from wild-type and ts1 virions was investigated by micrococcal nuclease digestion and electron microscopy. Partial digestion of wild-type and ts1 chromatin with micrococcal nuclease generated a multimeric DNA smear devoid of the 200 basepair nucleosome repeating pattern characteristic of cellular chromatin. However, 11 S monomer cores of 150 basepairs were detectable. The chromatin of ts1 (39 degrees C) was more resistant to digestion by micrococcal nuclease. Two-dimensional electrophoresis of the monomer core showed that wild-type core contained protein VII while ts1 (39 degrees C) core contained PVI and PVII. Protein V appears to be located on the variable-length intermonomer region. Crosslinking studies suggest that proteins PVII and VII exist in dimeric form within the monomer core. Electron microscopy revealed a 5.5-fold-condensed two-micron-long beaded structure with about 200 monomer particles spaced irregularly. Based on these observations, a model for adenovirus prochromatin and chromatin is proposed that differs in important aspects from the model proposed previously (Corden, J., Engelking, H.M. and Pearson, G.D. (1976) Proc. Natl. Acad. Sci. USA 73, 401-404).

The appearance of DNase I hypersensitive sites at the 5' end of the late SV40 genes is correlated with the transcriptional switch

DNase I digestion of the SV40 nuclear chromosome late in infection reveals three hypersensitive sites on the late side of the Bg1 I site. Two of these sites at bp 370, 270 correspond to the 5' side of the late transcripts while the third at bp 190, to a region that is required for early transcription. Early in infection, as well as in an SV40 transformed cell line and a T-Ag negative revertant (deleted in the coding region for T-Ag) only one of these sites is present - the one associated with early transcription. Thus, the positions of these major hypersensitive sites are related to the differential expression of the early and late genes. The presence of the characteristic hypersensitive site corresponding to "early" region expression in the revertant, where large T antigen is not synthesized, but where the early "promotor" is intact, indicates that large T antigen is not responsible for this particular hypersensitive site. Additional minor specific DNase I cuts were found on the early genes, at early times only, at 300, 550, 850 bp from Bg1 I site. In the transformed cell line, one of these minor cuts is found about 350-400 bp from the Bg1 I site and in the revertant, where this region is deleted, a new site is created at 100 bp.

Structure of chromatin at deoxyribonucleic acid replication forks: prenucleosomal deoxyribonucleic acid is rapidly excised from replicating simian virus 40 chromosomes by micrococcal nuclease

Replicating simian virus 40 (SV40) chromosomes were found to be similar to other eukaryotic chromosomes in that the rate and extent of micrococcal nuclease (MNase) digestion were greater with replicating than with nonreplicating mature SV40 chromatin. MNase digestion of replicating SV40 chromosomes, pulse labeled in either intact cells or nuclear extracts, resulted in the rapid release of nascent DNA as essentially bare fragments of duplex DNA (3-7S) that had an average length of 120 base pairs and were degraded during the course of the reaction. In addition, nucleosomal monomers, equivalent in size to those from mature chromosomes, were released. On the other hand, MNase digestion of uniformly labeled mature SV40 chromosomes resulted in the release of only nucleosomal monomers and oligomers. The small nascent DNA fragments released from replicating chromosomes represented prenucleosomal DNA (PN-DNA) from the region of replication forks that encompasses the actual sites of DNA synthesis and includes Okazaki fragments. Predigestion of replicating SV40 chromosomes with both Escherichia coli exonuclease III (3'-5') and bacteriophage T7 gene 6 exonuclease (5'-3') resulted in complete degradation of PN-DNA. This result, together with the observation that isolated PN-DNA annealed equally well to both strands of SV40 restriction fragments, demonstrated that PN-DNA originates from both sides of replication forks. Over 90% of isolated Okazaki fragments annealed only to the retrograde DNA template. The characteristics of isolated PN-DNA were assessed by examining its sensitivity to MNase and single strand specific S1 endonuclease, sedimentation behavior before and after deproteinization, buoyant density in CsCl after formaldehyde treatment, and size on agarose gels. In addition, it was observed that MNase digestion of purified SV40 DNA also resulted in the release of a transient intermediate similar in size to PN-DNA, indicating that a DNA-protein complex is not required to account for the appearance of PN-DNA. These and other data provide a model of replicating chromosomes in which DNA synthesis occurs on a region of replication forks that is free of nucleosomes and is designated as prenucleosomal DNA.

Replication of SV40 chromatin in extracts from eggs of Xenopus laevis

Simian virus 40 (SV40) nucleoprotein complexes were prepared from lytically infected cells and used as primer-templates for DNA replication in protein extracts from Xenopus eggs. We found that nucleoprotein containing replicating SV40 DNA served as primer-template while nucleoprotein with nonreplicating SV40 DNA was ineffective. In vitro DNA synthesis begins with short DNA fragments ("Okazaki fragments") which are, in later steps, joined to give unit length SV40 DNA strands, suggesting that in vivo initiated rounds of replication are completed in vitro in the Xenopus system. This conclusion is supported by a restriction enzyme analysis showing that in vitro DNA synthesis occurs in fragments distal to the SV40 origin of replication. Our studies indicate that SV40 DNA replication in Xenopus extracts can be used an an experimental system to study the biochemistry of replicative DNA chain elongation in vitro.

N-Acetoxy-acetylaminofluorene reacts preferentially with a control region of intracellular SV40 chromosome

Many chemical carcinogens or their metabolites react with DNA; thus it is of interest to determine what effect chromosomal structure has on these reactions. The chromosome of simian virus 40 (SV40) is well suited for such studies; like chromatin of eukaryotic cells, it is organized into nucleosomes. The nucleotide sequence of SV40 is known, together with much about the pattern of viral gene expression and DNA replication, and the structure of the viral chromosome. We have investigated the binding of the ultimate carcinogen, N-acetoxy-acetylaminofluorene (AAAF), to specific regions of the SV40 chromosome in situ in the intact infected cell. The results, reported here, indicate that a region containing regulatory functions on the intracellular SV40 chromosome has unique structural properties which render it more susceptible to attack by AAAF than the rest of the SV40 genome. The preferential binding of AAAF to regulatory regions of chromatin may have implications for the mechanism of action of this and similar carcinogens.

Quantitation of transcribing native simian virus 40 minichromosomes extracted from CV1 cells late in infection

Simian virus 40 transcriptional complexes could be extracted from CV1 cells late in infection and separated from the bulk of inactive viral chromatin. Sucrose gradient sedimentation, cesium sulfate equilibrium density gradient centrifugation, and electron microscopy indicated that the viral transcriptional complexes corresponded to at least 0.5 to 1% of the viral minichromosomes extracted, about 5,000 copies per cell.