Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin

Transcription and genome integrity

Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.

DNA conformational transitions induced by supercoiling control transcription in chromatin

Regulation of transcription in eukaryotes is considered in the light of recent findings demonstrating the presence of negative and positive superhelical tension in chromatin. This tension induces conformational transitions in DNA duplex. Particularly, the transition into A-form renders DNA accessible and waylaying for initiation of transcription producing RNA molecules long known to belong to the A-conformation. Competition between conformational transitions in various DNA sequences for the energy of elastic spring opens a possibility for understanding of fine tuning of transcription at a distance.

Measurement of the linking number change in transcribing chromatin

The in vivo-initiated, transcribing simian virus 40 (SV40) minichromosome was analyzed to determine its DNA linking number change, i.e. the difference between the linking number of the minichromosomal DNA and that of relaxed bare DNA. As part of this measurement, the linking number change due to the in vivo-initiated RNA polymerase II was determined, the first time a value for this quantity has been reported. The topological contribution of the polymerase was combined with values determined for constrained and non-constrained linking number contributions from the native transcription complex chromatin to yield the linking number change for the complex. The linking number change of the native non-transcribed SV40 minichromosome was independently determined and was found to be virtually the same as that for the chromatin of the transcription complex. This indicates that there is little difference between the two structures. The plausibility of several current models for the contribution of chromatin structure to transcription regulation is discussed in light of this finding.

Recognition and alignment of homologous DNA sequences between minichromosomes and single-stranded DNA promoted by RecA protein

The incorporation of DNA into nucleosomes and higher-order forms of chromatin in vivo creates difficulties with respect to its accessibility for cellular functions such as transcription, replication, repair and recombination. To understand the role of chromatin structure in the process of homologous recombination, we have studied the interaction of nucleoprotein filaments, comprised of RecA protein and ssDNA, with minichromosomes. Using this paradigm, we have addressed how chromatin structure affects the search for homologous DNA sequences, and attempted to distinguish between two mutually exclusive models of DNA-DNA pairing mechanisms. Paradoxically, we found that the search for homologous sequences, as monitored by unwinding of homologous or heterologous duplex DNA, was facilitated by nucleosomes, with no discernible effect on homologous pairing. More importantly, unwinding of minichromosomes required the interaction of nucleoprotein filaments and led to the accumulation of circular duplex DNA sensitive to nuclease P1. Competition experiments indicated that chromatin templates and naked DNA served as equally efficient targets for homologous pairing. These and other findings suggest that nucleosomes do not impede but rather facilitate the search for homologous sequences and establish, in accordance with one proposed model, that unwinding of duplex DNA precedes alignment of homologous sequences at the level of chromatin. The potential application of this model to investigate the role of chromosomal proteins in the alignment of homologous sequences in the context of cellular recombination is considered.

DNA topology and a minimal set of basal factors for transcription by RNA polymerase II

Immunoglobulin heavy chain (IgH) gene transcription in vitro can be reconstituted with a minimal reaction containing only TATA-binding protein (TBP), TFIIB, and RNA polymerase II (pol II) when the template is negatively supercoiled. Transcription from linear DNA templates containing either the IgH or the adenovirus major late promoters (MLPs) requires in addition TFIIF, TFIIE, TFIIH, and a fraction containing TFIIA and TFIIJ. Promoters vary in their activities in the minimal reaction. Initiation at the adenovirus MLP site was not observed in this reaction, even with templates containing negative superhelical density. When only TBP, TFIIB, and pol II were present in the reaction, the more negatively supercoiled the IgH template DNA was, the more active the transcription. It is suggested that the free energy of supercoiling promotes the formation of an open complex for initiation of transcription by the minimal set of transcription factors.

B-DNA to Z-DNA structural transitions in the SV40 enhancer: stabilization of Z-DNA in negatively supercoiled DNA minicircles

During replication and transcription, the SV40 control region is subjected to significant levels of DNA unwinding. There are three, alternating purine-pyrimidine tracts within this region that can adopt the Z-DNA conformation in response to negative superhelix density: a single copy of ACACACAT and two copies of ATGCATGC. Since the control region is essential for both efficient transcription and replication, B-DNA to Z-DNA transitions in these vital sequence tracts may have significant biological consequences. We have synthesized DNA minicircles to detect B-DNA to Z-DNA transitions in the SV40 enhancer, and to determine the negative superhelix density required to stabilize the Z-DNA. A variety of DNA sequences, including the entire SV40 enhancer and the two segments of the enhancer with alternating purine-pyrimidine tracts, were incorporated into topologically relaxed minicircles. Negative supercoils were generated, and the resulting topoisomers were resolved by electrophoresis. Using an anti-Z-DNA Fab and an electrophoretic mobility shift assay, Z-DNA was detected in the enhancer-containing minicircles at a superhelix density of -0.05. Fab saturation binding experiments demonstrated that three, independent Z-DNA tracts were stabilized in the supercoiled minicircles. Two other minicircles, each with one of the two alternating purine-pyrimidine tracts, also contained single Z-DNA sites. These results confirm the identities of the Z-DNA-forming sequences within the control region. Moreover, the B-DNA to Z-DNA transitions were detected at superhelix densities observed during normal replication and transcription processes in the SV40 life cycle.

Immunocytochemical detection of DNA topoisomerase type II in primary breast carcinomas: correlation with clinico-pathological features

DNA topoisomerase type II (DT-II) is a major component of interphase nuclear matrix fractions, present in S-phase of the cell cycle. A series of 80 carcinomatous breast surgical samples was evaluated by immunohistochemistry, using a polyclonal antibody in a comparison with Ki-67 antiserum. A correlation with clinico-pathological data was also performed. Infiltrating ductal and lobular carcinomas constantly express DT-II with varying intensity of nuclear staining; a similar immunohistochemical pattern is observed with Ki-67. A frequent co-expression of DT-II and Ki-67 is encountered with double immunostaining; accordingly to these data, a linear relationship is evident when linear regression is employed. In addition, significant relationships between DT-II values and tumour size, histological grade and node involvement are shown, while an inverse correlation is appreciable between DT-II and oestrogen receptors and progesterone receptors. DT-II may be considered to be an additional operational marker for the proliferating fraction of cells in breast carcinomas.

Relationship of histone acetylation to DNA topology and transcription

An autonomously replicating plasmid constructed from bovine papiloma virus (BPV) and pBR322 was stably maintained as a nuclear episome in a mouse cell culture. Addition to a cell culture of sodium butyrate (5 mM) induced an increase in plasmid DNA supercoiling of 3-5 turns, an increase in acetylation of cellular histones, and a decrease in plasmid transcription by 2- to 4-fold. After withdrawal of butyrate, DNA supercoiling began to fluctuate in a wave-like manner with an amplitude of up to 3 turns and a period of 3-4 h. These waves gradually faded by 24 h. The transcription of the plasmid and acetylation of cellular histones also oscillated with the same period. The wave-like alterations were not correlated with the cell cycle, for there was no resumption of DNA replication after butyrate withdrawal for at least 24 h. In vitro chemical acetylation of histones with acetyl adenylate also led to an increase in the superhelical density of plasmid DNA. The parallel changes in transcription, histone acetylation, and DNA supercoiling in vivo may indicate a functional innerconnection. Also, the observed in vivo variation in the level of DNA supercoiling directly indicates the possibility of its natural regulation in eukaryotic cells.

High rotational mobility of DNA in animal cells and its modulation by histone acetylation

DNA rotational mobility in a bovine papilloma virus (BPV)-based minichromosome, autonomously replicating in mouse cells, was studied using topoisomer analysis in temperature shift experiments. It was found that in live cells the average number of topological turns increased by six in the course of temperature shift through a range of 37 degrees C. This comprised approximately 85% of the total potential mobility of naked plasmid DNA. DNA rotation in isolated nuclei was found to be 3.5-4.0 turns per 37 degrees C in 100 mM NaCl - much higher than in all experiments with animal cells reported thus far. In low salt mobility was considerably lowered. Attempts to extract minichromosomes from nuclei allowed isolation of no more than 10% of minichromosomal DNA, with could indicate a very high proportion of transcriptionally active minichromosomes in the intracellular population. Growing cells in the presence of sodium butyrate resulted not only in an increase in the level of plasmid superhelicity and a decrease of its transcription (as we report in the accompanying publication) but also reduced rotational mobility of plasmid DNA threefold (from 6 to 2 turns per 37 degrees C). The decrease in DNA rotational mobility after butyrate treatment was also partially manifested in isolated nuclei (especially at lower ionic strength). To check whether histone acetylation is directly responsible for DNA immobilization, we performed in vitro acetylation of histones using acetyl adenylate. This resulted in severe DNA immobilization in experiments using both up and down temperature shifts.

A. E. Braunstein Plenary Lecture. Nuclear skeleton, DNA domains and control of replication and transcription

Chromosomal DNA is organized in loops or domains of about 100 kb. Their ends seem to be attached to special protein skeletal structures. The DNA-attachment sites can be subdivided into permanent and transient types. The permanent or constitutive attachment sites, which are retained in all types of cells (including those inactive in replication and transcription), either coincide with or are located close to replication origins. This observation provides a simple way for isolation of DNA fragments containing replication origins. Such fragments from the chicken alpha-globin gene domain and other regions of the chicken genome contain DNA sequences which interact with nuclear proteins present in dividing cells, but absent from non-dividing cells. Several new consensus sequences interacting with nuclear proteins were detected. The 5' end region of the alpha-globin gene domain containing a replication origin was found to possess enhancer activity lacking tissue specificity. Hence, the domain organization of DNA is related to the organization of replication process. Other sets of data indicate that the integrity of DNA domains is important for maintaining transcription within the domain. According to these data, even a single nick at an distance of about 100 kbp seems to be sufficient for blocking transcription within the whole domain at the stage of RNA elongation. Thus, topological integrity of DNA may be an important factor involved in formation of active chromatin.

Topological properties of bovine papillomavirus type 1 (BPV-1) DNA in episomal nucleoprotein complexes: a model system for chromatin organization in higher eukaryotes

Sedimentation analysis of isolated episomal bovine papillomavirus type 1 (BPV-1) nucleoprotein complexes in sucrose gradients and subsequent separation of the purified DNA in chloroquine gels revealed different classes of molecules, varying in their degree of superhelicity. Since torsionally stressed DNA favors the adoption of secondary structures, we employed the single-strand-specific S1 nuclease to detect such structural alterations in both naked DNA and native chromatin. Direct examination of nuclease digestion products in chloroquine gels showed that neither the naked DNA nor the BPV-1 nucleoprotein complexes in isolated nuclei were cleaved randomly by the enzyme. Instead, there was a strict dependence on nuclease susceptibility and the degree of supercoiling, strongly suggesting that the structural features detected by S1 nuclease are due to the occurrence of torsionally stressed viral chromatin. Mapping analysis using the indirect end-labeling method demonstrated an S1-nuclease cleavage site adjacent to 20 homopurine residues known to be hypersensitive to S1 attack. Furthermore, direct methylation experiments with viral chromatin in isolated nuclei indicated that only circular, covalently closed nucleoprotein complexes served as substrate, whereas linearized BPV-1 chromatin was not susceptible to exogenously added Hhal methylase. This observation raises the possibility that the modulation of topology in nucleosomally organized DNA might also play a role in eukaryotic DNA methylation.

Paranemic structures of DNA and their role in DNA unwinding

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.

Binding of the glucocorticoid receptor induces a topological change in plasmids containing the hormone-responsive element of mouse mammary tumor virus

Glucocorticoid hormones stimulate transcription of the mouse mammary tumor virus (MMTV) promoter by means of an interaction of the hormone receptor with a set of upstream DNA-binding sites called the hormone-responsive element (HRE). In an attempt to understand the underlying molecular mechanism, we have analyzed the influence of receptor binding on the topological state of plasmids carrying different parts of the HRE. Incubation of negatively supercoiled plasmids containing the intact HRE with the 94-kD purified glucocorticoid receptor, followed by extensive digestion with topoisomerase I, leads to a distribution of topoisomers shifted by two turns toward positively supercoiled circles. If relaxed plasmids are incubated with receptor and treated with topoisomerase I, the average linking number of the resulting distribution of topoisomers is also increased by two with respect to the controls. This effect depends on the presence of an intact HRE and is almost undetectable with the 40-kD form of the receptor. Thus, binding of the hormone receptor to functional DNA regulatory sites located in closed circular plasmids results in a topological change that could be related to the hormonal activation of transcription.

The nucleoskeleton and the topology of transcription

Transcription is conventionally believed to occur by passage of a mobile polymerase along a fixed template. Evidence for this model is derived almost entirely from material prepared using hypotonic salt concentrations. Studies on subnuclear structures isolated using hypertonic conditions, and more recently using conditions closer to the physiological, suggest an alternative. Transcription occurs as the template moves past a polymerase attached to a nucleoskeleton; this skeleton is the active site of transcription. Evidence for the two models is summarised. Much of it is consistent with the polymerase being attached and not freely diffusible. Some consequences of such a model are discussed.

Structure of transcriptionally active chromatin: radiological evidence for requirement of torsionally constrained DNA

Synthesis of alpha- and beta-globin RNA in DMSO-induced Friend's erythroleukemia cells and synthesis of immunoglobulin gamma- and kappa-chain RNA, total RNA, 5S RNA, and tRNA in mouse myeloma cells (MPC-11) was inhibited by gamma-irradiation. For all RNA species, synthesis decreased nearly exponentially as a function of radiation dose, whereas RNA size distributions, turnover rates, and specific activities of radioactively labeled RNA were affected only insignificantly. D37 values for the loss of synthesis of various RNA species correspond to target sizes ranging from 21,000 to 53,000 kd, or 30-80 kbp of DNA. These target sizes are several-fold larger than the structural genes in question; however, they correspond well with the size of DNA loops, or "domains" constrained by the nuclear matrix. The data suggest that the eukaryotic transcription unit is the torsionally constrained chromatin loop, transcription of which may be inactivated, or significantly reduced by a DNA single-strand break.

Molecular aspects of estrogen receptor activation factor (E-RAF) function

The estrogen receptor activation factor (E-RAF)-mediated binding of the receptor-estrogen complex to uterine nuclei was found to involve at least two classes of nuclear macromolecules: (1) the DNA, and (2) a proteinacious component. Evidences are presented to show that at least a portion of (2) is represented by the nuclear RNA polymerases. The receptor-estrogen complex associated in vivo with the nuclear RNA polymerases existed in two distinct forms which sedimented at 3.8 S and 4.8 S on sucrose density gradients. Almost 2/3 of the total radioactivity was associated with the 3.8 S species. Saturation kinetics of the two forms showed that while the 4.8 S form displayed characteristics similar to the classical type I nuclear binding site, the features displayed by the 3.8 S form were closely similar to those of the nuclear type II site. The 4.8 S species is a DNA binding form while the 3.8 S form is non-DNA binding. Anti-E-RAF IIA IgG cross-reacted with both the binding components. Goat uterine E-RAF I, IIA and IIB were purified to homogeneity as described earlier. While E-RAF IIA and IIB destabilized the native DNA structure and induced separation of the DNA strands, E-RAF I performed the opposite function. The reactions required the presence of ATP; all three of them displayed DNA-dependent ATPase activity. In an in vitro transcription system which contained purified RNA polymerase B (rat liver enzyme) and goat uterine DNA, E-RAF IIA and IIB enhanced transcription 7-fold over the control while E-RAF I totally suppressed the transcription process, irrespective of whether it was stimulated earlier by the other two E-RAF forms or not. This E-RAF property remained unchanged even after its association with the 4 S receptor-estrogen complex forming 5 S complex.

Control region of SV40 minichromosomes is preferentially cleaved by single-strand specific S1 nuclease

We have analysed S1 sensitivity of SV40 minichromosomes isolated from the nuclei of infected cells at the late stage of infection. We show that a fraction of purified minichromosomes is sensitive towards double-strand cleavage by S1 nuclease. The pattern of specific cleavage reminiscent of that found for subcloned fragment under supercoiling is superimposed upon apparently random double-strand cuts along the entire regulatory region. Therefore, the cleavage sites are not exclusively confined to the regions with the reported alternate DNA conformation.

Plasticity of DNA conformation around the Drosophila melanogaster alcohol dehydrogenase gene under torsional stress

Genomic DNA of eukaryotes is thought to be organized into multiple topological domains whose conformation can be independently regulated by torsional stress. We have demonstrated the formation of altered DNA structures around the Drosophila melanogaster alcohol dehydrogenase (Adh) gene by sensitivity to endonucleases and by binding single-strand binding (SSB) protein. Several altered DNA structures were detected only on torsionally stressed DNA at specific sites. Some corresponded to the two initiation cap sites and the poly(A) addition sites and others were found in the 5'-flanking regions of both the adult and larval cap sites and in the 3'-flanking region of the Adh gene. In particular, the 5'-flanking regions both exhibited a plasticity of DNA conformation according to the strength of torsional stress and the concentration of Mg2+. SSB protein bound preferentially to the non-coding regions of the Adh gene only on torsionally stressed DNA and not on relaxed or linear DNA. The observed binding preference appeared to correspond to the thermodynamic stability of the base-pairs involved. These results suggest that DNA conformation is specifically organized around the Adh gene for gene function. The plasticity of DNA may play a role in the regulation of transcriptional activation.

Supercoiling of intracellular DNA can occur in eukaryotic cells

The supercoiling of 2 micron DNA in yeast by a process or processes that generate positively and negatively supercoiled domains was shown by the use of yeast DNA topoisomerase mutants expressing Escherichia coli DNA topoisomerase I, an enzyme that relaxes negative supercoils specifically. Intracellular 2 micron DNA becomes positively supercoiled in yeast top1 top2 ts strains expressing the E. coli enzyme when neither one of the yeast DNA topoisomerases I and II is functional. Examination of the linking number distributions of plasmids bearing the inducible promoters of GAL1 and GAL10 genes indicates that the generation of supercoiled domains of opposite signs is related to transcription.

A domain model for eukaryotic DNA organization: a molecular basis for cell differentiation and chromosome evolution

A model for eukaryotic chromatin organization is presented in which the basic structural and functional unit is the DNA domain. This simple model predicts that both chromosome replication and cell type-specific control of gene expression depend on a combination of stable and dynamic DNA-nuclear matrix interactions. The model suggests that in eukaryotes, DNA regulatory processes are controlled mainly by the intranuclear compartmentalization of the specific DNA sequences, and that control of gene expression involves multiple steps of specific DNA-nuclear matrix interactions. Predictions of the model are tested using available biochemical, molecular and cell biological data. In addition, the domain model is discussed as a simple molecular mechanism to explain cell differentiation in multi-cellular organisms and to explain the evolution of eukaryotic genomes consisting mainly of repetitive sequences and "junk" DNA.

Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes

The promoter for eukaryotic genes transcribed by RNA polymerase B can be divided into the TATA box (located at -30) and startsite (+1), the upstream element (situated between -40 and about -110), and the enhancer (no fixed position relative to the startsite). Trans-acting factors, which bind to these elements, have been identified and at least partially purified. The role of the TATA box is to bind factors which focus the transcription machinery to initiate at the startsite. The upstream element and the enhancer somehow modulate this interaction, possibly through direct protein-protein interactions. Another class of transcription factors, typified by viral proteins such as the adenovirus EIA products, do not appear to require binding to a particular DNA sequence to regulate transcription. The latest findings in these various subjects are discussed.

The chemical carcinogen, chloroacetaldehyde, modifies a specific site within the regulatory sequence of human cytomegalovirus major immediate early gene in vivo

The reaction of chemical carcinogens with DNA is well documented, but whether this interaction occurs at specific sites in chromatin is unknown. We have examined in vivo the reaction of a known carcinogen, chloroacetaldehyde, with the active and inactive major immediate early gene of human cytomegalovirus. We found that during active transcription of the gene, this chemical carcinogen reacts with a unique DNA site in the 5' flanking sequence of the major immediate early gene. However, no reaction was detected in infected nonpermissive cells in which the gene was inactive. The chloroacetaldehyde-reactive site is located at -836 +/- 10 bp from the mRNA cap site in the part of the regulatory region that can both negatively and positively affect promoter activity [Nelson et al., Mol Cell Biol 7:4125-4129, 1987]. These results suggest, at least in the case of chloroacetaldehyde, the possibility that the molecular mechanism of chemical carcinogenesis involves a chemical reaction at specific sites in chromatin within the sequences responsible for regulation of gene expression. Such carcinogen-DNA interaction occurs as a consequence of a non-B DNA structure that contains unpaired DNA bases existing at specific sites in chromatin.

Non-histone chromatin proteins that recognize specific sequences of DNA

Numerous chromatographic procedures have recently been developed to purify to near homogeneity various eukaryotic non-histone chromatin proteins that recognize and bind to specific sequences of DNA. In this brief review we have discussed a number of these different methods that we feel are important and probably represent the starting points for much of the future research work in this area. We view this coverage as being only an introduction, however, and strongly recommend that the reader consult the original papers for details of methods and protocols. We, nevertheless, hope that the information presented here will be of some assistance to those researchers and students who wish to become acquainted with the latest developments in this rapidly advancing field of chromatography. Although it is evident from what has been presented that the purification of each DNA sequence-specific non-histone chromatin protein initially starts with common or classical isolation and fractionation procedures, the final (and often crucial) steps of enrichment and purification often involve distinctive or unique procedures for each individual protein of interest. In many cases these final steps involve new techniques such as DNA sequence-specific bioaffinity and photoaffinity chromatography which not only ensure the isolation of specific protein species from complex mixtures but also result in a tremendous enrichment for nuclear proteins that are often present in the nucleus in extremely low concentrations. Furthermore, the entire process of protein purification has been remarkedly facilitated with the advent of high-performance liquid chromatographic and fast protein liquid chromatographic techniques which now allow for the very rapid separation and purification of proteins in a matter of minutes from mixtures that in the recent past would have required hours or days to purify. Thus, separation and purification techniques are now available that set the stage for the rapid isolation of rare, DNA sequence-specific, NHC nuclear proteins from almost any cellular source. It is therefore reasonable to anticipate that in the near future there will be major advances made in our understanding of the specific nuclear proteins that regulate gene expression in eukaryotic cells.

Sequence dependence of Drosophila topoisomerase II in plasmid relaxation and DNA binding

The sequence dependence of Drosophila topoisomerase II supercoil relaxation and binding activities has been examined. The DNA substrates used in binding experiments were two fragments from Drosophila heat shock locus 87A7. One of these DNA fragments includes the coding region for the heat shock protein hsp70, and the other includes the intergenic non-coding region that separates two divergently transcribed copies of the hsp70 gene at the locus. The intergenic region was previously shown to have a much higher density of topoisomerase cleavage sites than the hsp70 coding region. Competition nitrocellulose filter binding assays demonstrate a preferential binding of the intergene fragment, and that binding specificity increases with increasing ionic strength. Dissociation kinetics indicate a greater kinetic stability of topoisomerase II complexes with the intergene DNA fragment. To study topoisomerase II relaxation activity, we used supercoiled plasmids that contained the same fragments from locus 87A7 cloned as inserts. The relative relaxation rates of the two plasmids were determined under several conditions of ionic strength, and when the plasmid substrates were included in separate reactions or when they were mixed in a single reaction. The relaxation properties of these two plasmids can be explained by a coincidence of high-affinity binding sites, strong cleavage sites, and sites used during the catalysis of strand passage events by topoisomerase II. Sequence dependence of topoisomerase II catalytic activity may therefore parallel the sequence dependence of DNA cleavage by this enzyme.

Topological characterization of the simian virus 40 transcription complex

We have used sedimentation analysis as well as agarose gel electrophoresis to characterize the topological state of the DNA of the Simian Virus 40 (SV40) transcription complex. We found that the complex DNA contained constrained topological tension, presumably resulting from nucleosome-like structures, but no detectable unconstrained (i.e., relaxable) topological tension. These results contradict previous conclusions that the SV40 transcription complex contains only unconstrained topological tension. Our findings are also the opposite of what has been proposed to be the case for the 5S gene analyzed in Xenopus oocytes. Thus the proposal that expression from the 5S gene is associated with substantial topological tension is not valid for expression from the SV40 late gene.

SV40 enhancer-binding factors are required at the establishment but not the maintenance step of enhancer-dependent transcriptional activation

We have used temperature-sensitive COS cells to design delayed competition experiments in which competition for simian virus 40 (SV40) enhancer factors occurs after enhancer-dependent transcription has been established. The results demonstrate that competition for SV40 enhancer-binding factors has no effect on enhancer-dependent transcription after transcription has been established at the SV40 early promoter. These data show that the enhancer and factors that bind to it are involved in the establishment of stable transcription complexes, although they do not show whether enhancer factors are an integral part of the transcription complexes. Furthermore, the results of delayed competition experiments with a replicating test plasmid are consistent with the possibility that enhancer-dependent stable transcription complexes could be maintained after DNA replication.

Structure of in-vivo transcribing chromatin as studied in simian virus 40 minichromosomes

In order to study the structure of chromatin during transcription, individual in-vivo transcribing simian virus 40 (SV40) minichromosomes were analyzed in the electron microscope after crosslinking the nascent RNA strands with different psoralen derivatives to the template DNA. Since psoralen crosslinks the DNA between nucleosomes, spreading of the crosslinked DNA and DNA-RNA complexes reveals single-stranded bubbles at positions where nucleosomes were located. We found that the transcribing SV40 minichromosomes contained a similar number of nucleosomes as did the minichromosomes without crosslinked nascent RNA. The nascent RNA was crosslinked in about equal proportions either in single-stranded bubbles of nucleosomal length or in continuously crosslinked regions between bubbles, in contrast with control experiments with ribosomal chromatin of Dictyostelium. Treatment of SV40 minichromosomes with 1.2 M-NaCl before and during photocrosslinking with psoralen led to the disappearance of the single-stranded bubbles. Since no bubbles could be detected at the attachment sites of the RNA molecules when the nucleosomes were disrupted in high salt, and since in about half of the molecules the RNA was attached to fully crosslinked linker DNA, we assume that the single-stranded bubbles with crosslinked RNA are not due to protection by the elongating RNA polymerase II complex, but are rather due to nucleosome-like structures. At the resolution level of single nucleosomes, these results imply for the first time that nucleosome-like structures (perhaps modified compared with "normal" nucleosomes) on SV40 minichromosomes do not prevent transcription elongation by RNA polymerase II.

Topoisomerase II cleavage in chromatin

We have examined the effect of the anti-tumor drug VM-26 on purified Drosophila topoisomerase II, and used this drug to map (putative) topoisomerase II cleavage sites in chromatin. These studies indicate that VM-26 interferes with the strand breakage-rejoining catalytic cycle. VM-26 appears to stabilize the topoisomerase-II-cleavable complex and markedly enhances the formation of double-strand breaks in naked DNA. VM-26 also stimulates the formation of double-strand breaks in isolated Drosophila nuclei. Analysis of the parameters of the VM-26-stimulated cleavage reaction in nuclei strongly suggests that the double-strand scissions are generated by endogenous topoisomerase II. Finally, we have examined the distribution of (putative) cleavage sites for endogenous topoisomerase II in the chromatin of the 87A7 heat shock locus and the histone repeat unit. We have found that there are prominent VM-26-induced cleavage products from the 5' ends of the 87A7, the two heat shock protein 70 genes, and in the intergenic spacer separating these genes. Moreover, the pattern of VM-26-induced cleavage products is altered in nuclei prepared from heat-shocked cells. In the case of the histone repeat unit, only minor VM-26-induced cleavage products are observed in nuclei (in spite of the fact that experiments on naked DNA indicate that the histone repeat contains many major cleavage sites for purified topoisomerase II). These findings suggest that the nucleoprotein organization of different DNA segments may be important in determining whether specific sites are accessible to endogenous topoisomerase II in nuclei.

Expression of transfected DNA depends on DNA topology

Supercoiled DNAs, especially those containing enhancers, yield markedly higher levels of expression than linearized DNA when transfected into CV-1 cells or L cells. Different templates, linear or supercoiled, enhancer-containing or not, saturate for expression at 2 micrograms DNA per dish, suggesting that one role for enhancers and supercoiling is to increase the efficiency with which the same limiting component is used. Plasmids containing only enhancers or only promoters do not compete for expression with an enhancer-driven gene. However, plasmids that contain both enhancers and promoters do complete, suggesting that a second role for enhancers is to increase the binding of a limiting transcription factor. Linear and supercoiled enhancer-promoter plasmids compete equivalently. This suggests that supercoiling affects the ability of transcription factors to activate a given promoter, once bound.

Transcription of eukaryotic ribosomal RNA gene

Remarkable advances have been made in the identification of the promoter regions for the ribosomal RNA genes from lower and higher eukaryotes. There has been some progress in the elucidation of the factors that control transcription of the ribosomal RNA gene. The characterization of the transcription factors are crucial for the understanding of the molecular mechanisms of ribosomal gene expression.

Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites

Introduction of torsional stress into active chromatin domains requires that linear DNA molecules be anchored in vivo to impede free rotation. While searching for these anchorage elements, we have localized a nuclear matrix association region (MAR) within the mouse immunoglobulin kappa gene that contains two topoisomerase II sites and is adjacent to the tissue-specific enhancer. The same matrix contact occurs when the kappa locus is in germ-line (inactive) or rear-ranged (transcribed) configurations. This constitutive anchorage site partitions the gene into V-J and C region chromatin domains. We demonstrate that at least 10,000 similar and evolutionarily conserved MAR binding sites exist in the nucleus. We propose that these sites, in association with topoisomerase II and possibly in conjunction with enhancers, play fundamental roles in the functional organization of chromatin loop domains.

Structure of transcriptionally active chromatin

Transcriptionally active or potentially active genes can be distinguished by several criteria from inactive sequences. Active genes show both an increased general sensitivity to endonucleases like DNase I or micrococcal nuclease and the presence of nuclease hypersensitive sites. Frequently, the nuclease hypersensitive sites are present just upstream of the transcription initiation site covering sequences that are crucial for the promoter function. Viral or cellular transcription enhancer elements are also associated with DNase I hypersensitive sites. At least for the SV40 enhancer, it was shown by electronmicroscopic studies that the DNase I hypersensitive DNA segment is excluded from nucleosomes. It is highly plausible that the binding of regulatory proteins to enhancer or promoter sequences is responsible for the exclusion of these DNA segments from nucleosomes and for the formation of nuclease hypersensitive sites. We speculate that the binding of such proteins may switch on a change in the conformation and/or the protein composition of a chromatin segment or domain containing one to several genes. Biochemical analysis of fractionated nucleosome particles or of active and inactive chromatin fractions have revealed differences in the composition as well as in the degree of modification of histones in these two subfractions of the chromosome. However, until present it is impossible to define unambiguously what are the crucial structural elements that distinguish between particles present on active and inactive chromatin.

Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution

Chemical probes sensitive to alterations in DNA conformation, especially Z-DNA, have been identified. These permit cleavage of DNA at sites of unusual structure, the results of which can be displayed on a sequencing gel. Using supercoiled plasmids containing inserts of d(C-G)16 and d(C-A)31 X d(T-G)31, it was found that hydroxylamine and osmium tetraoxide react preferentially with cytosines and thymines, respectively, near B-DNA-Z-DNA junctions; diethylpyrocarbonate reacts more strongly with purines within Z-DNA regions; and dimethylsulfate and diethylsulfate react more strongly with guanines in Z-DNA that are out of phase with the usual pattern of purine-pyrimidine alternation. Our results show that B-Z boundaries are mobile and that with increasing torsional strain, the Z-DNA regions can expand to include nonalternating nucleotide sequences.

Electron microscopic evidence for the cruciform structure in intracellular SV40 DNA

The conformation of intracellular SV40 DNA during lytic infection of CV-1 cells was studied by the psoralen crosslinking technique. Analysis of the crosslinked SV40 DNA in the electron microscope revealed a rare population (0.1%) with a cruciform structure at coordinates 0.62 +/- 0.05 or at 0.37 +/- 0.05 of the SV40 genome. The implication of this observation in relation to SV40 DNA replication is discussed.

Chromatin structure of the potential Z-forming sequence (dT-dG)n X (dC-dA)n. Evidence for an "alternating-B" conformation

The sequence (dT-dG)n X (dC-dA)n is the most abundant purine-pyrimidine dinucleotide repeat in eukaryotic genomes. This sequence and certain others that contain alternating purine-pyrimidine residues have been shown to adopt the left-handed, Z-DNA conformation in vitro when subjected to negative torsional stress or elevated ionic strengths. We have asked whether (dT-dG)n X (dC-dA)n tracts exist in topologically constrained Z-form structures in vivo by examining the chromatin organization of these sequences in cultured mouse cell nuclei. We find that these elements are quantitatively packaged into typical core particles which are embedded in canonical polynucleosomal arrays. In addition, these sequences neither flank nor reside within regions of chromatin that are preferentially sensitive to S1 nuclease. These characteristics suggest that these tracts do not exist predominantly in the Z-form in vivo. Furthermore, employing techniques that permit prominent hybridization to DNA fragments as short as 18 bases, we provide evidence that in vivo, most (dT-dG)n X (dC-dA)n elements instead adopt an "alternating-B" conformation on the nucleosomal surface.

Novobiocin blocks the Drosophila heat shock response

In the studies reported here we show that the antibiotic novobiocin, an in vitro inhibitor of topoisomerase II, blocks the Drosophila heat shock response. If novobiocin is added prior to induction, there is no detectable expression of the Drosophila heat shock genes. Moreover, analysis of the chromatin organization of the 87A7 heat shock locus indicates that the antibiotic prevents the structural alterations which normally accompany heat induction. When novobiocin is added after induction, transcription appears to be rapidly turned off, and the chromatin organization of the 87A7 locus is "fixed" in an "active" configuration. Novobiocin also prevents the re-establishment of the pre-induced 87A7 chromatin organization which occurs during recovery from heat shock. We have also presented data suggesting that this antibiotic blocks transcription at 25 degrees C. These findings raise the possibility that topoisomerase II may be required in eukaryotes for both gene activation and deactivation.

In vivo mapping of DNA topoisomerase II-specific cleavage sites on SV40 chromatin

The antitumor drug, m-AMSA (4'-(9-acridinylamino)-methanesulfon-m-anisidide), is known to interfere with the breakage-reunion reaction of mammalian DNA topoisomerase II by blocking the enzyme-DNA complex in its putative cleavable state. Treatment of SV40 virus infected monkey cells with m-AMSA resulted in both single- and double-stranded breaks on SV40 viral chromatin. These strand breaks are unusual because they are covalently associated with protein. Immunoprecipitation results suggest that the covalently linked protein is DNA topoisomerase II. These results are consistent with the proposal that the drug action in vivo involves the stabilization of a cleavable complex between topoisomerase II and DNA in chromatin. Mapping of these double-stranded breaks on SV40 viral DNA revealed multiple topoisomerase II cleavage sites. A major topoisomerase II cleavage site was preferentially induced during late infection and was mapped in the DNAase I hypersensitive region of SV40 chromatin.

Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence

Using supercoiled plasmids containing a (CG)16 sequence downstream of a promoter, it is shown that purified E. coli RNA polymerase can transcribe through the sequence when it is in the B helical form. However, the polymerase together with its nascent transcript is blocked at the boundary of the CG sequence proximal to the promoter when the template is negatively supercoiled to flip the CG sequence to the left-handed Z-form. S1 nuclease mapping of in vivo transcripts from an E. coli gyrase temperature-sensitive mutant harboring the plasmids indicates that the bulk of the transcripts at either permissive or nonpermissive temperatures can proceed through the CG sequence, suggesting that the sequence is normally in the B helical form in vivo. The almost total blockage of transcription in vitro by the (CG)16 sequence in a highly negatively supercoiled DNA is not observed for a d(CA)21 X d(TG)21 insert.