Changes in DNA topology can modulate in vitro transcription of certain RNA polymerase III genes

Noncoding DNA in lipofection of HeLa cells-a few insights

In cationic carrier-mediated gene delivery, the disproportional relationship between the quantity of delivered DNA and the amount of encoded protein produced is a well-known phenomenon. The numerous intracellular barriers which need to be overcome by pDNA to reach the nucleoplasm play a major role in it. In contrast to what one would expect, a partial replacement of coding pDNA by noncoding DNA does not lead to a decrease in transfection efficiency. The mechanism underlying this observation is still unclear. Therefore, we investigated which constituents of the transfection process might contribute to this phenomenon. Our data reveal that the topology of the noncoding plasmid DNA plays a major role. Noncoding pDNA can be used only in a supercoiled form to replace coding pDNA in Lipofectamine lipoplexes, without a loss in transfection levels. When noncoding pDNA is linearized or partly digested, it diminishes the transfection potential of coding pDNA, as does noncoding salmon DNA. The difference in transfection efficiencies could not be attributed to diverse physicochemical characteristics of the Lipofectamine lipoplexes containing different types of noncoding DNA or to the extent of their internalization. At the level of endosomal release, however, nucleic acid release from the endosomal compartment proceeds faster when lipoplexes contain noncoding salmon DNA. Since the half-life of pDNA in the cytosol hardly exceeds 90 min, it is conceivable that prolonged release of coding pDNA from complexes carrying supercoiled noncoding pDNA may explain its positive effect on transfection, while this depot effect does not exist when noncoding salmon DNA is used.

Presence of negative torsional tension in the promoter region of the transcriptionally poised dihydrofolate reductase gene in vivo

DNA topology has been suggested to play an important role in the process of transcription. Negative torsional tension has been shown to stimulate both pre-initiation complex formation and promoter clearance on plasmid DNA in vitro. We recently showed that genomic DNA in human cells contains localized torsional tension. In the present study we have further characterized and mapped torsional tension in the dihydrofolate reductase (DHFR) gene in Chinese hamster ovary (CHO) cells and investigated the effects of differential rates of transcription on the magnitude and location of this tension. Using psoralen photo-cross-linking in conjunction with X-irradiation, we found that relaxable psoralen hypersensitivity was specifically localized to the promoter region of the serum-regulated DHFR gene in serum-stimulated, but not in serum-starved, cells. Moreover, this hypersensitivity did not appear to be caused by transcription elongation, since it persisted in cells in which transcription of the DHFR gene had been reduced by the transcription inhibitor 5,6-dichloro-1-beta-D-ribofurano-sylbenzimidazole (DRB). We suggest that the generation of negative torsional tension in DNA may play an important role in gene regulation by poising genes for transcription.

A model for systemic lupus erythematosus based on chromatin disruption by polyamines

Here it is hypothesized that some autoimmune disorders, such as systemic lupus erythematosus, result in part from overexpression of polyamines which leads to disruption of chromatin structure. Disruption of inactive chromatin, such as the inactive X chromosome, exposes sites of unrepaired DNA damage. Repair is then hampered by the polyamines. Disruption also facilitates transcription at previously sequestered sites. Especially interesting are RNA polymerase III sites in highly repeated sequences such as the Alu sequence. Transcription and translation from these sites could create RNA and polypeptides not normally expressed. These could be antigenic either individually or in association with other cellular components. Interactions of polyamines in the nucleus and with the membrane could also lead to polyamine facilitated apoptosis.

Characterization of Ustilago maydis DNA binding protein one (UBP1)

The DNA binding properties of a protein from the lower eukaryote Ustilago maydis have been characterized. Using both filter binding and gel retention assays, we demonstrate that this protein, termed UBP1 (Ustilago binding protein one), binds preferentially to DNA molecules lacking chain interruptions. The introduction of DNA breaks by a restriction enzyme or a purified nuclease, from Ustilago maydis, causes the dissociation of protein-DNA complexes. UBP1 stimulates the relaxation of negatively supercoiled DNA, mediated by Ustilago type I topoisomerase, through a mechanism most likely involving the association of UBP1 with the DNA rather than with the topoisomerase. The prebinding of UBP1 to DNA templates, subsequently assembled into minichromosomes, results in the development of a disorganized nucleosomal array. Possible roles for UBP1 in processes that involve changes in DNA topology, such as chromatin assembly, are discussed.

The glucocorticoid receptor precludes the binding of a transcriptional repressor protein to the long terminal repeat of the mouse mammary tumor virus

The long terminal repeat (LTR) of the mouse mammary tumor virus was used as a template to examine the dual binding parameters of the glucocorticoid-receptor (GR) and a repressor protein termed Inhibitory Factor 1 (IF1). The receptor binds specifically to the glucocorticoid response element and precludes the binding of IF1 to its juxtaposed binding site within the LTR. When the two DNA targets are separated by the insertion of an additional 52 base pairs, coincident binding of both proteins is observed. Gel retention assays reveal three distinct nucleoprotein complexes. The first complex consists of the receptor and the LTR, the second is comprised of IF1 and DNA and the third is a multiprotein-DNA complex consisting of the GR, IF1 and DNA, migrating at a higher molecular weight position. The inhibition of IF1 binding by the presence of prebound GR leads to the repression of transcription of juxtaposed genes. The GR may act to block access of a sequence, used by the cell to titrate repressor proteins and facilitate the onset of gene expression.

Positive regulation of tRNA gene expression by the mouse mammary tumor virus-long terminal repeat in vitro

The mouse mammary tumor virus long terminal repeat (MMTV-LTR) participates in the control of gene expression by providing a series of important DNA binding sites at which trans-acting factors interact. Among these factors are the steroid receptor, nuclear factor I (NFI) and the TATA box factor (TFIID). The binding of these proteins facilitates the assembly of a transcriptionally competent complex, that includes RNA polymerase II, and activates the expression of juxtaposed genes in cis. A particular DNA sequence, distinct from previously identified regulatory elements, was found in the present study to activate gene expression in trans. The sequence is located between nucleotides +3 and +43 near the 3' terminus of the LTR. This sequence binds a protein that may actively repress the expression of genes that are not located immediately in cis. This protein was purified by ion exchange chromatography and has an approximate molecular weight of 31,000 daltons, as judged by SDS-PAGE. Gel retardation experiments reveal that progressively larger protein--DNA complexes are formed when the amount of this factor is increased relative to the DNA binding site. Furthermore, this protein was found to preferentially aggregate DNA molecules containing the LTR sequence between bases +3 and +43. These results reveal the existence of a unique modulatory role for the LTR in regulating gene expression in trans.

In vitro transcription of the c-myc first exon may be influenced by the extent of chromatin assembly

The first exon of the human c-myc gene can be transcribed by either RNA polymerase II or RNA polymerase III. The molecular factors contributing to polymerase selection are not yet completely defined. We have examined the role of chromatin structure in regulating transcription by RNA polymerase III. Using as competitor a pol III gene in both a cis and trans arrangement, we demonstrate that c-myc gene expression is facilitated from templates containing a minimal number of fully assembled nucleosomes. The removal of excess histones by DNA titration leads to an elevated level of c-myc expression. These results suggest that either the c-myc expression is inhibited when the template is fully packaged into chromatin or that the affinity of RNA polymerase for the regulatory elements of this exon is such that a template, devoid of histones, is required for transcriptional initiation.

In vitro analysis of a type I DNA topoisomerase activity from cultured tobacco cells

The role of DNA topoisomerases in plant cell metabolism is currently under investigation in our laboratory. Using a purified type I topoisomerase from cultured tobacco, we have carried out a biochemical characterization of enzymatic behavior. The enzyme relaxes negatively supercoiled DNA in the presence of MgCl2, and to a lesser extent in the presence of KCl. Phosphorylation of the topoisomerase does not influence its activity and it is not stimulated by the presence of histones H1 or H5. The enzyme may act in either a processive or distributive manner depending on reaction conditions. The anti-tumor drug, camptothecin, induces significant breakage by the enzyme on purified DNA molecules unless destabilized by the addition of KCl. The tobacco topoisomerase I can catalyze the formation of stable nucleosomes on circular DNA templates, suggesting a role for the enzyme in chromatin assembly.

In vitro chromatin assembly promoted by the Xenopus laevis S-150 cell-free extract is enhanced by treatment with RNase A

Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence of RNA in the assembly process. Under reaction conditions that inhibit nucleosome formation (+ EDTA), pretreatment of the extract with RNase A revives the chromatin assembly machinery while the rate of DNA supercoiling is stimulated significantly. Addition of purified RNA blocks DNA supercoiling. Taken together, these data suggest that the parameters surrounding in vitro chromatin assembly are variable and subject to modulation by endogenous factors.

The structure and role of RNA polymerases in Plasmodium

During the past few years the characterization of several Plasmodium falciparum RNA polymerase subunits has revealed potentially significant differences between the corresponding subunits of the host and parasite enzymes(1-3). The largest subunits of P. falciparum RNA polymerase II and III contain enlarged variable domains that separate conserved domains in these subunits. The partially characterized beta and beta '-like subunits of an organellar P. falciparum RNA polymerase also appear to be distinct from the host RNA polymerases. In this review David Bzik discusses the structure and role of RNA polymerases in Plasmodium.

cis-acting enhancement of RNA polymerase III gene expression in vitro

The Xenopus laevis S-150 cell-free extract catalyzes in vitro transcription of several RNA polymerase III genes. Among these are the Xenopus 5S RNA gene (somatic type) and the Xenopus methionine tRNA gene. In this report we present an analysis of the transcriptional activity of these two genes either in trans-competition experiments or when the genes are co-localized in the same circular plasmid. In the "cis" arrangement, elevated levels of 5S and tRNA gene expression are observed, which are dependent on the relative orientation of the two genes (convergent or in tandem) and the distance between them. The results of these analyses reveal important parameters affecting the expression of juxtaposed genes.

Reaction parameters of TFIIIA-induced supercoiling catalyzed by a Xenopus laevis cell-free extract

In addition to its fundamental role of nucleating the formation of stable transcription complexes, the Xenopus laevis 5S RNA specific transcription factor, TFIIIA, promotes a variety of DNA-associated metabolic reactions. We report that TFIIIA can induce a DNA supercoiling catalyzed by the Xenopus laevis S-150 cell-free extract on plasmids containing a single copy of the Xenopus 5S RNA gene (somatic-type). Stimulated supercoiling occurs in the presence of high concentrations of ATP (4 mM) and at a factor to DNA ratio of 1 through a mechanism most likely involving type I topoisomerase. The highest level of stimulated supercoiling occurs when TFIIIA is incubated with DNA prior to the addition of the S-150 extract. Taken together, the experiments outlined in this report establish a reliable and seminal system in which TFIIIA-induced DNA supercoiling can be observed reproducibly.

DNA superhelicity enhances the assembly of transcriptionally active chromatin in vitro

Using an in vitro chromatin assembly system, we analyzed the influence of DNA superhelicity on the development of transcriptionally active minichromosomes. Plasmid DNA molecules containing either a Xenopus borealis 5S RNA gene or an X. laevis methionine tRNA gene were utilized as templates for the assembly of chromatin. Both plasmids were processed into active minichromosomes if introduced as supercoiled molecules into the extract (S-150). The degree of superhelicity is a determining factor in the assembly of active chromatin. Molecules containing varying superhelical densities were processed into minichromosomes with different transcriptional activities. The absence of supercoils leads to the assembly of chromatin with substantially lower transcriptional activity. Assembled minichromosomes are stable enough to be isolated by sucrose gradient centrifugation while retaining their transcriptional phenotype. The formation of nucleosomes with a periodic spacing occurred with the same efficiency and to the same degree regardless of the initial DNA topology. Hence, a determining factor in the development of transcriptionally active chromatin may be the initial superhelicity of the DNA molecule to which activator (trans-acting factors) or repressor (histones) proteins bind. Once the chromatin assembly process has begun, the transcriptional activity of the resulting minichromosome may already have been determined.