Transcription of DNA and chromatin with calf thymus RNA polymerase B in vitro

Ultrastructural methods for nucleic acid detection by immunocytology

In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.

Robert Feulgen Prize Lecture 1995. New approaches to in situ detection of nucleic acids

The present paper reviews recent results obtained by different molecular biology-based, immunocytological approaches to the localization and identification of nucleic acids in sections of biological material. Examples of sensitive, high-resolution detection methods for RNA, DNA or specialized DNA regions are presented. Special emphasis is placed on the potential values and limitations of these new methods.

Control of RNA polymerase binding to chromatin by variations in linker histone composition

We have measured the frequency of initiation sites in chromatin for RNA polymerase in vitro as a function of the composition of linker histones (H1 and its analogues). In linker histone-depleted chromatin, RNA chain initiation appears to be restricted to the exposed linker DNA. On titration with purified linker histones, initiation is further restricted to an extent determined by the amount and type of linker histone, and the source of depleted chromatin. The extent of repression is correlated with the capacity of linker histones to induce the formation of higher-order structure in the complex. The results suggest that the effects of linker histones are mediated through the higher-order structure of chromatin, which prevents access of polymerase to the linker DNA. Accordingly, we find that structures imposed by the linker histones after polymerase binding are not inhibitory. Microscopy reveals that the higher-order structure in partially condensed chromatin is discontinuous, with solenoidal units spaced by sections of unravelled nucleosomes. Since salt stimulation of linker histone exchange does not result in derepression of linkers in our assay, we conclude that the distribution of higher-order units in chromatin is static and that the linker histones exchange between high-affinity sites in established units. We have previously shown that the globin gene is selectively unfolded in tissues that express the gene. The present results suggest that the transcriptional activity of specific genes is maintained by differential linker histone binding within chromatin.

Modulation of early mRNA synthesis in lectin-induced lymphocyte activation--an association with a possible factor

Two phases of early mRNA synthesis were observed in lectin-induced lymphocyte activation. At 0-2 h, lectin-treated lymphocytes showed a considerable decrease in nuclear RNA polymerase II activity as compared with that of untreated cells and, at later periods, a reverse increase was observed. Such modulation of mRNA synthesis is not due to the change of RNA polymerase II, but a possible factor in nuclei. This factor represses RNA chain initiation and stimulates chromatin-dependent RNA elongation catalyzed by RNA polymerase II. It was characterized to be a 10-30 kDa sugar-containing molecule and the physiological significance of this factor is discussed from the viewpoint of the transcriptional regulation.

A novel factor for DNA-dependent RNA polymerase II in rat liver nuclei

The author found, in rat liver nuclei, a novel factor which exhibited a strong inhibitory effect on RNA chain initiation by various classes of RNA polymerases (I, II and III) using an exogenous DNA template. The molecular weight of this factor was estimated to be 70 K daltons, and its activity was not affected by treatment with trypsin, RNase A, lipase C, alpha-amylase and heat. However, its activity was inactivated by a digestion of glycosidases. The molecule is shown to contain a considerable amount of sugars by physicochemical analysis. In addition, it is elucidated that the factor is not heparin which has a similar biological activity.

An examination of models for chromatin transcription

Structural studies have revealed that chromatin is composed of repeating units or nucleosomes having two distinct domains, the nucleosome core and the linker region. The nucleosome core comprises 146 base pairs of DNA wound in one and three quarter turns around an octamer of histones made up of two symmetrical tetramers (1). It may be inferred on topological grounds that this structure must be perturbed during chromatin transcription and replication since the histone core bridges the supercoil which blocks the passage of polymerase along the template and prevents the unwinding of DNA required for enzymatic copying. A number of mechanisms for freeing the DNA template may be envisaged, and one detailed model, based on symmetrical dissociation of the histone tetramers, has been proposed (2). Here we present evidence against such unpairing or indeed any detachment of histones from the octamer during chromatin transcription, and we give reasons for favouring a transcriptional mechanism based upon the separation of the octamer from at least one of the DNA.

In vitro transcription of chromatin containing histones hyperacetylated in vivo

The culture of cells in the presence of sodium n-butyrate causes an accumulation of histones that are highly acetylated. When chromatin containing these histones was transcribed with E. coli RNA polymerase, an increase in the template activity compared to control chromatin was observed. Titration of chromatin with polymerase under both reinitiating and non-reinitiating conditions showed there was no increase in the number of regions available for transcription. Comparison of the kinetics for single and multiple rounds of transcription indicated that the rate of elongation was increased and probably the rate of reinitiation as well. Comparison of the size of transcripts from control and acetylated chromatin showed a small increase in the average size of transcripts from acetylated chromatin. When transcription was compared using partially purified HeLa polymerase, an increase was also seen. Studies under various ionic conditions showed that control chromatin required a higher salt concentration for optimum activity than did acetylated chromatin. In addition, at the optimum salt concentration for each chromatin, there was very little difference in the transcriptional activity using exogenous HeLa RNA polymerase.

Transcriptionally active RNA polymerases from Morris hepatomas and rat liver. Elucidation of the mechanism for the preferential increase in the tumour RNA polymerase I

The amount and/or activity of DNA-dependent RNA polymerase I, Ii and III from resting liver, regenerating liver and a series of Morris hepatomas (5123D, 7800, 7777, 3924A) were determined after extraction of the enzymes from whole tissue homogenates and subsequent fractionation by DEAE-Sephadex column chromatography. When compared with resting liver, the tumours exhibited a characteristic enzyme pattern in which polymerase I, but not II, was increased. The increase in RNA polymerase I was proportional to the tumour growth rates. Alterations in polymerase III were confined to the most rapidly proliferating hepatomas. By contrast, all classes of RNA polymerase were found to be increased during liver regeneration. Relative to resting liver, the fastest growing tumour, 3924A, exhibited the highest activities and/or amounts of RNA polymerase I (8-fold) and III (5-fold) per g of tissue. These alterations in the tumour RNA polymerases were reflected in corresponding increases in the transcriptionally active (bound or chromatin-associated) enzyme population. The mechanisms underlying the augmented synthesis of RNA in vitro by bound polymerase I from hepatoma 3924A were elucidated by product analysis. The results indicated that, relative to liver RNA polymerase I, the tumour enzyme produced more nascent RNA chains and elongated these chains at a faster rate. The number of 3'-termini, as measured by incorporation into uridine, was higher in the hepatoma even under conditions which prevented re-initiation. suggesting increased amount of transcriptionally active RNA polymerase I in the tumour.

Features of in vitro puffing and RNA synthesis in polytene chromosomes of Chironomus

In order to elucidate the causal relation between RNA synthesis and puffing in polytene chromosomes, salivary gland nuclei and chromosomes from Chironomus tentans and C. pallidivittatus (Diptera, Chironomidae) were isolated in the native state under controlled and optimized conditions. The behavior of the polytene chromatin in vitro as compared to that in vivo was studied morphologically and autoradiographically. It was shown that the absence of cytologically visible puffing does not necessarily indicate transcriptional quiescence. Under suitable conditions all potential puff sites incorporate the radioactive precursor simultaneously. This can be seen in vivo and even more clearly in chromosomes decondensed by 340-400 mM NaCl in vitro. Potential puff sites therefore appear to be permanently equipped with RNA-polymerases, and there is always a basic low level of transcriptive activity. Experimental shrinking of Balbiani rings and other puffs by dimethylsulfoxide (DMSO) or heat shock in vivo, leaves the genes in the collapsed puffs still transcriptionally active, although to a reduced extent. Light optically visible puffing is therefore not a necessary prerequisite for RNA synthesis, while, conversely, RNA synthesis is required for puff formation.

Regulation of transcription by DNA-bound non-histone nuclear proteins

Purified non-histone proteins from mouse mammary cells bind specifically to homologous DNA or chromatin. Complexes of non-histone protein with DNA or chromatin, isolated on agarose columns, were transcribed with both Escherichia coli RNA polymerase and RNA polymerase B from calf thymus. The fact that complexing of DNA with non-histone proteins increases transcription by E. coli RNA polymerase but not by RNA polymerase B suggests different mechanisms of transcription by these two enzymes. Similar experiments with mouse and Drosophila chromatin indicate that non-histone proteins specifically stimulate the transcription of mouse chromatin by RNA polymerase B. Non-histone proteins stimulate the transcription of mouse mammary tumor virus sequences in chromatin by RNA polymerase B but not by E. coli RNA polymerase. We conclude that those non-histone proteins bound specifically to chromatin are able to activate the transcription of specific genes by eukaryotic RNA polymerase.

Non-random nature of 2-acetylaminofluorene-induced alterations of DNA template capacity

Male rats were fed a diet containing 0.03% (w/w) 2-acetylaminofluorene (AAF) and their hepatic DNA was isolated and transcribed with E. coli RNA polymerase. Ingestion of the carcinogen-containing diet for 4 days substantially reduced the template capacity of the isolated DNA. This reduction in template capacity was due to an apparent decreased RNA chain size (up to 50%), with no significant changes in initiation or re-initiation of RNA synthesis. This premature termination of RNA synthesis was accompanied, in some instances, by a reduced rate of RNA chain elongation. When the rats were returned to a basal diet for 7 days following 4 days of AAF ingestion, template capacity and RNA chain size returned to control values. Fractionation of hepatic chromatin on a glycerol gradient revealed that inhibition of DNA template capacity occurs on portions exhibiting characteristics of expressed, as well as those with characteristics of repressed, segments of the genome. In contrast, the DNA isolated from a small, highly condensed chromatin fraction (15% of total chromatin-DNA) showed no significant reduction in total template capacity. Analysis of the fidelity of RNA synthesis on this DNA template was performed by determining the rate of addition of individual nucleotide triphosphates to a growing RNA chain. Large reductions in the rates of adenosine and uridine polymerization were observed while no changes in guanosine or cytidine polymerization were found. This suggests the presence of functionally significant carcinogen-induced modifications of adenine. The inhibition in the rate of adenosine and uridine polymerization was reversed when the animals were placed on a basal diet after AAF ingestion.

Initiation and elongation of polyribonucleotide chains on rat ventral-prostate chromatin transcribed by homologous ribonucleic acid polymerase B

The characteristics of initiation of RNA synthesis and the elongation of RNA chains on rat ventral-prostate chromatin by RNA polymerase B were investigated by two methods. 1. Initiation was carried out under low-salt conditions with three ribonucleoside triphosphates, and elongation was begun in the absence of reinitiation by the addition of the fourth ribonucleoside triphosphate and increasing the salt concentration. 2. Stable initiation complexes were formed by preincubation of enzyme with template at 37 degrees C, elongation was started by the addition of all four ribonucleoside triphosphates and reinitiation or spurious RNA synthesis was prevented by rifamycin AF/013. The latter method gave more reliable results. The dependence of those parameters on the androgenic status of the animal was studied. During the first 24h after castration, elongation was mainly affected, whereas after 72h a smaller number of initiation sites for RNA polymerase B on chromatin was evident. Considerable diurnal variations in the various parameters were observed. Changes in the relative concentrations of the chromatin-associated proteins were also observed after castration. In the rat ventral-prostate gland androgenic steroids may not only influence one stage of the transcriptional process, but may affect many factors involved in the control of gene expression.

Template activity of calf thymus DNA modified by a dihydrodiol epoxide derivative of benzo[a]pyrene

The purpose of the present study was to determine the effects of covalent binding to DNA of a reactive derivative of benzo[a]pyrene on template activity during in vitro transcription with RNA polymerase. Calf thymus deoxyribonucleic acid, modified by reaction with (+/-)-7beta,8alpha-dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene, was transcribed with Escherichia coli DNA-dependent RNA polymerase. With increasing levels of modification, there was a progressive inhibition of transcription. The inhibition was much greater under conditions where continuous reinitiation of transcription occurred than under conditions where only one RNA chain was synthesized per initiation site. This suggested that the modified sites block the movement of polymerase along the template and prevent recycling of the enzyme. Consistent with this interpretation were analyses of RNA transcripts on sucrose density gradients which showed a progressive decrease in average RNA chain length as the extent of template modification increased. In contrast to the inhibitory effect on chain elongation, evidence was obtained that the modified DNA had an increase in the number of initiation sites for transcription. These results are consistent with separate physical studies indicating that modification of DNA by this benzo[a]pyrene derivative can induce small localized regions of denaturation.

On the initiation of mammalian RNA polymerase at single-strand breaks in DNA

Mammalian RNA polymerase B is able to initiate at single-strand breaks in the DNA template. A 3'-OH end at a nick is required for initiation whereas the 5'-end may be either -- OH or phosphate. The 3'-OH group does not function as a primer. An appreciable part of the newly synthesized RNA started at a nick remains associated with the DNA in hydrid form. Initiation of exogeneous RNA polymerase B on chromatin exhibits similar requirements.

Organisation of genes for ribosomal RNA in Physarum polycephalum

Physarum polycephalum nucleolar satellite DNA has been analysed by restriction enzyme digests and hybridisation to ribosomal RNA. The nucleolar DNA is isolated as molecules of molecular weight 39 X 10(6). The positions of sites of endo R-EcoRI and endo R-HindIII digestion have been determined accurately in the whole molecule. The endo R-EcoRI sites and one endo R-HindIII site are within the26-S rRNA complementary sequence and the other endo R-HindIII site is within the 19-S rRNA complementary sequence. The sites are arranged symmetrically about the centre of the molecule as if it were a palindrome.

RNA chain elongation on a chromatin template

The rate of RNA chain elongation has been measured with DNA and chromatin as template. RNA propagation on chromatin is about 50% of the rate found with DNA. Kinetic experiments demonstrate that the inhibition is not due to interference with the addition of the nucleoside triphosphates. Analysis of the dependence of propagation on the Tm of DNA shows that the chromatin proteins interfere with the translocation of the RNA polymerase along the DNA template.

Control of RNA synthesis by chromatin proteins

The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA.

Chromatin-bound DNA-dependent RNA polymerase in developing pea cotyledons

The pattern of cotyledon development in three varieties of Pisum sativum has been defined in terms of cell number, DNA and RNA content and chromatin, bound RNA polymerase activity. Variation was observed in the relative periods of growth by cell division and cell expansion between the three varieties. The mean DNA content per cotyledon cell during growth by cell expansion increased to approximately 50C in one variety, 30C in the second variety and 15C in the third variety. The pattern of chromatin-bound RNA polymerase activity during development suggested that some of the DNA above the 2C level may contribute to RNA synthesis in two of the three varieties studied. In the third variety the RNA polymerase activity decreases throughout the phase of increase in DNA per cell. The chromatin-bound RNA polymerase activity per cell was correlated with the rate of RNA increase per cell.

Separation of lymphocyte chromatin into template-active fractions with specificity for eukaryotic RNA polymerase II or prokaryotic RNA polymerase

When chromatin prepared from WI-L2 lymphocytes by low salt extraction and shearing is centrifuged on a glycerol gradient, one area of the gradient yields chromatin enriched in template activity for Escherichia coli DNA-dependent RNA polymerase (EC 2.7.7.6; nucleosidetriphosphate:RNA nucleotidyltransferase) as compared to Saccharomyces cerevisiae RNA polymerase II (or B). Another area yields chromatin preferred by the eukaryotic enzyme. Kinetic studies indicate that the differences in activity cannot be explained by differences in affinity of the enzymes for the various templates. The DNA isolated from either fraction has a molecular weight of 8.5 X 106. The "yeast active" fraction seems enriched in proteins. Mixing experiments indicate that the yeast enzyme does not alter the template in such a way as to improve it for the bacterial enzyme.