Quantitation of elongating form A and B RNA polymerases in chick oviduct nuclei and effects of estradiol

The JAK-STAT pathway at twenty

We look back on the discoveries that the tyrosine kinases TYK2 and JAK1 and the transcription factors STAT1, STAT2, and IRF9 are required for the cellular response to type I interferons. This initial description of the JAK-STAT pathway led quickly to additional discoveries that type II interferons and many other cytokines signal through similar mechanisms. This well-understood pathway now serves as a paradigm showing how information from protein-protein contacts at the cell surface can be conveyed directly to genes in the nucleus. We also review recent work on the STAT proteins showing the importance of several different posttranslational modifications, including serine phosphorylation, acetylation, methylation, and sumoylation. These remarkably proficient proteins also provide noncanonical functions in transcriptional regulation and they also function in mitochondrial respiration and chromatin organization in ways that may not involve transcription at all.

Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on

We adapted the nuclear run-on method to measure changes in the rate of RNA polymerase II (pol II) transcription of repetitive elements and transposons in the female germ line of Drosophila melanogaster. Our data indicate that as little as an approximately 1.5-fold change in the rate of transcription can be detected by this method. Our nuclear run-on protocol likely measures changes in transcriptional elongation, because rates of transcription decline with time, consistent with a low rate of pol II re-initiation in the isolated nuclei. Surprisingly, we find that the retrotransposon gypsy and the repetitive sequence mst40 are silenced posttranscriptionally in fly ovaries.

Transcription factories: quantitative studies of nanostructures in the mammalian nucleus

Transcription by the three nuclear RNA polymerases is carried out in transcription factories. This conclusion has been drawn from estimates of the total number of nascent transcripts or active polymerase molecules and the number of transcription sites within a cell. Here we summarise the variety of methods used to determine these parameters, discuss their associated problems and outline future prospects.

The path of transcripts from extra-nucleolar synthetic sites to nuclear pores: transcripts in transit are concentrated in discrete structures containing SR proteins

The route taken by transcripts from synthetic sites in the nucleus to the cytoplasm has been under scrutiny for years, but details of the pathway remain obscure. A new high-resolution method for mapping the pathway is described; HeLa cells are grown in Br-U so that the analogue is incorporated into RNA and exported to the cytoplasm, before Br-RNA is localized by immuno-electron microscopy. After exposure to low concentrations of Br-U for short periods, cells grow normally. Br-RNA is first found in several thousand extra-nucleolar transcription sites or factories (diameter 50–80 nm), before appearing in several hundred new downstream sites (diameter 50–80 nm) each minute; subsequently, progressively more downstream sites become labelled. These sites can be isolated on sucrose gradients as large nuclear ribonucleoprotein particles of approximately 200 S. Later, Br-RNA is seen docked approximately 200 nm away from approximately 20% nuclear pores, before exiting to the cytoplasm. Individual downstream sites are unlikely to contain individual transcripts; rather, results are consistent with groups of transcripts being shipped together from synthetic sites to pores. A subset of SR proteins are excellent markers of this pathway; this subset is concentrated in tens of thousands of sites, which include transcription, downstream and docking sites. Growth in high concentrations of Br-U for long periods is toxic, and Br-RNA accumulates just inside nuclear pores.

Numbers and organization of RNA polymerases, nascent transcripts, and transcription units in HeLa nuclei

Using HeLa cells, we have developed methods to determine 1) the number of RNA polymerases that are active at any moment, 2) the number of transcription sites, and 3) the number of polymerases associated with one transcription unit. To count engaged polymerases, cells were encapsulated in agarose, permeabilized, treated with ribonuclease, and the now-truncated transcripts extended in [32P]uridine triphosphate; then, the number of growing transcripts was calculated from the total number of nucleotides incorporated and the average increment in length of the transcripts. Approximately 15, 000 transcripts were elongated by polymerase I, and approximately 75,000 were elongated by polymerases II and III. Transcription sites were detected after the cells were grown in bromouridine for <2.5 min, after which the resulting bromo-RNA was labeled with gold particles; electron microscopy showed that most extranucleolar transcripts were concentrated in approximately 2400 sites with diameters of approximately 80 nm. The number of polymerases associated with a transcription unit was counted after templates were spread over a large area; most extranucleolar units were associated with one elongating complex. These results suggest that many templates are attached in a "cloud" of loops around a site; each site, or transcription "factory," would contain approximately 30 active polymerases and associated transcripts.

Ultrastructural localization of active genes in nuclei of A431 cells

We have studied the ultrastructural localization of active genes in nuclei of the human epidermoid carcinoma cell line A431. Nascent RNA was labeled by incorporation of 5-bromouridine 5'-triphosphate, followed by pre-embedment or postembedment immunogold labeling and electron microscopy using ultrasmall gold-conjugated antibodies and silver enhancement. This combination of techniques allowed a sensitive and high resolution visualization of RNA synthesis in the nucleus. Transcription sites were identified as clusters of 3-20 gold particles and were found throughout the nucleoplasm. The clusters had a diameter of less than 200 nm. The distribution of clusters of gold particles in nuclei is preserved in nuclear matrix preparations. Nascent RNA is associated with fibrillar as well as with granular structures in the matrix. A431 nuclei contained on average about 10,000 clusters of gold particles. This means that each cluster represents transcription of probably one active gene or, at most, a few genes. Our study does not provide evidence for aggregation of active genes. We found transcription sites distributed predominantly on the surface of electron-dense nuclear material, probably lumps of chromatin. This supports a model of transcription activation preferentially on the boundary between a chromosome domain and the interchromatin space.

Active RNA polymerases are localized within discrete transcription “factories' in human nuclei

Nascent transcripts in permeabilized HeLa cells were elongated by approximately 30–2,000 nucleotides in Br-UTP or biotin-14-CTP, before incorporation sites were immunolabelled either pre- or post-embedding, and visualized by light or electron microscopy. Analogues were concentrated in approximately 2,100 (range 2,000-2,700) discrete sites attached to a nucleoskeleton and surrounded by chromatin. A typical site contained a cluster (diameter 71 nm) of at least 4, and probably about 20, engaged polymerases, plus associated transcripts that partially overlapped a zone of RNA polymerase II, ribonucleoproteins, and proteins rich in thiols and acidic groups. As each site probably contains many transcription units, these results suggest that active polymerases are confined to these sites, which we call transcription ‘factories’. Results are consistent with transcription occurring as templates slide past attached polymerases, as nascent RNA is extruded into the factories.

The structural basis of nuclear function

Most models for transcription and replication involve polymerases that track along the template. We review here experiments that suggest an alternative in which polymerization occurs as the template slides past a polymerase fixed to a large structure in the eukaryotic nucleus--a "factory" attached to a nucleoskeleton. This means that higher-order structure dictates how and when DNA is replicated or transcribed.

Replication and transcription sites are colocalized in human cells

HeLa cells synchronized at different stages of the cell cycle were permeabilized and incubated with analogues of nucleotide triphosphates; then sites of incorporation were immunolabeled with the appropriate fluorescent probes. Confocal microscopy showed that sites of replication and transcription were not diffusely spread throughout nuclei, reflecting the distribution of euchromatin; rather, they were concentrated in ‘foci’ where many polymerases act together. Transcription foci aggregated as cells progressed towards the G1/S boundary; later they dispersed and became more diffuse. Replication was initiated only at transcription sites; later, when heterochromatin was replicated in enlarged foci, these remained sites of transcription. This illustrates the dynamic nature of nuclear architecture and suggests that transcription may be required for the initiation of DNA synthesis.

Fluorescent labeling of nascent RNA reveals transcription by RNA polymerase II in domains scattered throughout the nucleus

Several nuclear activities and components are concentrated in discrete nuclear compartments. To understand the functional significance of nuclear compartmentalization, knowledge on the spatial distribution of transcriptionally active chromatin is essential. We have examined the distribution of sites of transcription by RNA polymerase II (RPII) by labeling nascent RNA with 5-bromouridine 5'-triphosphate, in vitro and in vivo. Nascent RPII transcripts were found in over 100 defined areas, scattered throughout the nucleoplasm. No preferential localization was observed in either the nuclear interior or the periphery. Each transcription site may represent the activity of a single gene or, considering the number of active pre-mRNA genes in a cell, of a cluster of active genes. The relation between the distribution of nascent RPII transcripts and that of the essential splicing factor SC-35 was investigated in double labeling experiments. Antibodies against SC-35 recognize a number of well-defined, intensely labeled nuclear domains, in addition to labeling of more diffuse areas between these domains (Spector, D. L., X. -D. Fu, and T. Maniatis. 1991. EMBO (Eur. Mol. Biol. Organ.) J. 10:3467-3481). We observe no correlation between intensely labeled SC-35 domains and sites of pre-mRNA synthesis. However, many sites of RPII synthesis colocalize with weakly stained areas. This implies that contranscriptional splicing takes place in these weakly stained areas. These areas may also be sites where splicing is completed posttranscriptionally. Intensely labeled SC-35 domains may function as sites for assembly, storage, or regeneration of splicing components, or as compartments for degradation of introns.

Visualization of focal sites of transcription within human nuclei

HeLa cells were encapsulated in agarose microbeads, permeabilized and incubated with Br-UTP in a 'physiological' buffer; then sites of RNA synthesis were immunolabelled using an antibody that reacts with Br-RNA. After extending nascent RNA chains by < 400 nucleotides in vitro, approximately 300-500 focal synthetic sites can be seen in each nucleus by fluorescence microscopy. Most foci also contain a component of the splicing apparatus detected by an anti-Sm antibody. alpha-amanitin, an inhibitor of RNA polymerase II, prevents incorporation into these foci; then, using a slightly higher salt concentration, approximately 25 nucleolar foci became clearly visible. Both nucleolar and extra-nucleolar foci remain after nucleolytic removal of approximately 90% chromatin. An underlying structure probably organizes groups of transcription units into 'factories' where transcripts are both synthesized and processed.

Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcripts

Many trypanosome genes are expressed as part of large polycistronic transcription units. This finding suggests that regulation of mRNA biogenesis may emphasize RNA-processing reactions more so than in other organisms. This study was undertaken to understand the temporal order of two RNA-processing reactions, trans splicing and polyadenylation, in the maturation of trypanosome mRNAs in vivo. Kinetic studies revealed rapid trans splicing of alpha-tubulin, beta-tubulin, and actin pre-mRNAs within 1 to 2 min after synthesis of the 3' splice site. Furthermore, following blockage of pre-mRNA synthesis, newly synthesized spliced leader RNA cannot be used for trans splicing, suggesting that trypanosomes do not accumulate substantial amounts of pre-mRNA which can provide splice acceptor sites. Thus, trans splicing is cotranscriptional. In addition, we show that trans splicing precedes polyadenylation in the processing of trypanosome tubulin pre-mRNAs.

Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcripts

Many trypanosome genes are expressed as part of large polycistronic transcription units. This finding suggests that regulation of mRNA biogenesis may emphasize RNA-processing reactions more so than in other organisms. This study was undertaken to understand the temporal order of two RNA-processing reactions, trans splicing and polyadenylation, in the maturation of trypanosome mRNAs in vivo. Kinetic studies revealed rapid trans splicing of alpha-tubulin, beta-tubulin, and actin pre-mRNAs within 1 to 2 min after synthesis of the 3' splice site. Furthermore, following blockage of pre-mRNA synthesis, newly synthesized spliced leader RNA cannot be used for trans splicing, suggesting that trypanosomes do not accumulate substantial amounts of pre-mRNA which can provide splice acceptor sites. Thus, trans splicing is cotranscriptional. In addition, we show that trans splicing precedes polyadenylation in the processing of trypanosome tubulin pre-mRNAs.

Maturation of polycistronic pre-mRNA in Trypanosoma brucei: analysis of trans splicing and poly(A) addition at nascent RNA transcripts from the hsp70 locus

Numerous protein-coding genes of the protozoan Trypanosoma brucei are arranged in tandem arrays that are transcribed polycistronically. The pre-mRNA transcripts are processed by trans splicing, leading to the addition of a capped 39-nucleotide (nt) miniexon and by poly(A) addition. We wished to determine the order of the RNA processing events at the hsp70 locus and address the potential occurrence of cotranscriptional RNA processing. We determined the rate of transcriptional elongation at the hsp70 locus in isolated nuclei, which measured between 20 and 40 nt/min. This low rate of RNA chain elongation allowed us to label the 3' end of hsp70 nascent RNA with a short (about 180-nt) 32P tail. The structure of the labeled nascent hsp70 RNA could then be analyzed by RNase T1 and RNase T1/RNase A mapping. We show that the trans splicing of hsp70 pre-mRNA did not occur immediately after the synthesis of the 3' splice acceptor site, and nascent RNA molecules that contained about 550 nt of RNA beyond the 3' splice acceptor site still had not acquired a miniexon. In contrast, nascent RNA with a 5' end that mapped to the polyadenylation site of the hsp70 genes could be detected, indicating that maturation of the pre-mRNA in trypanosomes involves a rapid cleavage of the nascent hsp70 RNA (within seconds after synthesis of the site) for poly(A) addition. Our data suggest that polycistronic pre-mRNA is unlikely to be synthesized in toto and rather appears to be processed cotranscriptionally by cleavage for poly(A) addition.

Maturation of polycistronic pre-mRNA in Trypanosoma brucei: analysis of trans splicing and poly(A) addition at nascent RNA transcripts from the hsp70 locus

Numerous protein-coding genes of the protozoan Trypanosoma brucei are arranged in tandem arrays that are transcribed polycistronically. The pre-mRNA transcripts are processed by trans splicing, leading to the addition of a capped 39-nucleotide (nt) miniexon and by poly(A) addition. We wished to determine the order of the RNA processing events at the hsp70 locus and address the potential occurrence of cotranscriptional RNA processing. We determined the rate of transcriptional elongation at the hsp70 locus in isolated nuclei, which measured between 20 and 40 nt/min. This low rate of RNA chain elongation allowed us to label the 3' end of hsp70 nascent RNA with a short (about 180-nt) 32P tail. The structure of the labeled nascent hsp70 RNA could then be analyzed by RNase T1 and RNase T1/RNase A mapping. We show that the trans splicing of hsp70 pre-mRNA did not occur immediately after the synthesis of the 3' splice acceptor site, and nascent RNA molecules that contained about 550 nt of RNA beyond the 3' splice acceptor site still had not acquired a miniexon. In contrast, nascent RNA with a 5' end that mapped to the polyadenylation site of the hsp70 genes could be detected, indicating that maturation of the pre-mRNA in trypanosomes involves a rapid cleavage of the nascent hsp70 RNA (within seconds after synthesis of the site) for poly(A) addition. Our data suggest that polycistronic pre-mRNA is unlikely to be synthesized in toto and rather appears to be processed cotranscriptionally by cleavage for poly(A) addition.

Activated ribosomal RNA synthesis in regenerated rat liver upon inhibition of protein synthesis

Cycloheximide (Cyh), administered at a dose of 5 mg/kg body wt blocks protein synthesis in normal rat liver (NRL) and regenerating rat liver (RRL). The rate of synthesis of 45S pre-rRNA in RRL, studied after RNA labelling in vivo is activated 2.8 times. Pre-r RNA synthesis in RRL is more sensitive to the stopped translation, but never falls down to the level in NRL. The major contribution to the rDNA transcription activation in RRL comes from the 20-fold increase in the number of pol I molecules engaged in the transcription, the elongation rate being 1.4-fold accelerated. Cyh quenches partially the enhanced rDNA transcription in RRL: the number of pol I molecules and their elongation rate are about 1.7-fold and 1.5-fold higher, respectively, than the corresponding values in NRL after Cyh treatment. The results show that two different mechanisms control the number and the rate of initiation and elongation of RNA polymerase I in rat liver; one of them depends on continuous protein synthesis and can be inactivated by Cyh, the other is Cyh resistant.

Regulation of amyloid A gene expression in cultured cells

Serum amyloid A (SAA) proteins are secreted by mammalian liver in response to inflammatory stimuli. Both transcriptional and posttranscriptional mechanisms have been shown to regulate the 2,000-fold increase in SAA mRNA after injection of endotoxin into mice. We report here the characterization of a cell line derived from mouse liver (BNL) in which the expression of SAA3 mRNA is regulated. In this model, SAA3 mRNA accumulated in response to conditioned medium from the mouse macrophage P388D1 cell line with kinetics similar to that seen in mouse liver (C. A. Lowell, R. S. Stearman, and J. F. Morrow, J. Biol. Chem. 261:8453-8461, 1986). In in vitro nuclear transcription assays, the SAA3 gene was transcribed equally in induced and uninduced cells. In addition, in steady-state RNA studies treatment with conditioned medium allowed the cells to rapidly accumulate SAA3 mRNA without an apparent change in half-life. These observations suggest that conditioned medium contains a factor(s) that acts directly on hepatocytes to regulate SAA3 mRNA processing.

Kinetics of expression of the gene encoding the 65-kilodalton DNA-binding protein of herpes simplex virus type 1

The 65-kilodalton DNA-binding protein (65KDBP) of herpes simplex virus type 1, encoded by gene UL42, is required for herpes simplex virus origin-dependent DNA replication (C.A. Wu, N.J. Nelson, D.J. McGeoch, and M.D. Challberg, J. Virol. 62:435-443, 1988). We found by indirect immunofluorescence with monoclonal antibody to 65KDBP that the protein was first detectable at 3 h postinfection. It localized first to the inner periphery of the nucleus, but accumulated in large globular compartments within the nucleus by 6 h postinfection in a pattern similar to that displayed by the major DNA-binding protein ICP8. Immune electron microscopy revealed that 65KDBP was associated with the marginated heterochromatin at the early times, but migrated further into the nucleus at late times when the only discernible areas devoid of 65KDBP were the nucleoli and heterochromatin. The 65KDBP gene is a member of the beta kinetic class as determined by the ability of the mRNA to be expressed at significant levels even in the absence of viral DNA synthesis. Furthermore, in the presence or absence of the DNA polymerase inhibitor phosphonoacetic acid, the patterns of accumulation of protein as well as mRNA were virtually indistinguishable from those displayed by the model beta genes encoding ICP8 and thymidine kinase. Nuclear run-on experiments demonstrated that maximum rates of 65KDBP gene transcription occurred prior to the maximum rate of progeny viral DNA synthesis and confirmed that the expression of the 65KDBP gene is regulated at the level of transcriptional initiation.

Steady-state and nuclear run-on analyses of transcription in a temperature-sensitive Chinese hamster cell mutant with a defect in RNA metabolism

We have further characterized a temperature-sensitive mutant of Chinese hamster lung fibroblasts in tissue culture with a defect in RNA metabolism. The mutant phenotype is reflected in transcription in crude extracts or in isolated nuclei, when these are made from cells shifted to the nonpermissive temperature; however, differential heat inactivation between mutant and wild-type extracts cannot be demonstrated with cell-free systems. We tentatively conclude that the mutation may affect initiation of transcription which cannot be observed in our in vitro systems. Partially purified RNA polymerase I, II, and III fractions are indistinguishable from wild type. A temperature shift does not affect transcription by RNA polymerase III measured with intact cells or by nuclear run-on experiments. The nuclear run-on and other experiments suggest that RNA polymerase II-dependent transcription is inhibited before RNA polymerase I-dependent transcription. This conclusion is also supported by Northern analyses of selected mRNAs in nonsynchronized and synchronized cells after a shift to the nonpermissive temperature.

Regulation of amyloid A gene expression in cultured cells

Serum amyloid A (SAA) proteins are secreted by mammalian liver in response to inflammatory stimuli. Both transcriptional and posttranscriptional mechanisms have been shown to regulate the 2,000-fold increase in SAA mRNA after injection of endotoxin into mice. We report here the characterization of a cell line derived from mouse liver (BNL) in which the expression of SAA3 mRNA is regulated. In this model, SAA3 mRNA accumulated in response to conditioned medium from the mouse macrophage P388D1 cell line with kinetics similar to that seen in mouse liver (C. A. Lowell, R. S. Stearman, and J. F. Morrow, J. Biol. Chem. 261:8453-8461, 1986). In in vitro nuclear transcription assays, the SAA3 gene was transcribed equally in induced and uninduced cells. In addition, in steady-state RNA studies treatment with conditioned medium allowed the cells to rapidly accumulate SAA3 mRNA without an apparent change in half-life. These observations suggest that conditioned medium contains a factor(s) that acts directly on hepatocytes to regulate SAA3 mRNA processing.

Transcriptional regulation of hemoglobin switching in chicken embryos

We used recombinant chicken deoxyribonucleic acid clones containing embryonic and adult beta-globin genes and "runoff" endogenous nuclear transcription to investigate the expression of embryonic and adult beta-globin genes during hematopoiesis in the developing chicken embryo. Purified, cloned deoxyribonucleic acids were digested with various restriction enzymes, separated on agarose gels, blotted to nitrocellulose, and annealed with purified nuclear [32P]ribonucleic acid synthesized in vitro from embryonic or adult red cell nuclei. Transcription of the respective globin genes was assayed by hybridization of nuclear [32P]ribonucleic acid to specific restriction fragments containing adult or embryonic coding sequences. Our results indicate that little, if any, transcription from the adult or embryonic beta-globin genes is detectable in the heterologous red cell nuclei, even under conditions in which ribonucleic acid processing probably does not occur.

Transcription of three actin genes and a repeated sequence in isolated nuclei of sea urchin embryos

The relative transcription of three unlinked actin genes of the sea urchin Strongylocentrotus purpuratus was measured in isolated nuclei, at several stages during embryonic development. Transcription of two cytoskeletal actin genes, CyI and CyIIIa, was first detected in 64-128 cell embryos. At the early stages, the CyIIIa gene is several-fold more active per embryo than CyI. The relative transcription of these two genes changes as development proceeds so that by the pluteus stage the CyI gene is at least twice as active per embryo as the CyIIIa gene. Both the time of initial detection of transcription of these two genes and the shift in their relative transcription during development correspond closely with the appearance and relative abundance in embryos of the mRNAs from these genes. Transcription of the muscle actin gene M was first detected in nuclei from pluteus stage embryos and thus also closely correlates with the first appearance of the muscle actin gene mRNA in embryos. The tight temporal coupling of the appearance in embryos of mRNA from these genes and the detection of their transcription in nuclei suggests that the regulation of their expression is in large part transcriptional. In addition to examining the transcription of these actin genes, we discovered that a member of an actively transcribed repeated sequence family is located upstream of the muscle actin-coding sequence. This sequence, which is present at least several hundred times within the genome and hybridizes strongly to RNA synthesized by RNA polymerase III at cleavage stages and to RNA synthesized in nuclei from pluteus stage embryos, shows little hybridization at blastula and gastrula stages.

Rapid enhancement of beta 2-interferon/B-cell differentiation factor BSF-2 gene expression in human fibroblasts by diacylglycerols and the calcium ionophore A23187

The expression in human fibroblasts of the beta 2-interferon (IFN-beta 2) gene, which is now recognized to be identical to the gene encoding B-cell differentiation factor BSF-2, is enhanced by several cytokines that affect cell growth (tumor necrosis factor, interleukin 1, platelet-derived growth factor, and beta 1-interferon). We have examined the possibility that IFN-beta 2 gene expression is regulated through activation, by diacylglycerol, of the protein kinase C pathway. The synthetic diacylglycerols 1,2-dioctanoylglycerol (diC8) and 1-oleoyl-2-acetylglycerol strongly enhanced IFN-beta 2, but not IFN-beta 1, gene expression in human fibroblasts (FS-4 strain). An increase in IFN-beta 2 mRNA level was detected within 15 min after addition of diC8 (290 microM) to FS-4 cells and was maximal approximately 20 hr later. An increase in IFN-beta 2 gene transcription was detected within 5 min of addition of diC8, and the rate of transcription was near-maximal by 15-30 min. The enhancement of IFN-beta 2 gene expression by diC8, interleukin 1, or tumor necrosis factor was not prevented by H8, a preferential inhibitor of cAMP- and cGMP-dependent protein kinases, but was blocked by H7, an inhibitor of protein kinase C as well as of cyclic nucleotide-dependent protein kinases. diC8 was found to protect FS-4 cells from the cytopathic effect of vesicular stomatitis virus; this protection was blocked by polyclonal or monoclonal antibodies that neutralize IFN-beta, suggesting that the antiviral effect was due to the secretion of IFN-beta 2 by the diC8-treated fibroblasts. The calcium ionophore A23187 (1-10 microM) also elicited an increase in the level of IFN-beta 2 mRNA in FS-4 fibroblasts; appropriate combinations of A23187 and diC8 had at least an additive effect in enhancing IFN-beta 2 mRNA levels. These results show that protein kinase C-activating or [Ca2+]-elevating agents rapidly increase the expression of the IFN-beta 2 gene in human fibroblasts.

Effect of cytokinins on ribosomal RNA gene expression in excised cotyledons of Cucurbita pepo L

Excised pumpkin (Cucurbita pepo L.) cotyledons were used to investigate the effects of two different types of cytokinins: N(6)-benzyladenine and N1-(2-chloro-4-pyridyl)-N2-phenylurea on RNA synthesis in isolated nuclei. Treatment of cotyledons with both cytokinins resulted in a rapid enhancement of nuclear RNA-polymerase-I activity (EC 2.7.7.6). Maximum stimulation of RNA polymerase I, responsible for rRNA synthesis, was observed 4-6 h after the start of cytokinin action. The activity of RNA polymerase II was stimulated much more slowly and to a lesser extent. Uridine 5'-monophosphate-uridine analysis of the alkalidigested nascent pre-rRNA chains showed that the stimulation of RNA-polymerase-I activity was the consequence of an increase of the polyribonucleotide-clongation rate. No significant change in the number of transcribing enzyme molecules was defected after hormone treatment (86·10(3) RNA-polymerase-I molecules per diploid genome).Indications that de-novo protein synthesis is necessary for cytokinin-mediated RNA-polymerase stimulation were derived from experiments showing inhibition by cycloheximide.

Effects of glucocorticoid and cycloheximide on the activity and amount of RNA polymerase I in nuclei of rat liver

The activity of the template-engaged form of RNA polymerase I from livers of adrenalectomized rats was about 50-60% of that of normal control rats, and increased about 2-fold at 6 h after the administration of dexamethasone. However, no change was found in the activity of the 'free' form of RNA polymerase I or the template-engaged form of RNA polymerase II. Immunochemical studies using guinea-pig anti-(RNA polymerase I) serum disclosed that the total number of RNA polymerase I molecules did not vary during the treatment with dexamethasone. Cycloheximide caused a rapid decrease in the template-engaged form of RNA polymerase I activity in normal rats and in dexamethasone-treated (6 h) adrenalectomized rats, to the value in adrenalectomized rats, but affected it only slightly in adrenalectomized rats. The elongation rate of rRNA-precursor synthesis in liver nuclei was not affected by a change in the concentration of circulating dexamethasone. From these results, it is concluded that about half the rRNA-precursor synthesis in rat liver is regulated by glucocorticoids, probably through the synthesis of short-lived protein(s) which may play a role in conversion of the 'dormant' form of RNA polymerase I into the 'engaged' form.

The effect of age on the induction of tyrosine aminotransferase and tryptophan oxygenase genes by physiological stress

Expression of the genes coding for tyrosine aminotransferase and tryptophan oxygenase in rats is induced in response to cold stress. We have studied the effect of ageing on this induction. The induction of tyrosine aminotransferase activity in young adult rats (10 months) was about twice that observed with old rats (25 months). This difference between the two age groups was also observed when the steady-state level of tyrosine aminotransferase mRNA was measured by hybridization with a specific DNA probe. However, when the transcription rate of the gene was measured by in vitro elongation of nascent RNA in isolated nuclei, no difference was detected. In contrast to the results with tyrosine aminotransferase, induced tryptophan oxygenase enzyme and mRNA levels did not show an age-dependent difference. These results suggest that there is, with ageing, an impairment in post-transcriptional regulation of the synthesis of tyrosine aminotransferase. The regulation of tryptophan oxygenase, on the other hand, is similar in the two age groups.

Histone synthesis and deposition in the G1 and S phases of hepatoma tissue culture cells

Hepatoma tissue culture cells were synchronized in G1 and in S phase in order to examine the level of synthesis of different histone types and to determine the rate, timing, and location of their deposition onto DNA. We observe a basal level of synthesis in G1 (5% of that seen in S phase) for H2A.1, H2A.2, H3.2, H2B, and H4. The minor histone variants X and Z are synthesized at 30% of the rate observed in S cells. The rate of synthesis of the ubiquinated histones uH2A.1,2 is not as depressed in G1 cells as seen for H2A.1 and H2A.2. Histones synthesized in G1 are not deposited on the DNA of these cells at equivalent rates. Thus, histones H3.2 and H4 are not deposited significantly until S phase begins, at which time deposition occurs selectively on newly synthesized DNA. The deposition of H2A.1, H2A.2, H2B, X, and Z proceeds in G1; however, it occurs to a 2-4-fold lower extent than seen for the deposition of H1, HMG 14, and HMG 17. The deposition of all histones synthesized in S phase occurs rapidly, but there are variations in the sites of deposition. Thus, newly synthesized H3.1, H3.2, and H4 deposit primarily on newly replicated DNA whereas H2A.1, H2A.2, uH2A.1, 2, and H2B deposit only partially on new DNA (30%) and mostly on old. H1, HMG 14, and HMG 17 are deposited in an apparently fully random manner over the chromatin. To interpret these observations, we propose a model which includes a measure of histone exchange on the chromatin fiber. The model emphasizes the dynamics of histone-histone and histone-DNA interactions in regions of active genes and at replication forks.

Screening of lambda library for differentially expressed genes using in vitro transcripts

We present an improved approach to the screening of eucaryotic libraries for differential gene expression. Previous techniques have generated probe via the harvesting of cellular poly(A)+ RNA and synthesizing labeled cDNA probe using reverse transcriptase. In our approach we prepare labeled RNA probe via in vitro transcription. Unlike cDNA preparation, in vitro transcription (i) directly reflects the ongoing rate of gene expression, and (ii) allows one to assess expression of genes whose transcripts are not polyadenylated. To make this approach practical for the screening of a large library, we modified and optimized existing in vitro transcription techniques, enhancing manyfold the [alpha-32P]UTP incorporation into mRNA, while almost completely suppressing rRNA incorporation. In addition, we developed a simple procedure for making precise replicate dot blots of very large quantities of lambda-phage library DNA. By combining our techniques of in vitro transcription and replicate blotting, we are able to approach detection of a twofold difference in gene expression over a greater than 1000-fold range in overall expression. Our single-clone amplification and dot-blotting technique resulted in nearly the same number of lambda-phage DNA copies per dot for all members of the library. This feature allows us to assign genes to different expression classes, as well as to detect any alterations in expression. We demonstrate our approach by screening the drosophila genomic DNA library with in vitro transcripts from drosophila tissue culture cells. Screening of the entire drosophila genomic library at the 99% probability level is readily achieved.

Interferon action: transcriptional control of a gene specifying a 56,000-Da protein in Ehrlich ascites tumor cells

The exposure of cells to interferons enhances the accumulation of particular mRNAs and of the corresponding proteins. A cDNA clone (clone 202) complementary to an mRNA (202 mRNA) whose level is enhanced over 12-fold in mouse Ehrlich ascites tumor cells upon exposure to beta-interferon for 10 hr has previously been isolated. The level of this mRNA was also increased in other beta-interferon-responsive mouse cell lines (i.e., L929, L1210S) but not in a line (L1210R) which is not responsive to beta-interferon. The extent of induction in Ehrlich ascites tumor cells depended on the beta-interferon concentration and reached its maximal level between 300 and 1000 units of interferon/ml. Nuclei isolated from Ehrlich ascites tumor cells which had been exposed to beta-interferon produced in vitro more 202 specific RNA than nuclei from control Ehrlich ascites tumor cells: an increase in this production was detectable 2 hr after beginning the exposure of the cells to 1000 units/ml of beta-interferon and the increase reached its maximal level, around 18-fold, after 18 hr exposure. Much, if not all of this increase, appeared to be due to an increase in the rate of synthesis of the RNA and not to a decrease in its rate of turnover. The 202 mRNA was translated in a reticulocyte lysate into a 56,000-Da protein.

Correlation in isolated nuclei of template-engaged RNA polymerase II, ovalbumin mRNA synthesis, and estrogen receptor concentrations

Template-engaged and total RNA polymerase II molecules were quantitated in isolated nuclei at various stages of estrogen withdrawal and secondary stimulation by using [3H]amanitin titration assays. Estrogen receptors, RNA transcriptional activity, and ovalbumin mRNA were also measured, and comparisons were made between these parameters to determine whether any significant correlations exist. In isolated nuclei, the highest positive correlations existed between template-engaged RNA polymerase II, ovalbumin mRNA synthesis in vitro, and estrogen receptor concentration. Interestingly, restimulation of estrogen-withdrawn chicks results in replenishment of RNA polymerase II activity to prewithdrawal levels within 4 h; however, the recovery of the numbers of template-engaged polymerase II molecules, ovalbumin gene transcription, and nuclear receptor binding lags behind. These findings suggest that the estrogen effect on RNA polymerase activity is more rapid than the increase in template-engaged RNA polymerase II and ovalbumin-specific gene transcription. The excellent correlation that exists between nuclear estrogen receptor concentrations, template-engaged RNA polymerase II, and ovalbumin gene transcription strongly supports the hypothesis that estrogen receptors mediate RNA polymerase II binding to sequences associated with preferential transcription of the ovalbumin gene.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Posttranslational phosphorylation of specific chromosomal proteins and transcription of hnRNA genes in isolated nuclei: retention of in vivo sensitivity to 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)

The rapidly turning over phosphorylation of specific nuclear nonhistone proteins, especially 42-, 33-, and 30-kDa polypeptides, and its relation to the transcriptional activity of hnRNA genes was investigated in isolated nuclei from salivary gland cells of Chironomus tentans. Incubation conditions promoting the phosphorylation of nonhistone proteins as well as the transcriptional activity of RNA polymerase II were established. The pattern of 32P incorporation into the nonhistone proteins found in isolated nuclei resembled that obtained in experiments with intact cells, and the endogenous RNA polymerase II retained its ability to reinitiate the transcription under in vitro assay conditions. In addition, the in vivo sensitivity of the phosphorylation of 42-, 33-, and 30-kDa polypeptides, like the sensitivity of the initiation of hnRNA transcription to 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), were preserved in the nuclear preparation. The experimental data taken together provide further support for the idea that the activation of hnRNA genes is causally related to the phosphorylation of specific nonhistone proteins.

Glucocorticoids modify the rate of ribosomal RNA synthesis in rat thymus cells by regulating the polymerase elongation rate

The mechanism by which glucocorticoids inhibit RNA polymerase A activity, and hence rRNA synthesis, in rat thymus cells has been investigated. Studies of the intranuclear distribution of RNA polymerase A between chromatin bound ("engaged") and unbound ("free") forms revealed that the steroid-mediated inhibition of the activity of the "engaged" form of the enzyme was not accompanied by significant changes in "free" pool activity. In the presence of rifamycin AF/0-13, an inhibitor of re-initiation of RNA polymerase A, the rate of [3H]UMP incorporation into RNA was slower in nuclei from steroid-treated cells than in those from control cells, although in both conditions similar plateau levels of UMP incorporation were attained. Direct measurements of the numbers of transcribing RNA polymerase A molecules and of elongation rates showed that the inhibition of pre-rRNA synthesis was the result of a decrease in enzyme elongation rate; no significant change was observed in the number of transcribing enzymes. The steroid-induced inhibition of pre-rRNA synthesis was selectively abolished by mild proteolysis of nuclei, suggesting the involvement of a labile, regulatory glucocorticoid-induced protein. It is concluded that glucocorticoid treatment of rat thymus cells decreases 45S rRNA synthesis primarily by decreasing the polyribonucleotide elongation rate of RNA polymerase A, possibly by modification of the enzyme.

Activation of pS2 gene transcription is a primary response to estrogen in the human breast cancer cell line MCF-7

We have shown previously that an increase in the level of accumulated pS2 mRNA is first detectable in MCF-7 cells after 3 hr of estradiol treatment. Using in vitro nuclear run-on transcription with nuclei prepared from MCF-7 cells grown in the presence of estradiol or in estradiol-stripped medium, we demonstrate here that expression of the pS2 gene is controlled by estrogen at the transcriptional level. Induction of transcription is a very early event that is already apparent within 15 min after addition of estradiol to the culture medium. In addition, pretreatment of the cells with the protein synthesis inhibitor cycloheximide does not prevent induction of pS2 gene transcription, indicating that it corresponds to a primary effect of estrogen. The pS2 gene in MCF-7 cells represents a unique example of a human gene whose transcription is directly controlled by estrogen.

Dexamethasone increases the number of RNA polymerase II molecules transcribing integrated mouse mammary tumor virus DNA and flanking mouse sequences

In mouse Ltk- cells that were transfected with recombinant bacteriophage DNA containing a complete proviral copy of an integrated endogenous mouse mammary tumor virus (MMTV) with its flanking cellular sequences, the newly acquired MMTV proviruses were transcribed in a glucocorticoid-responsive fashion. After hormone treatment of selected cell clones in culture we isolated the nuclei, elongated the nascent RNA chains in vitro, and determined the number of RNA polymerase II molecules on the transcribed MMTV DNA as well as on the flanking mouse DNA sequences. We found that the specific increase in the polymerase loading after hormone treatment is proportional to the increase in the amount of stable MMTV mRNA. When the DNA sequences which are responsible for hormone-receptor binding and for the increased MMTV mRNA levels were deleted, no increase in RNA polymerase II loading on MMTV DNA was observed. Nuclear RNA chains which were transcribed in response to hormone treatment were detected not only from the transfected MMTV DNA but also from the mouse DNA sequences adjacent to the 3' end of the provirus.

Chromatin-bound and free RNA polymerase A activities in rat thymus cells following glucocorticoid treatment

Treatment of rat thymus cell suspensions with dexamethasone resulted in inhibition of engaged RNA polymerase A, without significant change in free pool activity. Studies with the re-initiation inhibitor, rifamycin AF/0-13, and measurements of numbers of RNA polymerase A molecules and of elongation rates showed that the inhibition of pre-rRNA synthesis resulted from a decrease in elongation rate. This effect was selectively abolished by mild proteolysis of nuclei. It is concluded that glucocorticoid treatment of rat thymus cells suppresses 45 S rRNA synthesis primarily by decreasing the polyribonucleotide elongation rate, rather than by effecting a change in enzyme redistribution or concentration.

Dihydrofolate reductase gene expression in cultured mouse cells is regulated by transcript stabilization in the nucleus

Methotrexate-resistant cells, which contain a 500-fold amplification of dihydrofolate reductase (DHFR) genes, were used as a model system for studying the regulation of DHFR gene expression during growth stimulation. We have shown that a threefold increase in DHFR mRNA levels following growth stimulation results from a corresponding increase in DHFR mRNA production (i.e., delivery to the cytoplasm) and is not the result of a change in DHFR mRNA half-life. We previously showed that the increase in DHFR mRNA production during growth stimulation is not accompanied by an increase in the relative rate of transcription of the DHFR gene. This suggested that changes in DHFR mRNA production during growth stimulation are due to changes in the stability of DHFR transcripts in the nucleus. Using continuous labeling experiments in vivo comparing the stability of DHFR RNA with specific reference sequences, we show that in growing cells most DHFR transcripts were converted to mRNA, whereas in resting cells the majority of DHFR transcripts were rapidly degraded in the nucleus. There was no significant difference in the rate of processing and transport of stable DHFR transcripts. Therefore, changes in the stability of DHFR RNA in the nucleus control the amount of mRNA available for translation in the cytoplasm.

Dexamethasone increases the number of RNA polymerase II molecules transcribing integrated mouse mammary tumor virus DNA and flanking mouse sequences

In mouse Ltk- cells that were transfected with recombinant bacteriophage DNA containing a complete proviral copy of an integrated endogenous mouse mammary tumor virus (MMTV) with its flanking cellular sequences, the newly acquired MMTV proviruses were transcribed in a glucocorticoid-responsive fashion. After hormone treatment of selected cell clones in culture we isolated the nuclei, elongated the nascent RNA chains in vitro, and determined the number of RNA polymerase II molecules on the transcribed MMTV DNA as well as on the flanking mouse DNA sequences. We found that the specific increase in the polymerase loading after hormone treatment is proportional to the increase in the amount of stable MMTV mRNA. When the DNA sequences which are responsible for hormone-receptor binding and for the increased MMTV mRNA levels were deleted, no increase in RNA polymerase II loading on MMTV DNA was observed. Nuclear RNA chains which were transcribed in response to hormone treatment were detected not only from the transfected MMTV DNA but also from the mouse DNA sequences adjacent to the 3' end of the provirus.

Regulation of histone mRNA production and stability in serum-stimulated mouse 3T6 fibroblasts

We measured the content and metabolism of histone mRNA in mouse 3T6 fibroblasts during a serum-induced transition from the resting to growing state. The content of several histone H3 and H2b mRNAs was measured by an S1 nuclease procedure. All of these increase in parallel by a factor of about 50 during S phase. However, the rate of H3 gene transcription increased only fivefold during this period, as determined in an in vitro transcription assay. This suggests that histone mRNA content is also controlled at the posttranscriptional level. When resting cells were serum stimulated in the presence of cytosine arabinoside, the rate of H3 gene transcription increased to about the same extent as that in control-stimulated cells. However, cytoplasmic H3 mRNA content increased only five to seven-fold. The half-life of H3 mRNA during S phase was about 4 to 5 h. When cytosine arabinoside was added to cells in the S phase, the half-life of the message decreased to about 15 min. The rapid turnover of H3 mRNA was prevented when the drug was added in the presence of cycloheximide or puromycin. The rate of H3 gene transcription decreased by only 35% after treatment with cytosine arabinoside. These results suggest that H3 gene transcription is not tightly coupled to DNA replication but is controlled temporally during the resting to growing transition. However, there is a correlation between the rate of DNA synthesis and the stability of histone H3 mRNA.

In vitro and in vivo analysis of the control of dihydrofolate reductase gene transcription in serum-stimulated mouse fibroblasts

We have studied the rate of transcription of the gene for dihydrofolate reductase (DHFR) in mouse 3T6 fibroblasts during serum-induced transitions between the resting (G0) and growing states. As a model system, we have used a methotrexate-resistant 3T6 cell line that overproduces DHFR and its mRNA about 300-fold, yet regulates the expression of the DHFR gene in the same manner as normal 3T6 cells. In previous studies, we showed that the rate of production of cytoplasmic DHFR mRNA relative to total mRNA is about 4 times lower in resting than in exponentially growing cells. The rate increases to the growing value by about 15 hr following serum stimulation of the resting cells. This increase appeared to be controlled by regulating the rate of synthesis of DHFR hnRNA. In this study, we analyze the transcription of the DHFR gene in more detail. We use a variety of labeling times and RNA extraction procedures to measure the rate of synthesis of DHFR hnRNA relative to total hnRNA in pulse-labeled cells or in nuclei isolated from cells at various times following serum stimulation. The amount of labeled DHFR RNA is determined by DNA-excess filter hybridization. In all cases, the relative rate of synthesis of DHFR hnRNA increases at the same time, and to the same extent, as the rate of production of DHFR mRNA, suggesting that the increase in DHFR mRNA production is due to a corresponding increase in the rate of transcription of the DHFR gene. The increase in DHFR gene transcription is not blocked by cytosine arabinoside, showing that the increase does not depend on gene duplication. In isolated nuclei, DHFR RNA synthesis is inhibited by alpha-amanitin (1 microgram/ml), indicating that the DHFR gene is transcribed by RNA polymerase II. Others have shown that when stationary phase cells are stimulated to proliferate, the increase in DHFR mRNA content is controlled primarily at the post-transcriptional level. Therefore, it appears that the rate of production of DHFR mRNA is controlled by different biochemical mechanisms when cells are in different physiological states.