Transcription of specific genes in isolated nuclei by exogenous RNA polymerases

The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance

A 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3'-ends during repair. Another is synthesis of 5'ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.

Externally added DNA molecules support initiation of transcription in isolated nuclei from petunia

Nuclei isolated from protoplasts transfected with the pUC8CaMVCAT and pDO432 plasmids were able to support, in run off experiments, the synthesis of specific transcripts as was evident from analysis by dot blot hybridization. Also the addition of the above plasmids to nuclei, prepared from non-transfected protoplasts, supported the synthesis of specific transcripts. Dot blot analysis showed that most of the transcripts obtained were complementary to the relevant gene sequences. alpha-Amanitin, at concentrations which are known to block the activity of RNA polymerase II, significantly inhibited the synthesis of specific transcripts by the isolated nuclei. The transcription activity was found to be predominantly associated with the nuclear fraction while the transcription products (RNA molecules) appeared in the supernatant obtained following sedimentation of the nuclei.

Specific transcription and reinitiation of class III genes in wheat embryo nuclei and chromatin

Chromatin isolated from wheat germ embryos has a transcription efficiency for RNA polymerase III (pol III) closely approaching that for isolated wheat germ nuclei. Transcription in nuclei and chromatin is inhibited 5-10-fold by the addition of heparin, suggesting that free pol III molecules bind to chromatin and initiate transcription during thein vitro incubation. Nuclei were shown to have similar transcriptional activity in potassium chloride and potassium acetate. Nuclei and chromatin exhibited different salt optima for transcription. Neither nuclei nor chromatin were strongly stimulated by exogenous protein fractions. The data presented here suggest that in wheat germ nuclei the complete transcriptional apparatus is stably bound to the chromatin. Wheat germ nuclei may serve therefore as an enriched source for a solublein vitro transcription system.

The measurement of the production of tRNAMet1 in the Friend erythroleukemia cell

We have used the gene for tRNAMet1 as a hybridization probe to measure the production of tRNAMet1 in the Friend erythroleukemia cell. In this cell, the relative concentration of tRNAMet1 (i.e., the percentage of total steady-state tRNA representing tRNAMet1) is 1.60 +/- 0.18. To study the relative synthesis of tRNAMet1, cells were labeled in vivo with [3H]uridine for periods ranging from 4 to 24 h, and the tRNA was isolated. The fraction of newly-synthesized tRNA representing tRNAMet1 (1.72% +/- 0.11) does not change when different in vivo labeling times are used. This value is similar to the relative concentration of tRNAMet1 in the older steady-state tRNA (1.61% +/- 0.18). The similar relative synthesis values using different labeling times, plus evidence presented that the total tRNA population decays homogeneously (t 1/2 = 110 h) indicate that tRNAMet1 has a cytoplasmic stability similar to the general tRNA population, and that its concentration relative to the tRNA population is established within the nucleus or soon after exiting the nucleus. Measurements of the synthesis of tRNAMet1 in isolated nuclei, relative to the synthesis of total RNA polymerase III transcripts, showed that this relative synthesis (0.291% +/- 0.017) is only 17% of the relative concentration of tRNAMet1 in the cytoplasm, which may reflect the presence of sequences other than tRNA in total nuclear polymerase III transcripts.

Synthesis of 5S rRNA and putative precursor tRNAs in nuclei isolated from wheat embryos

Nuclei isolated from wheat embryos synthesize 4.5S precursor tRNAs and 5S rRNA in vitro. The precursor tRNAs can be processed to 4S tRNAs. Transcription of the tRNA and 5S rRNA genes is carried out by endogenous RNA polymerase III, and addition of exogenous wheat RNA polymerase III results in increased transcription on these genes. A number of experimental results suggest that proper initiation and accurate transcription of the tRNA and 5S rRNA genes occurs with isolated wheat nuclei.

Specific modulation of the transcription of cloned avian vitellogenin II gene by estradiol-receptor complex in vitro

Avian vitellogenin-cauliflower mosaic virus hybrid gene is effectively transcribed in vitro in the homologous embryonic liver nuclei system. The transcription of the hybrid gene is modulated by the addition of an estradiol-receptor preparation that has been shown to bind selectively to an upstream region of cloned vitellogenin gene. Stimulation of the transcription of cloned vitellogenin hybrid gene by estradiol receptor is alpha-amanitin sensitive, hormone dependent, and promoter specific. Simian virus 40 and Escherichia coli promoters are not stimulated by the estradiol-receptor complex. The endogenous silent vitellogenin II gene (wild type) present in the nuclei is not turned on by the addition of estradiol-receptor complex. Deletion or inversion of the DNA sequence where the estradiol-receptor complex binds results in the complete suppression of the in vitro stimulation of transcription by estradiol receptor. Correct initiation of the transcription was demonstrated by primer extension studies of the newly synthesized RNA.

Transcription renders chromatin resistant to micrococcal nuclease digestion

When isolated HeLa cell nuclei were preincubated under transcription conditions with excess E. coli RNA polymerase, chromatin DNA became relatively resistant to digestion by micrococcal nuclease. Quantitation of the DNA content in nuclei after enzyme digestion revealed that approximately twice as much nuclease was required to give the same levels of release of DNA fragments from transcribed as from untranscribed nuclei. Resistance increased with the amount of polymerase and with the time of preincubation. Since the resistance to nuclease was not observed in the presence of rifampicin or by preincubation without UTP, both RNA chain initiation and elongation were considered to be essential for the manifestation of resistance. However, when DNase 1 was used as a probe, such a change in chromatin DNA was not detected.

Transfer RNA and ribosomal RNA are synthesized from the same pyrimidine nucleotide pool

We have tested the hypothesis [Wiegers, Kramer, Klapproth & Hilz (1976) Eur. J. Biochem. 64. 535-540] that the synthesis of rRNA in the nucleolus may have a partially independent supply of nucleoside triphosphates that is not completely suppressed when cells are supplied with exogenous nucleosides. For the slime mould, Physarum polycephalum, and Chinese hamster ovary cells in culture, the specific activities (3H/32P) of UMP and CMP in tRNA, which is synthesised in the nucleoplasm, and rRNA were compared after continuous labelling with [3H]uridine and [32P]phosphate. No differences were found, suggesting that transcription throughout the nucleus draws on a common supply of pyrimidine triphosphates that is uniformly labelled from exogenous [3H]uridine. As a control of the radioactive labelling schedule, a similar experiment was carried out with the prokaryote, Escherichia coli, and identical results were obtained.

Synthesis of low molecular weight RNA components in cells with a temperature-sensitive polymerase II

AF 8 cells are a mutant cell line of baby hamster kidney cells with a temperature-sensitive polymerase II activity. When these cells grow at the non-permissive temperature (40 degrees C) the syntheseis of low molecular weight RNA components D, C and A is preferentially inhibited, whereas the synthesis of rRNA, tRNA, 5 S RNA and component L is affected only a little or not at all. These results indicate that polymerase II catalyzes the synthesis of components D, C and A.

Modulation of transcription from chromatin assembled in vitro

A small plasmid DNA was assembled into chromatin in vitro by incubation in an extract prepared frog eggs of Xenopus laevis. The plasmid DNA contrained the regulatory region of the Escherichia coli lac operon, the transcription of which is under positive regulation by catabolite activator protein (CAP) and negative regulation by lac repressor. After incubation in the egg extract the plasmid DNA acquired approximately 60% of the predicted maximum number of nucleosomes. Chromatin was treated with protein and DNA cross-linking agents prior to transcriptin in order to demonstrate that regions of the DNA organized into nucleosomes served as templates for transcription. Cross-linking abolished transcription of chromatin but had no effect on transcription of the DNA, suggesting that transcription of untreated chromatin was not solely attributable to nucleosome-free regions. In support of this conclusion, the average size of the RNA transcribed from chromatin was approximately 1000 bases, which was approximately 5 times longer than the average distance between nucleosomes. Transcription of in vitro assembled plasmid chromatin by E. coli RNA polymerase was stimulated by catabolite activator protein. The CAP-mediated stimulation of transcription was detectable as an increase in total transcription that was specific to chromatin made from a plasmid containing the lac regulatory DNA sequences. The specific increase in the amount of RNA whose synthesis was initiated within the lac region was demonstrated by hybridization of transcription products to complementary DNA fragments bound to nitrocellulose filters. Preliminary investigation of the action of lac repressor suggested that it also modulated transcription from the chromatin template.

Transcription of Friend virus proviral sequences in isolated nuclei

Transcription studies using isolated Friend nuclei and Escherichia coli polymerase are presented. Combination of the techniques of thiol-Sepharose chromatography and cDNA-Sepharose hybridisation has resulted in a system in which the transcription of the Friend virus proviral sequences with endogenous and E. coli polymerase can be examined. The results show that the percentage of Friend viral-specific sequences in RNA transcribed by E. coli RNA polymerase and by endogenous RNA polymerase in isolated nuclei are similar. The percentage of viral-specific sequences synthesized in isolated nuclei is similar to that found in Friend cell nuclear RNA.

In vitro synthesis of a 5S RNA precursor by isolated nuclei of rat liver and HeLa cells

Isolated rat liver nuclei were incubated under appropriate conditions in the presence of 0.5 micrograms/ml alpha-amanitin and an RNAase inhibitor prepared from cytosol fraction, together with alpha-32P-UTP or alpha-32P-CTP and three other nucleoside triphosphates. RNA extracted by an SDS-hot phenol procedure was fractionated with sucrose density gradient centrifugation followed by acrylamide gel electrophoresis. Fingerprint analysis of the in vitro synthesized "5S" RNA, which was slightly larger than mature 5S RNA on gel electrophoresis, showed that it contained all the sequences of mature 5S RNA except for the oligonucleotide at the 3' end. Instead, it contained two additional spots which were not present in mature 5S RNA. Analysis of the extra spots revealed that they were derived from the 3' end of the in vitro synthesized "5S RNA, which were sequenced tentatively as -CUUGAUGCUUoh (extra sequence underlined). The 5' end of the product was (p)pGU--. Isolated HeLa cell nuclei synthesized similar sized "5S" RNA under the same conditions. We conclude from these results that in isolated nuclei of these mammalian cells RNA polymerase III starts transcription of 5S RNA gene at the same site as the 5' end of mature 5S RNA, proceeds toward the 3' direction and stops at a site probably 8 nucleotides downstream from the 3' end of mature 5S RNA. Experiments with a short pulse and with various "chases" have demonstrated the presence of a short-lived precursor 5S RNA which is similar in size and sequence to in vitro "5S" RNA, suggesting that 5S RNA is synthesized in vivo as a longer precursor molecular as demonstrated in this in vitro system, and is rapidly processed into mature 5S RNA.

Effects of cytosol on transcription in isolated simian-virus-40-infected nuclei

The transcription in vitro of nuclei isolated from monkey kidney cells infected with simian virus 40 was stimulated by a cytosol fraction from the same uninfected cells. Transcription in nuclei was inhibited 60--80% by 0.1 microgram/ml of alpha-amanitin, in the presence or in the absence of the cytosol preparation. Treatment of nuclei after transcription in vitro with 0.02 M EDTA preferentially solubilized viral-specific RNA partially bound to the viral chromatin. The increase in incorporation into total RNA seen in the presence of cytosol was not paralleled by any detectable increase in transcription of viral sequences as shown by RNA . DNA hybridizations.

Biosynthesis of low molecular weight RNA in mouse myeloma cells

The low molecular weight RNAs in the nucleus and cytoplasm of mouse myeloma cells have been characterized. There are major nuclear species (other than 5-S and tRNA), four of which contain 'capped' 5' termini. There are three major small cytoplasmic RNAs none of which contain 'caps'. The biosynthesis of the nuclear species when studied using [3H]adenosine as an RNA precursor is characterized by a rapid, transient appearance in the cytoplasm, followed by fixation in the nucleus. Within 15 min, the amount in the cytoplasm has reached a steady-state level maintained for 60 min, while the accumulation in nuclei is linear after a short lag (less than 5 min). When biosynthesis is studied using [Me-3H]methionine as a precursor, much less labeled RNA is present in the cytoplasm, suggesting that methylation may immediately precede fixation into the nucleus.

Analysis of RNA initiated in isolated mouse myeloma nuclei using purine nucleoside 5'[gamma-S]triphosphates as affinity probes

The purine ribonucleoside triphosphate analogues adenosine 5'[gamma-S]triphosphate and guanosine 5'[gamma-T]triphosphate were used as affinity probes for studying RNA chain initiation in isolated nuclei from the mouse myeloma 66.2 cell line. Transcripts initiated with either nucleotide analogue were isolated by affinity chromatography on a mercury-agarose affinity column. The binding was specific and dependent upon the inclusion of the sulfur nucleotide analogues in the in vitro synthetic reaction. Several lines of evidence indicate that the affinity-labeled RNA is initiated in vitro. First, the sulfur nucleotide is recovered in high yield as a single nucleoside 5'[gamma-S]triphosphate 2',3'-monophosphate product following alkaline hydrolysis of RNA bound to the affinity column. Second, authentic ribosomal 5S RNA is known to initiate with GTP; in vitro 5S RNA is bound to mercury-agarose only if [gamma-S]GTP is used as the affinity label in the synthesis, and not if [gamma-S]ATP is used. Under the conditions studied, nuclei incorporated 1.2--2.4 pmole of UMP per 10(6) nuclei per min, and the rate of synthesis was unaffected by substitution of the nucleotide analogues for the normal nucleotides. The percentage of the total RNA synthesized that was incorporated into sequences initiated in vitro was 7.8 +/- 1.5% with [gamma-S]ATP and 9.6 +/- 6.4% with [gamma-S]GTP. The size of the total RNA synthesized, determined by sedimentation on sucrose density gradients containing dimethylsulfoxide, ranged from less than 5S to 45S, and the size of the affinity-labeled sequences ranged from less than 5S to 28S. Approximately half of the incorporation into RNA initiated in vitro was sensitive to a concentration of alpha-amanitin which selectively inhibits polymerase II activity. Most of the remaining incorporation into initiated sequences can be abolished by concentrations of alpha-amanitin that are inhibitory for polymerase III activity. Over 70% of the total incorporation into ribosomal 5S RNA transcripts was into sequences initiated in vitro. This initiation was catalyzed by polymerase III and was specific for GTP as the initiating nucleotide. The RNAase T1 fingerprint of the newly initiated 5S RNA indicates that this gene is accurately initiated and faithfully elongated in vitro. The use of these affinity label probes provides much greater sensitivity for studying the initiation of RNA in vitro.