RNA polymerase I transcription in confluent cells: Rb downregulates rDNA transcription during confluence-induced cell cycle arrest.

When 3T6 cells are confluent, they withdraw from the cell cycle. Concomitant with cell cycle arrest a significant reduction in RNA polymerase I transcription (80% decrease at 100% confluence) is observed. In the present study, we examined mechanism(s) through which transcription of the ribosomal genes is coupled to cell cycle arrest induced by cell density. Interestingly with an increase in cell density (from 3 - 43% confluence), a significant accumulation in the cellular content of hyperphosphorylated Rb was observed. As cell density increased further, the hypophosphorylated form of Rb became predominant and accumulated in the nucleoli. Co-immunoprecipitation experiments demonstrated there was also a significant rise in the amount of hypophosphorylated Rb associated with the rDNA transcription factor UBF. This increased interaction between Rb and UBF correlated with the reduced rate of rDNA transcription. Furthermore, overexpression of recombinant Rb inhibited UBF-dependent activation of transcription from a cotransfected rDNA reporter in either confluent or exponential cells. The amounts or activities of the rDNA transcription components we examined did not significantly change with cell cycle arrest. Although the content of PAF53, a polymerase associated factor, was altered marginally (decreased 38%), the time course and magnitude of the decrease did not correlate with the reduced rate of rDNA transcription. The results presented support a model wherein regulation of the binding of UBF to Rb and, perhaps the cellular content of PAF53, are components of the mechanism through which cell cycle and rDNA transcription are linked. Oncogene (2000) 19, 3487 - 3497

Different populations of progesterone receptor-steroid complexes in binding to specific DNA sequences: effects of salts on kinetics and specificity.

We previously reported evidence for two subpopulations of several classes of steroid receptors that could be distinguished by their requirement of a low molecular weight factor (Mr=700-3000 Da) for binding to nonspecific, calf thymus DNA-cellulose [Cavanaugh, A. H. and Simons Jr., S. S., Journal of Steroid Biochemistry and Molecular Biology, 48, 433-446 (1994)]. This factor appeared to be enriched in (NH4)2SO4 precipitates of nuclear extracts. Using human progesterone receptors (PRs) and biologically active DNA sequences in a modified avidin/biotin-coupled DNA (ABCD) binding assay, we now report a factor-mediated increase in PR binding to specific DNA sites that was indistinguishable from that seen with nonspecific sites. The main advantages of this modified assay are that both kinetic and equilibrium binding of receptor-steroid complexes to DNA can be directly monitored in solution. The ability of either Sephadex G-50 chromatography or sodium arsenite to prevent that binding which is increased by added factor supported the existence of PR subpopulations that are independent of the acceptor DNA sequence. The factor was found, surprisingly, to be low concentrations (> or = 5 mM) of (NH4)2SO4, which anomalously is partially excluded from Sephadex G-10 columns, and can be mimicked by some salts but not sodium arsenite. Kinetic analyses demonstrated that the mechanism of action of salt was to accelerate the rate of binding of PR. Salt also had a much greater effect on the nonspecific binding of PR, such that the ratio of specific to nonspecific DNA binding was greatest at elevated salt concentrations (approximately 75 mM) that afforded submaximal levels of PR binding to specific DNA sites. Further analysis of the DNA-bound receptors revealed that the smaller, A-form of PR is preferentially bound to specific DNA sequences both in the presence and in the absence of various salt concentrations. Thus, the differences in DNA binding of PR +/- salt do not correlate with the preferential binding of A or B isoform. The unequal behavior of PR subpopulations and/or isoforms for binding to specific DNA sequences offers added mechanisms for selective transcriptional regulation of genes in intact cells.

Androgen regulation of ribosomal RNA synthesis in LNCaP cells and rat prostate.

Androgen-dependent growth of prostate tissue has been well documented. An additional prerequisite for cellular growth is the accumulation of ribosomes. It is thus reasonable to hypothesize that ribosomal DNA (rDNA) transcription in prostate tissue must be stimulated by androgen either directly or indirectly. This hypothesis was tested using both LNCaP cells, an androgen-dependent tissue culture line and in a rat animal model. Nuclear run-on assays confirmed that the administration of DHT to LNCaP cells resulted in a two- to three-fold increase in the rate of rRNA synthesis when compared to cells maintained in the absence of androgen. Enzymatic analysis and Western blots were carried out to measure the amount (activity and mass) of RNA polymerase I in DHT treated LNCaP cells. These assays demonstrated that neither the catalytic activity of RNA polymerase I nor the amount of the enzyme varied in response to DHT. However, Western blots revealed that the amount of the auxiliary RNA polymerase I transcription factor UBF, was significantly increased (two- to three-fold) in cells grown in the presence of DHT. Similar experiments were carried out with prostatic tissue obtained from orchiectomized rats maintained on either placebo or testosterone pellets. In this model, both the catalytic activity as well as the amount of RNA polymerase I protein decreased. However, in agreement with the tissue culture model, UBF protein decreased in prostates from orchiectomized rats and was maintained in animals supplemented with testosterone. These lines of evidence are consistent with the hypothesis that androgens stimulate rRNA synthesis by increasing the quantities of the components of the rDNA transcription system.

The species-specific RNA polymerase I transcription factor SL-1 binds to upstream binding factor.

Transcription of the 45S rRNA genes is carried out by RNA polymerase I and at least two trans-acting factors, upstream binding factor (UBF) and SL-1. We have examined the hypothesis that SL-1 and UBF interact. Coimmunoprecipitation studies using an antibody to UBF demonstrated that TATA-binding protein, a subunit of SL-1, associates with UBF in the absence of DNA. Inclusion of the detergents sodium dodecyl sulfate and deoxycholate disrupted this interaction. In addition, partially purified UBF from rat cell nuclear extracts and partially purified SL-1 from human cells coimmunoprecipitated with the anti-UBF antibody after mixing, indicating that the UBF-SL-1 complex can re-form. Treatment of UBF-depleted extracts with the anti-UBF antibody depleted the extracts of SL-1 activity only if UBF was added to the extract prior to the immunodepletion reaction. Furthermore, SL-1 activity could be recovered in the immunoprecipitate. Interestingly, these immunoprecipitates did not contain RNA polymerase I, as a monospecific antibody to the 194-kDa subunit of RNA polymerase I failed to detect that subunit in the immunoprecipitates. Treatment of N1S1 cell extracts with the anti-UBF antibody depleted the extracts of SL-1 activity but not TFIIIB activity, suggesting that the binding of UBF to SL-1 is specific and not solely mediated by an interaction between UBF and TATA-binding protein, which is also a component of TFIIIB. These data provide evidence that UBF and SL-1 interact.

Activity of RNA polymerase I transcription factor UBF blocked by Rb gene product.

The protein encoded by the retinoblastoma susceptibility gene (Rb) functions as a tumour suppressor and negative growth regulator. As actively growing cells require the ongoing synthesis of ribosomal RNA, we considered that Rb might interact with the ribosomal DNA transcription apparatus. Here we report that (1) there is an accumulation of Rb protein in the nucleoli of differentiated U937 cells which correlates with inhibition of rDNA transcription; (2) addition of Rb to an in vitro transcription system inhibits transcription by RNA polymerase I; (3) this inhibition requires a functional Rb pocket; and (4) Rb specifically inhibits the activity of the RNA polymerase I transcription factor UBF (upstream binding factor) in vitro. This last observation was confirmed by affinity chromatography and immunoprecipitation, which demonstrated an interaction between Rb and UBF. These results indicate that there is an additional mechanism by which Rb suppresses cell growth, namely that Rb directly represses transcription of the rRNA genes.

Metal oxyanion stabilization of the rat glucocorticoid receptor is independent of thiols.

The ability of sodium molybdate, both to stabilize the steroid binding activity of glucocorticoid receptors and to prevent the activation of receptor-steroid complexes to a DNA binding species, has long been thought to involve thiols. Two receptor thiols in particular, Cys-656 and Cys-661 of rat receptors, have been suspected. The requirements for the action of molybdate, as well as two other metal oxyanions (tungstate and vanadate) known to exert the same effects as molybdate, have now been examined with receptors in which these thiols, or a third cysteine in the steroid binding cavity (Cys-640), have been mutated to serine. No mutation prevented any metal oxyanion from either stabilizing steroid-free receptors or blocking the activation of complexes for binding to nonspecific or specific DNA sequences. Thus, Cys-640, Cys-656, and Cys-661 are not required for any of the effects of molybdate, tungstate, or vanadate with rat glucocorticoid receptors. Studies with hybrid receptors, and with a 16-kDa steroid binding core fragment containing only 3 cysteines at positions 640, 656, and 661, indicated that no cysteine of the rat receptor was needed to maintain responsiveness to molybdate. Even when all of the thiol groups in crude cytosol were blocked by reaction with excess methyl methanethiol-sulfonate, each metal oxyanion was still able to stabilize the steroid binding of receptors. These results argue that molybdate, tungstate, and vanadate each interact with the receptor or an associated nonreceptor protein(s) in a manner that does not require thiols. An indirect mechanism of molybdate action was evaluated in light of the recent report that the whole cell actions are mediated by increased levels of intracellular cGMP. Under cell-free conditions, however, the effects of molybdate could not be reproduced by cGMP derivatives. Evidence consistent with a direct effect was that molybdate, tungstate, or vanadate each modified the kinetics of proteolysis of wild type receptors at 0 degrees C by trypsin, presumably due to induced conformational changes of the receptor. This alteration of trypsin digestion constitutes yet another effect of metal oxyanions on the glucocorticoid receptor.

Factor-assisted DNA binding as a possible general mechanism for steroid receptors. Functional heterogeneity among activated receptor-steroid complexes.

We previously reported that activated glucocorticoid receptor-steroid complexes from rat HTC cell cytosol exist as at least two sub-populations, one of which requires a low molecular weight (700-3000 Da) factor(s) for binding to DNA. This factor is removed by Sephadex G-50 chromatography and is found predominantly in extracts of crude HTC cell nuclei. We have now determined that factor is not limited to HTC cells since an apparently identical factor(s) was found in nuclear extracts of rat kidney and liver as well as human HeLa and MCF-7 cells. Furthermore, the DNA binding of a sub-population of human glucocorticoid receptors depends on factor. While these results were obtained with agonist (dexamethasone) bound receptors, a sub-population of HTC cell receptors covalently labeled by the antiglucocorticoid dexamethasone 21-mesylate also displayed factor-dependent DNA binding. This receptor heterogeneity was not an artifact of cell-free activation since the cell-free nuclear binding of dexamethasone mesylate labeled complexes was, as in intact cells, less than that for dexamethasone bound complexes. Earlier results suggested that the increased DNA binding with factor involved a direct interaction of receptor with factor(s). We now find that the factor-induced DNA binding is retained by amino terminal truncated (42 kDa) glucocorticoid receptors from HTC cells. Thus the ability of receptor to interact with factor(s) is encoded by the DNA and/or steroid binding domains. Two dimensional gel electrophoresis analysis of dexamethasone-mesylate labeled 98 kDa receptors revealed multiple charged isoforms for both sub-populations but no differences in the amount of the various isoforms in each sub-population. Finally, activated progesterone and estrogen receptor complexes were also found to be heterogeneous, with a similar, if not identical, small molecular weight factor(s) being required for the DNA binding of one sub-population. The observations that functional heterogeneity of receptors is not unique to glucocorticoid receptors, whether bound by an agonist or antagonist, and that the factor(s) is neither species nor tissue specific suggests that factor-assisted DNA binding may be a general mechanism for all steroid receptors.

Arsenite and cadmium(II) as probes of glucocorticoid receptor structure and function.

Low concentrations of arsenite, but not arsenate, and Cd2+ blocked steroid binding to the glucocorticoid receptors of HTC cells. Inhibition by arsenite was faster and occurred at lower concentrations than for Cd2+. Half-maximal inhibition of [3H]dexamethasone binding was seen after a 30-min preincubation with approximately 7 microM arsenite. The effect of arsenite and of Cd2+ appears to be mediated by a reaction with vicinal dithiols of the receptor as shown by (a) the reversal of arsenite inhibition by much lower concentrations of dithiothreitol (approximately 0.1 mM) than of beta-mercaptoethanol (approximately 10 mM); (b) the ability of both arsenite and Cd2+ to block [3H]dexamethasone 21-mesylate labeling of receptors but not of other thiol-containing proteins; and (c) the known selectivity of arsenite and of Cd2+ for reactions with vicinal dithiols. Arsenite forms a tight complex with these vicinal dithiols since the removal of loosely associated arsenite by gel exclusion chromatography did not reverse the inhibition of steroid binding. The effect of other ions on steroid binding was also examined. Half-maximal inhibition of binding occurred with approximately 5 microM selenite, whereas up to 300 microM Zn2+ was without effect. Much higher concentrations of arsenite were required for effects on unactivated and activated complexes. Arsenite slowly induced a loss of unactivated complexes but rapidly inhibited a portion of the DNA binding of activated complexes. Any effect on activation occurred at arsenite concentrations equal to or higher than those that inhibited DNA binding. In contrast, Cd2+ concentrations similar to those that block steroid binding caused a biphasic loss of unactivated complexes and a marginal loss of activated complexes. This is the first report of effects of arsenite on glucocorticoid receptors. These results confirm directly our earlier hypothesis that steroid binding to rat glucocorticoid receptors involves a vicinal dithiol (Miller, N. R., and Simons, S. S., Jr. (1988) J. Biol. Chem. 263, 15217-15225) and show that arsenite is a potent new reagent for probing receptor structure and function.

Glucocorticoid receptor binding to calf thymus DNA. 1. Identification and characterization of a macromolecular factor involved in receptor-steroid complex binding to DNA.

Activation of receptor-steroid complexes to a form with high affinity for DNA is a poorly understood process involving multiple components in addition to the holoreceptor. Employing rat HTC cells as the source of glucocorticoid receptor, we show that maximal receptor binding to calf thymus DNA is mediated by a previously unknown small molecular weight factor. This factor can be removed from cytosolic preparations of receptor by gel filtration chromatography. Salt extraction of crude nuclear pellets afforded much larger amounts of a similar DNA-binding activity factor. The cytoplasmic factor and the more abundant nuclear factor were identical on the basis of their similar physical properties. The factor was precipitable in the crude state with (NH4)2SO4 and stable to heat as well as freezing and thawing. Chromatography on DNA-cellulose revealed that the factor itself did not bind to DNA. The factor could be filtered through a Centricon C-3 microconcentrator (molecular weight cutoff approximately 3000) but was excluded from Sephadex G-10 columns. These parameters enable us to determine an apparent molecular weight of 700-3000 for this factor. The presence of large amounts of this factor in nuclei accounts for the previously unexplained observation that, following size exclusion chromatography, more activated complexes bind to nuclei than to DNA. These data indicate that some, but not all, of the activated complexes require factor to be able to bind to DNA. The predominantly nuclear localization of this factor, coupled with its ability to increase DNA binding, attests to the biological relevance of this factor in the whole cell action of receptor-glucocorticoid complexes.

Glucocorticoid receptor binding to calf thymus DNA. 2. Role of a DNA-binding activity factor in receptor heterogeneity and a multistep mechanism of receptor activation.

In the preceding paper [Cavanaugh, A. H., & Simons, S. S., Jr. (1990) Biochemistry (preceding paper in this issue)], we characterized an apparently identical factor in the cytosol and the nuclear extract of HTC cells that is required for the DNA binding of approximately 43% of the activated receptor-glucocorticoid complexes. In the present study, both those activated complexes that are influenced by this factor and the role of this factor in the process of activation are examined. We find that sodium arsenite inhibits only the DNA binding of those complexes that require factor. Conversely, methyl methane-thiolsulfonate inhibits the DNA binding of only those complexes that are independent of factor. These results provide direct chemical evidence for two populations of activated complexes. Double-reciprocal plots revealed that the increase in DNA binding with endogenous factor occurred by recruiting new complexes for DNA binding as opposed to increasing the binding affinity of existing complexes. These results further suggest that factor associates only with the receptor-steroid complex and does not additionally interact with DNA. A saturable association of factor with complexes was indicated since the amount of available factor in cytosolic solutions decreased after activation of the complexes. Sodium molybdate is known to inhibit the activation of HTC cell receptor-steroid complexes. When factor was added to complexes that had been subjected to activating conditions in the presence of the inhibitor sodium molybdate, no increased DNA binding was observed.(ABSTRACT TRUNCATED AT 250 WORDS)

Hormonal regulation of transcription of rDNA. Initiation of transcription by RNA polymerase I in vitro.

Transcription of mouse rDNA in vitro proceeds by an ordered mechanism of at least three steps. The first reaction involves formation of stable preinitiation complexes (Wandelt, C., and Grummt, I., (1983) Nucleic Acids Res. 11, 3795-3809; Cizewski, V., and Sollner-Webb, B. (1983) Nucleic Acids Res. 11, 7043-7056). Such complexes form at reduced temperature and in the absence of nucleoside triphosphates. The data presented here identify a second intermediate in the process of initiatio. This intermediate, called the convertible complex, forms slowly or not at all at 10 degrees C. Formation of the convertible complex requires the presence of ATP plus CTP or the dinucleotide ApC. ATP may be replaced with 5'-adenylyl imidotriphosphate. It is concluded that formation of the convertible complex is associated with formation of the first phosphodiester bond of nascent pre-rRNA. In the presence of all four nucleoside triphosphates, the convertible complex undergoes conversion to an elongation complex. This represents the third discernible step in the transcription process. The elongation complex is distinguished from the convertible complex by virtue of the observation that formation of the latter is inhibited by heparin, Sarkosyl, and 150 mM KCl. The elongation complex is not significantly affected by any of these substances. Moreover, formation of the convertible complex requires the glucocorticoid-regulated initiation factor designated TFIC.

The effects of cycloheximide upon transcription of rRNA, 5 S RNA, and tRNA genes.

The effects of inhibitors of protein synthesis upon transcription have been re-examined. Cycloheximide (1 microgram/ml) inhibits incorporation of uridine into RNA of P1798.S20 lymphosarcoma cells. Filter hybridization studies indicate that labeling of pre-rRNA is inhibited 60-80% after 1 h and quantitative S1 nuclease mapping reveals a corresponding decrease in the amount of cellular pre-rRNA. Cycloheximide also inhibits labeling of 5 S RNA and tRNA, but incorporation of uridine into poly(A+) RNA is unaffected. Transcription experiments carried out in nuclei from cycloheximide-treated cells indicate that the inhibitor causes a selective decrease in the activity of RNA polymerases I and III. Cell-free extracts from P1798.S20 were used to transcribe the cloned mouse rRNA gene, Syrian hamster 5 S RNA gene, and the Drosophila tRNAArg gene. Extracts from cycloheximide-treated cells were inhibited in this respect. Transcription of rRNA and 5 S RNA genes was inhibited by 90% after 2 h and 50% inhibition occurred within 20-30 min. Transcription of the tRNA gene was inhibited 75% after 2 h with a half-time of approximately 1 h. Inhibition was due neither to a direct effect of cycloheximide nor to the presence of nucleases or diffusible inhibitors of transcription. Moreover, transcription of rDNA in extracts from cycloheximide-treated cells could be restored by the addition of a partially purified initiation factor preparation. The data indicate that inhibition of protein synthesis results in rapid depletion of transcription factors that are required for initiation by RNA polymerases I and III. Among these is the glucocorticoid-regulated rDNA initiation factor designated TFIC.

Hormonal regulation of transcription of rDNA: glucocorticoid effects upon initiation and elongation in vitro.

Various parameters of transcription of cloned mouse rDNA have been examined using extracts from control P1798 cells and from cells treated 24 h with 0.1 microM dexamethasone. Highly purified RNA polymerase I from either source catalyzes nucleotidyl transfer (elongation) at a rate of approximately 30 nucleotides/sec. Extracts from hormone-treated cells are capable of forming stable, preinitiation complexes. The rates of stable complex formation are the same in extracts from control and hormone-treated cells. Nevertheless, initiation of transcription does not occur in extracts from hormone-treated cells. Initiation in such extracts may be restored by the addition of a partially purified RNA polymerase I initiation factor, designated TFIC. The data indicate that initiation by RNA polymerase I is a multi-step process. The first step involves the formation of stable, preinitiation complexes, as demonstrated by a number of groups. Initiation, per se, requires an additional protein, TFIC. Glucocorticoids and perhaps other mitogenic agents regulate transcription of rDNA by influencing the amount or activity of TFIC.

Glucocorticoid inhibition of initiation of transcription of the DNA encoding rRNA (rDNA) in lymphosarcoma P1798 cells.

Cell-free extracts of lymphosarcoma P1798 cell culture lines support faithful initiation upon the cloned mouse DNA encoding rRNA (rDNA) promoter, whereas extracts from cells treated for 16 hr with 0.1 microM dexamethasone cannot. Extracts from both sources transcribe the cloned 5S RNA gene in vitro and mixing experiments further demonstrate that inhibition of transcription of rDNA in vitro is not due to nucleases or inhibitors of transcription present in extracts from glucocorticoid-treated cells. Incubation of extracts from control cells at 45 degrees C for 15 min inactivates RNA polymerase I and abolishes transcription. Activity can be restored by the addition of partially purified RNA polymerase I from control cells and hormone-treated cells. Moreover, extracts from hormone treated cells can be reconstituted by the addition of a partially purified, heat-stable transcription factor from control cells.

The relationship between the activity of DNA-dependent RNA polymerase I and the rate of synthesis of rRNA in hepatoma cells in culture.

Cell culture lines were established from the transplantable mouse hepatomas H6 and H129. Both cell lines had a doubling time about 30 h when maintained in medium containing 5% foetal bovine serum. H6 cells contained about 3-4 times more DNA-dependent RNA polymerase I (Pol I; ribonucleoside triphosphate--RNA nucleotidyltransferase, EC 2.7.7.6) than did H129 cells. Moreover, the H6-cell enzyme was more heat-labile than that from H129 cells. Steady-state contents of 28S rRNA were measured in both cell lines. Exponentially growing cultures of H6 cells contained about 6.5pg of 28S rRNA/cell, and similar cultures of H129 cells contained about 5.8pg/cell. Stationary cultures of both cell lines contained about 2pg of 28S rRNA/cell. By two different techniques, the half-time for turnover of 28S rRNA was estimated to be 16-17h for both H6 and H129 cells. Knowing the turnover rate and the steady-state concentration, one may calculate that both H6 and H129 cells synthesize 28S rRNA at a rate of about 0.25 pg/h per cell. The amount of template-bound Pol I activity was similar in nuclei isolated from H6 and H129 cell cultures. These data indicate that, although H6 cells contained 3-4 times more Pol I than did H129 cells, both cell lines synthesized rRNA at about the same rate.

DNA-dependent RNA polymerase I from hepatomas: comparison of activity levels and properties.

Activity levels of DNA-dependent RNA polymerase I (Pol I; ribonucleoside triphosphate: RNA ribonucleotidyl transferase, E.C. 2.7.7.6, eucaryotic type I) have been compared in five transplantable murine hepatomas and livers of three inbred mouse host strains. Three tumors (H6, H4 and H134) contained about 350-450 units of Pol I activity/g of tissue. Two hepatomas (H129 and BW7756) contained about 120-150 units of activity/g of tissue. Livers contained about 100-150 units/g of tissue. Chromatographic comparisons revealed that hepatoma Pol I is slightly less anionic than the liver enzyme. Thermal denaturation studies were carried out using Pol I partially purified from a high-activity line hepatoma (H6), a low-activity line hepatoma (H129) and livers of the appropriate host strains. Pol I from H6 tumors was denatured at 40 degrees C with a half-time of 2 min. The enzyme from H129 tumors and host livers was denaturated with a half-time of 7 min. These data indicate that hepatoma H6 expressed a structural variant of Pol I. This is the first Pol I variant ever reported.

Factors underlying infertility in the alcoholic.

In an effort to identify the factor(s) contributing to loss in sexual competence in alcoholics, a pilot study was made of the interrelationships of hepatic disease, plasma hormone levels and importnce in 35 male patients in an alcohol unit. Contrary to previous reports, impotence was not a direct concomitant of hepatic disease, elevated sex hormone-binding globulin capacity or hyperestrinism. The most significant aberration found was a nearly 30% lower mean free testosterone concentration which appeared to be secondary to a mean total testosterone concentration 20% below that of the subjects with normal sexual function. We conclude from this that impotence results from testicular secretion impaired by the action of alcohol or its metabolite, acetaldehyde.