5,6-dichloro-1-beta-ribofuranosylbenzimidazole enhances premature termination of late transcription of simian virus 40 DNA

CDK9: A Comprehensive Review of Its Biology, and Its Role as a Potential Target for Anti-Cancer Agents

Cyclin-dependent kinases (CDKs) are proteins pivotal to a wide range of cellular functions, most importantly cell division and transcription, and their dysregulations have been implicated as prominent drivers of tumorigenesis. Besides the well-established role of cell cycle CDKs in cancer, the involvement of transcriptional CDKs has been confirmed more recently. Most cancers overtly employ CDKs that serve as key regulators of transcription (e.g., CDK9) for a continuous production of short-lived gene products that maintain their survival. As such, dysregulation of the CDK9 pathway has been observed in various hematological and solid malignancies, making it a valuable anticancer target. This therapeutic potential has been utilized for the discovery of CDK9 inhibitors, some of which have entered human clinical trials. This review provides a comprehensive discussion on the structure and biology of CDK9, its role in solid and hematological cancers, and an updated review of the available inhibitors currently being investigated in preclinical and clinical settings.

The p38 signaling pathway upregulates expression of the Epstein-Barr virus LMP1 oncogene

The Epstein-Barr virus (EBV)-encoded LMP1 oncogene has a role in transformation, proliferation, and metastasis of several EBV-associated tumors. Furthermore, LMP1 is critically involved in transformation and growth of EBV-immortalized B cells in vitro. The oncogenic properties of LMP1 are attributed to its ability to upregulate anti-apoptotic proteins and growth signals. The transcriptional regulation of LMP1 is dependent on the context of cellular and viral proteins present in the cell. Here, we investigated the effect of several signaling pathways on the regulation of LMP1 expression. Inhibition of p38 signaling, using p38-specific inhibitors SB203580 and SB202190, downregulated LMP1 in estrogen-induced EREB2.5 cells. Similarly, p38 inhibition decreased trichostatin A-induced LMP1 expression in P3HR1 cells. Exogenous expression of p38 in lymphoblastoid cell lines (LCLs) led to an increase in LMP1 promoter activity in reporter assays, and this activation was mediated by the previously identified CRE site in the promoter. Inhibition of p38 by SB203580 and p38-specific small interfering RNA (siRNA) also led to a modest decrease in endogenous LMP1 expression in LCLs. Chromatin immunoprecipitation indicated decreased binding of CREB-ATF1 to the CRE site in the LMP1 promoter after inhibition of the p38 pathway in EREB2.5 cells. Taken together, our results suggest that an increase in p38 activation upregulates LMP1 expression. Since p38 is activated in response to stimuli such as stress or possibly primary infection, a transient upregulation of LMP1 in response to p38 may allow the cells to escape apoptosis. Since the p38 pathway itself is activated by LMP1, our results also suggest the presence of an autoregulatory loop in LMP1 upregulation.

Alternative polyadenylation produces two major transcripts of Alix

The mammalian adaptor protein Alix participates in multiple cellular processes. Since mouse Alix cDNA detects two distinct transcripts of approximately 3.5 and approximately 7.0 kb in various mouse tissues, it is possible that there exist isoforms of Alix protein that perform varied biological functions. In this study, we first demonstrate that four different anti-Alix monoclonal antibodies immunoblot the single Alix protein in nine different mouse tissues. We then show that the two transcripts of 3.2 and 6.4 kb are widely expressed in various human tissues and cell lines. These two transcripts are generated from the same Alix gene localizing at 3p22.3 via alternative polyadenylation, thus containing an identical open reading frame. However, the 3.2-kb transcript is much more active in translation than the 6.4-kb transcript in a randomly selected cell line. These results eliminate the possibility that the two transcript variants encode different isoforms of Alix protein and suggest that alternative polyadenylation is one of the mechanisms controlling Alix protein expression.

Contrasting effects of matrix protein on apoptosis in HeLa and BHK cells infected with vesicular stomatitis virus are due to inhibition of host gene expression

Vesicular stomatitis virus (VSV) is a potent inducer of apoptosis in host cells. Recently, it has been shown that two VSV products are involved in the induction of apoptosis, the matrix (M) protein, and another viral product that has yet to be identified (S. A. Kopecky et. al., J. Virol. 75:12169-12181, 2001). Comparison of recombinant viruses containing wild-type (wt) or mutant M proteins showed that wt M protein accelerates VSV-induced apoptosis in HeLa cells, while wt M protein delays apoptosis in VSV-infected BHK cells. Our hypothesis to explain these results is that both effects of M protein are due to the ability of M protein to inhibit host gene expression. This hypothesis was tested by infecting cells with an M protein mutant virus defective in the inhibition of host gene expression (rM51R-M virus) in the presence or absence of actinomycin D, another inhibitor of host gene expression. Actinomycin D accelerated induction of apoptosis of HeLa cells infected with rM51R-M virus and delayed apoptosis in BHK cells infected with rM51R-M virus, similar to the effects of wt M protein. The idea that the induction of apoptosis by M protein in HeLa cells is due to its ability to inhibit host gene expression was further tested by comparing the activation of upstream caspase pathways by M protein versus that by actinomycin D or 5,6-dichlorobenzimidazole riboside (DRB). Expression of M protein activated both caspase-8 and caspase-9-like enzymes, as did treatment with actinomycin D or DRB. Induction of apoptosis by M protein, actinomycin D, and DRB was inhibited in stably transfected HeLa cell lines that overexpress Bcl-2, an antiapoptotic protein that inhibits the caspase-9 pathway. A synthetic inhibitor of caspase-8, Z-IETD-FMK, did not inhibit induction of apoptosis by M protein, actinomycin D, or DRB. Taken together, our data support the hypothesis that the induction of apoptosis by M protein is caused by the inhibition of host gene expression and that the caspase-9 pathway is more important than the caspase-8 pathway for the induction of apoptosis by M protein and other inhibitors of host gene expression.

Expression, regulation, and activity of ABCA1 in human cell lines

Mutations in the ATP-binding cassette transporter A1 (ABCA1) gene cause familial high-density lipoprotein deficiency and Tangier disease. ABCA1 plays a crucial role in active apolipoprotein A-I (apoA-I) lipidation, a key step in reverse cholesterol transport. We compared ABCA1 transcriptional regulation and cholesterol efflux in human skin fibroblasts, monocyte-derived macrophages and hepatocytes (HepG2). 8-Br-cAMP did not increase ABCA1 transcription in these tissues compared to mouse macrophages. We found that ABCA1 is differentially regulated among tissues. While transcription in HepG2 appears to be constitutive, sterols stimulate ABCA1 transcription in fibroblasts and monocyte-derived macrophages. ApoA-I promoted cholesterol efflux in fibroblasts, macrophages, and HepG2. Cholesterol homeostasis in fibroblasts is tightly regulated, and ABCA1 mRNA closely follows the cellular mass of free cholesterol (dose- and time-dependent manner). To further determine the mechanism used by fibroblasts to maintain sterol balance, we used a competitive inhibition approach with geranylgeranyl pyrophosphate (GGPP) to block the LXR induction pathway. GGPP blocked basal, 22-(R)-hydroxycholesterol- and cholesterol-induced ABCA1 expression. Taken together, these results demonstrate that: (1) ABCA1 expression varies among tissues, and (2) cholesterol conversion to hydroxycholesterol is an important mechanism for the maintenance of cholesterol homeostasis in fibroblasts.

A selective effect of Mpl ligand on mRNA stabilization during megakaryocyte differentiation

Megakaryocytes, the platelet precursors, are induced to differentiate in response to Mpl ligand. Here we report that stability of the megakaryocyte-specific platelet factor 4 (PF4) mRNA is substantially augmented in the presence of Mpl ligand. This stabilization requires protein synthesis, but the 3'-untranslated region of PF4 mRNA is not sufficient for granting the effect. This cytokine also significantly or mildly stabilizes Mpl receptor or GAPDH mRNAs, respectively, in contrast to a previously reported lack of effect on P2Y(1) receptor mRNA. Our study is the first to suggest that Mpl ligand-induced lineage specification is also determined by message stabilization.

Rapid induction of nuclear transcripts and inhibition of intron decay in response to the polymerase II inhibitor DRB

The transcriptional inhibitor 5, 6-dichloro-1-beta-d-ribofuranosylbenzimidazole (DRB) is an adenosine analog that has been shown to cause premature transcriptional termination and thus has been a useful tool to identify factors important for transcriptional elongation. Here, we establish an efficient system for studying DRB-sensitive steps of transcriptional elongation. In addition, we establish two novel effects of DRB not previously reported: intron stabilization and the induction of long transcripts by a mechanism other than premature termination. We found that DRB had a biphasic effect on T-cell receptor-beta (TCRbeta) transcripts driven by a tetracycline (tet)-responsive promoter in transfected HeLa cells. In the first phase, DRB caused a rapid decrease (within five minutes) of pre-mRNA and its spliced intron (IVS1(Cbeta1)), consistent with the known ability of DRB to inhibit transcription. In the second phase (which began ten minutes to two hours after treatment, depending on the dose), DRB dramatically increased the levels of IVS1(Cbeta1)-containing transcripts by a mechanism requiring de novo RNA synthesis. DRB induced the appearance of short 0.4 to 0.8 kb TCRbeta transcripts in vivo, indicating DRB enhances premature transcriptional termination. A approximately 475 nt prematurely terminated transcript (PT) was characterized that terminated at an internal poly(A) tract in the intron IVS1(Cbeta1). We identified three other effects of DRB. First, we observed that DRB induced the appearance of heterodisperse TCRbeta transcripts that were too long ( approximately 1 kb to >8 kb) to result from the type of premature termination events previously described. Their production was not promoter-specific, as we found that long transcripts were induced by DRB from both the tet-responsive and beta-actin promoters. Second, DRB upregulated full-length normal-sized c-myc mRNA, which provided further evidence that DRB has effects besides regulation of premature termination. Third, DRB stabilized lariat forms of the intron IVS1(Cbeta1), indicating that DRB exerts post-transcriptional actions. We propose that our model system will be useful for elucidating the factors that regulate RNA decay and transcriptional elongation in vivo.

The binding of the alpha subunit of protein kinase CK2 and RAP74 subunit of TFIIF to protein-coding genes in living cells is DRB sensitive

In a previous report, we documented that a major portion of the nuclear protein kinase CK2alpha (CK2alpha) subunit does not form heterooligomeric structures with the beta subunit, but it binds tightly to nuclear structures in an epithelial Chironomus cell line. We report here that the CK2alpha, but not beta, subunit is co-localized with productively transcribing RNA polymerase II (pol II) on polytene chromosomes of Chironomus salivary gland cells. Likewise, the RAP74 subunit ofTFIIF, a potential substrate for CK2, is co-localized with pol II. The occupancies of chromosomes with the CK2alpha and RAP74 subunits are sensitive to DRB, an inhibitor of pol II-based transcription and the activity of CK2 and pol II carboxyl-terminal kinases. DRB alters the chromosomal distribution of the CK2alpha and RAP74 subunits: there is a time-dependent clearance from the chromosomes of CK2alpha and RAP74 subunits, which coincides in time the completion and release of preinitiated transcripts after addition of DRB. The results suggest that both the CK2alpha and RAP74 subunits travel with the elongating pol II molecules along the DNA template during the entire transcription cycle. No detectable re-association of CK2alpha and RAP74 with the promoters takes, however, place after the completion of the preinitiated transcripts in the presence of DRB. In contrast, the binding of hypophosporylated pol II and TFIIH to the active gene loci is not abolished by the DRB regimen. Our data are consistent with the possibility that in living Chironomus salivary gland cells, DRB interferes with the recruitment of TFIIF, but not of TFIIH, to the promoter by interference with the activity of the CK2alpha subunit enzyme and phosphorylation of RAP74 and thereby DRB blocks transcription initiation.

Lithium increases melanin-concentrating hormone mRNA stability and inhibits tyrosine hydroxylase gene expression in PC12 cells

Melanin-concentrating hormone (MCH) is a cyclic peptide involved in the regulation of food-intake behaviour and stress response in mammals. Expression of the MCH gene predominates in hypothalamic neurons. Mechanisms governing the regulation of expression of MCH gene in established cell lines were not explored yet. Here, we analysed the actions of nerve growth factor (NGF), dexamethasone, forskolin and lithium on MCH mRNA levels in the PC12 pheochromocytoma cell line. We compared them with those observed on tyrosine hydroxylase (TH) mRNA, constitutively expressed in PC12 cells, and neurotensin (NT) mRNA, taken as a control. In untreated cells, MCH RNA species of high molecular weight were found. Exposure of cells at a combination of NGF and lithium resulted in decreased expression of these MCH RNAs and in the transient production of mature MCH mRNA. Strikingly, after short exposure of PC12 cells to NGF, lithium per se elicited a marked increase in MCH mRNA levels whilst it exerted a potent inhibitory action on TH mRNA expression. Detailed investigations revealed that lithium enhanced MCH mRNA expression through post-transcriptional mechanisms whereas it regulated TH gene expression mainly at the level of transcription. These results demonstrate that lithium, an agent widely used for treatment of manic depressive illness, can exert an opposite effect on MCH and TH mRNA production in PC12 cells. The MCH gene system in NGF-treated PC12 cells provides a good opportunity for studying the effect of lithium on gene expression at post-transcriptional levels in a neuron-like cellular model.

P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro

To identify novel inhibitors of transcriptional activation by the HIV Tat protein, we used a combination of in vitro and in vivo Tat-dependent transcription assays to screen >100,000 compounds. All compounds identified blocked Tat-dependent stimulation of transcriptional elongation. Analysis of a panel of structurally diverse inhibitors indicated that their target is the human homolog of Drosophila positive transcription elongation factor b (P-TEFb). Loss of Tat transactivation in extracts depleted of the kinase subunit of human P-TEFb, PITALRE, was reversed by addition of partially purified human P-TEFb. Transfection experiments with wild-type or kinase knockout PITALRE demonstrated that P-TEFb is required for Tat function. Our results suggest that P-TEFb represents an attractive target for the development of novel HIV therapeutics.

A protein synthesis-dependent late phase of cerebellar long-term depression

Synthesis of new protein has been shown to be required for establishment of a late phase in hippocampal long-term potentiation. Whether a similar requirement is needed to produce the late phase of long-term depression (LTD) remains to be determined. Application of transcription inhibitors or of the translation inhibitor anisomycin, immediately, but not 30 min after glutamate/depolarization conjunction, attenuated a late phase of cerebellar LTD in culture. LTD, produced in a perforated outside-out macropatch of Purkinje neuron dendrite, which lacks nuclear material, returned to baseline values with a time course paralleling that observed with protein synthesis inhibitors in intact cultured Purkinje neurons. These findings suggest that there is a distinct late phase of cerebellar LTD that is dependent upon postsynaptic protein synthesis.

RNA polymerase II inhibitor, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) causes erythroleukemic differentiation and transcriptional activation of erythroid genes

Friend virus-transformed murine erythroleukemia (MEL) cells are a useful system for studying the regulation of erythroid growth and differentiation. As a manifestation of the leukemic process, these erythroblasts are blocked in their ability to terminally differentiate. However, this block is reversible as a variety of different agents are capable of inducing differentiation of these malignant erythroblasts. The mechanisms by which these agents cause differentiation remains unknown. We report here that 5,6-dichlorobenzimidazole (DRB), which inhibits RNA polymerase II by causing premature termination of transcription, induces differentiation of these cells, including the transcriptional activation of erythroid genes. The effects of DRB on nonerythroid gene expression and on cell growth are substantially different than that of the commonly used inducer, dimethyl sulfoxide (DMSO). The shared ability of DMSO, DRB, and other unrelated agents to induce erythroid gene expression in MEL cells while having differing effects on nonerythroid gene expression and on cell growth suggests that expression of the terminally differentiated phenotype represents a common pathway that can be triggered by different mechanisms.

Phosphorylation dependence of the initiation of productive transcription of Balbiani ring 2 genes in living cells

Using polytene chromosomes of salivary gland cells of Chironomus tentans, phosphorylation state-sensitive antibodies and the transcription and protein kinase inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), we have visualized the chromosomal distribution of RNA polymerase II (pol II) with hypophosphorylated (pol IIA) and hyperphosphorylated (pol II0) carboxyl-terminal repeat domain (CTD). DRB blocks labeling of the CTD with 32Pi within minutes of its addition, and nuclear pol II0 is gradually converted to IIA; this conversion parallels the reduction in transcription of protein-coding genes. DRB also alters the chromosomal distribution of II0: there is a time-dependent clearance from chromosomes of phosphoCTD (PCTD) after addition of DRB, which coincides in time with the completion and release of preinitiated transcripts. Furthermore, the staining of smaller transcription units is abolished before that of larger ones. The staining pattern of chromosomes with anti-CTD antibodies is not detectably influenced by the DRB treatment, indicating that hypophosphorylated pol IIA is unaffected by the transcription inhibitor. Microinjection of synthetic heptapeptide repeats, anti-CTD and anti-PCTD antibodies into salivary gland nuclei hampered the transcription of BR2 genes, indicating the requirement for CTD and PCTD in transcription in living cells. The results demonstrate that in vivo the protein kinase effector DRB shows parallel effects on an early step in gene transcription and the process of pol II hyperphosphorylation. Our observations are consistent with the proposal that the initiation of productive RNA synthesis is CTD-phosphorylation dependent and also with the idea that the gradual dephosphorylation of transcribing pol II0 is coupled to the completion of nascent pol II gene transcripts.

Expression of the transcription factor, Spi-1 (PU.1), in differentiating murine erythroleukemia cells Is regulated post-transcriptionally. Evidence for differential stability of transcription factor mRNAs following inducer exposure

Increased expression of the transcription factor Spi-1 (PU.1) results from retroviral insertion in nearly all Friend spleen focus-forming virus-transformed murine erythroleukemia cell lines and exposure of these cells to Me2SO, induces their differentiation and decreases Spi-1 mRNA level by 4-5-fold. While these results suggest that alterations in Spi-1 expression have significant effects on erythroblast growth and differentiation, neither the cause nor the effect of the decrease in Spi-1 expression that follows Me2SO exposure has been established. The experiments described here demonstrate that the effect of inducers on Spi-1 expression is regulated post-transcriptionally. Nuclear run-off transcriptions demonstrated that Spi-1 transcription was not decreased following Me2SO exposure. Additionally, expression of a recombinant Spi-1 mRNA under transcriptional control of a constitutively active Rous sarcoma virus promoter was regulated identically to endogenous Spi-1 mRNA. The ability of Me2SO to destabilize Spi-1 mRNA was selective, as the stability of the erythroid transcription factors GATA-1 and NF-E2 were not similarly effected. The effect of Me2SO on the stability of Spi-1 mRNA provides a novel means of altering gene expression in these cells and is likely to have significance for the differentiation of these cells.

Purification of P-TEFb, a transcription factor required for the transition into productive elongation

Production of full-length runoff transcripts in vitro and functional mRNA in vivo is sensitive to the drug 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). We previously proposed the existence of an activity, P-TEF (positive transcription elongation factor) that functions in a DRB-sensitive manner to allow RNA polymerase II elongation complexes to efficiently synthesize long transcripts (Marshall, N. F. and Price, D. H. (1992) Mol. Cell. Biol. 12, 2078-2090). We have fractionated nuclear extracts of Drosophila melanogaster Kc cells and identified three activities, P-TEFa, factor 2, and P-TEFb, that are directly involved in reconstructing DRB-sensitive transcription. P-TEFb is essential for the production of DRB-sensitive long transcripts in vitro, while P-TEFa and factor 2 are stimulatory. P-TEFb activity is associated with a protein comprising two polypeptide subunits with apparent molecular masses of 124 and 43 kDa. Using a P-TEFb-dependent transcription system, we show that P-TEFb acts after initiation and is the limiting factor in the production of long run-off transcripts.

Minute virus of mice infection modifies cellular transcription elongation

Our previous observations indicated that upon infection with minute virus of mice (MVM), Ehrlich ascites cells lose a transcription elongation activity which is essential for the readthrough of the MVM attenuator. This was monitored by the ability of extracts from uninfected but not from infected cells to support readthrough of the P4 attenuator when added to partially purified transcription elongation complexes. We have investigated the nature of this change in transcription elongation following MVM infection. In this communication, we show that infection of Ehrlich ascites cells with MVM leads to a general shift in the length of nascent mRNA synthesized in isolated nuclei and separated by sucrose gradients. Furthermore, infection leads to attenuation of transcription of the cellular gene c-fos but not c-myc. We show biochemical evidence to support a model by which, following MVM infection, there is a functional reduction in the activity of a TFIIS-like general transcriptional elongation activity.

Characterization of an inducible promoter system to investigate decay of stable mRNA molecules

We have developed a system in which the decay of stable mRNAs can be studied without the use of inhibitors of transcription. The Drosophila hsp70 heat shock promoter linked to the bovine growth hormone (BGH) gene was used to establish stable cell lines in which the BGH gene is transcribed in a conditional manner. The BGH mRNA is synthesized only after induction at 43 degrees C. Following a brief period of re-equilibration at 37 degrees C during which transcription of the heat shock-driven gene ceases, the stable BGH mRNA decays with typical first-order kinetics. Hence, the decay of the mRNA can be studied without assumptions regarding radioactive labeling of precursor pools or transcriptional inhibitors. The system is applicable to any stable mRNA.

Enhancement of hepatitis A propagation in tissue culture with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole

The adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) was found to increase the production of hepatitis A (HAV) antigen in two monkey kidney cell lines (Frhk-4 and Vero cells). DRB, a known inhibitor of the synthesis of messenger RNA, caused moderate changes in cell morphology. However, Frhk-4 cells could be maintained for several weeks at 80 microM of DRB, the concentration that caused maximal enhancement on HAV. DRB should be present from about the time of virus inoculation and its strongest effect was seen at low multiplicities of infection. Using radioimmunofocus assay it could be shown that DRB increased the amount of infectious virus. DRB treatment was applied in primary isolation of HAV from feces. In nine of ten strains HAV antigen expression was strongly increased and in six of the ten strains infectivity of harvested material increased by one 10log or more. DRB thus seems to be a useful enhancer of HAV growth in tissue culture.

Human RNA polymerase II can prematurely terminate transcription of the adenovirus type 2 late transcription unit at a precise site that resembles a prokaryotic termination signal

Premature termination of transcription has been demonstrated by eukaryotic RNA polymerase II at specific sites in the major late transcriptional unit of SV40 and in one of the transcriptional units of the parvovirus, minute virus of mice (MVM) (Y. Aloni and N. Hay, CRC Critical Reviews of Biochem., 18:327-383, 1985). In both cases the prematurely terminated (attenuated) RNA can be folded into a hairpin structure followed by U-residues that resemble a termination signal in prokaryotes. The experiments presented herein demonstrate premature termination of transcription 185 nucleotides (nt) downstream from the major late promoter of adenovirus type 2 (Ad2) in vivo, and in vitro in isolated nuclei and in HeLa whole cell extract. As in SV40 and MVM the attenuated RNA of Ad2 can be folded into a hairpin structure followed by U-residues. Transcription-termination was significantly reduced when ITP replaced GTP and when Br-UTP replaced UTP in the transcription reaction mixture, indicating that RNA secondary structure and the rU-dA interactions, respectively, are parts of the termination signal. Moreover, in isolated nuclei transcription-termination at the attenuation site occurred when the reaction mixture contained between 50-150 mM NaCl but not when it contained 300 mM NaCl. These results indicate that, at least in isolated nuclei, attenuation can be regulated. The possible involvement of termination factor(s) in the regulation of attenuation is discussed.

Simian virus 40 agnoprotein facilitates normal nuclear location of the major capsid polypeptide and cell-to-cell spread of virus

The simian virus 40 agnoprotein is a 61-amino-acid, highly basic polypeptide that is coded within the 5' leader of late 16S mRNAs. To better understand agnoprotein function and to more effectively differentiate cis-from trans-acting effects of an agnogene mutation, we constructed a mutant virus that carries a single-base-pair substitution and fails to produce agnoprotein. pm 1493 contains a T/A to A/T transversion at sequence position 335. This mutation converts the agnoprotein initiation codon from ATG to TTG, preventing synthesis of the protein. The mutant displays only a modest growth defect in CV-1P and AGMK cells and no defect in BSC-1 cells. Early-gene expression, DNA replication, synthesis of late viral products, and the kinetics of virion assembly all appear normal in pm 1493-infected CV-1P cells. Immunofluorescent studies, however, indicate that localization of the major capsid polypeptide VP1 is different in mutant- than wild-type virus-infected cells. Furthermore, the lack of agnoprotein led to inefficient release of mature virus from the infected cell. Agnogene mutants could be severely compromised in their ability to propagate in monkeys given their reduced capacity for cell-to-cell spread.

Transcriptionally active SV40 minichromosomes are restriction enzyme sensitive and contain a nucleosome-free origin region

A nucleosome-free region or gap containing the origin of replication and the transcriptional promoter elements is observed on 20 to 25% of the SV40 minichromosomes isolated at physiological ionic strength late in infection. We used the preferential sensitivity of the gapped minichromosomes to restriction enzymes to obtain sucrose gradient fractions containing 50 to 80% of gapped molecules. The same fractions are also enriched in RNA polymerase B (II) molecules engaged in transcription. Using electron microscopy, we demonstrate here that the transcriptional complexes are preferentially sensitive to restriction enzyme digestion, which indicate that they represent a subpopulation of the gapped minichromosomes.

Attenuation may regulate gene expression in animal viruses and cells

In eukaryotes, an abundant population of promoter-proximal RNA chains have been observed and studied, mainly in whole nuclear RNA, in denovirus type 2, and in SV40. On the basis of these results it has been suggested that a premature termination process resembling attenuation in prokaryotes occurs in eukaryotes. Moreover, these studies have shown that the adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) enhances premature termination, but its mode of action is not understood. The determination of the nucleotide sequences of SV40 and other viruses and cellular genes provide means for elucidating the nucleotide sequences involved in the attenuation mechanism. A model has recently been described in which attenuation and mRNA modulation in a feedback control system quantitatively regulate SV40 gene expression. The suggested mechanism described in this model opens up approaches to the investigation of attenuation and mRNA modulation as a possible mechanism whereby eukaryotes may regulate transcription in a variety of different circumstances.

Transcription of minute virus of mice, an autonomous parvovirus, may be regulated by attenuation

To characterize the transcriptional organization and regulation of minute virus of mice, an autonomous parvovirus, viral transcriptional complexes were isolated and cleaved with restriction enzymes. The in vivo preinitiated nascent RNA was elongated in vitro in the presence of [alpha-32P]UTP to generate runoff transcripts. The lengths of the runoff transcripts were analyzed by gel electrophoresis under denaturing conditions. On the basis of the map locations of the restriction sites and the lengths of the runoff transcripts, the in vivo initiation sites were determined. Two major initiation sites having similar activities were thus identified at residues 201 +/- 5 and 2005 +/- 5; both of them were preceded by a TATAA sequence. When uncleaved viral transcriptional complexes or isolated nuclei were incubated in vitro in the presence of [alpha-32P]UTP or [alpha-32P]CTP, they synthesized labeled RNA that, as determined by polyacrylamide gel electrophoresis, contained a major band of 142 nucleotides. The RNA of the major band was mapped between the initiation site at residue 201 +/- 5 and residue 342. We noticed the potential of forming two mutually exclusive stem-and-loop structures in the 142-nucleotide RNA; one of them is followed by a string of uridylic acid residues typical of a procaryotic transcription termination signal. We propose that, as in the transcription of simian virus 40, RNA transcription in minute virus of mice may be regulated by attenuation and may involve eucaryotic polymerase B, which can respond to a transcription termination signal similar to that of the procaryotic polymerase.

S1 mapping of purified nascent transcripts of simian virus 40

We purified nascent simian virus 40 late transcripts by incubating viral transcriptional complexes, isolated from infected BSC-1 cells, in a reaction mixture that contained mercurated CTP; RNA molecules that had incorporated mercurated residues in vitro were isolated by sulfhydrylcellulose affinity chromatography. The nascent RNA was hybridized to an end-labeled HindIII C probe fragment (0.646 to 0.86 map unit), and the hybrids were analyzed by S1 mapping. Most of the products of digestion corresponded to unspliced transcripts with 5' ends mapping at nucleotides 325, 260, and 195, which are positions of the 5' ends of mature, cytoplasmic late mRNA species. In addition, two minor products diagnostic of splicing at the acceptor junctions mapping at nucleotides 556 and 443 were detected. Because the abundance of these products was not diminished by repurifying the nascent RNA through a second round of sulfhydrylcellulose chromatography, these products did not originate from contaminating non-nascent RNA. Moreover, the generation of these products was not affected when a higher salt concentration and lower temperature were used for S1 digestion, conditions that should decrease artifactual cleavage by S1 in A + U-rich regions of colinear hybrids. Therefore, it is likely that some simian virus 40 RNA chains are spliced before release from the template.

Phosphorylation of some chromosomal nonhistone proteins in active genes is blocked by the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)

The distribution of rapidly phosphorylated chromosomal proteins between chromosome I, chromosome II + III, chromosome IV, and nuclear sap including the matrix was investigated in salivary gland cells of Chironomus tentans. Chromosome IV, which carries most active nonribosomal genes in the cell, was found to be enriched in four rapidly phosphorylated nonhistone polypeptides (Mr = 25,000, 30,000, 33,000, and 42,000) in parallel with the transcriptional activity rather than with the DNA content of the chromosome. Also the histones H2A and H4 are rapidly phosphorylated but the phosphorylation is proportional to the DNA content of each chromosome sample. The 32P-labeled Mr = 42,000 polypeptide immunologically cross-reacted with an antibody elicited against the transcription stimulatory factor S-II isolated from Ehrlich ascites tumor cells (Sekimizu, K., D. Mizuno, and S. Natori, 1979, Exp. Cell Res., 124:63-72). In addition, indirect immunofluorescence studies on chromosome IV with antisera against the stimulatory factor II revealed a selective staining of the active gene loci. The incorporation of 32P into three chromosome IV nonhistone polypeptides, especially into the Mr = 42,000 polypeptide, was lowered by 70-85% shortly after administration of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a likely inhibitor of heterogeneous nuclear RNA transcription at initiation level. The possibility of a causal relationship between inhibited phosphorylation of chromosomal proteins and blocked transcription of heterogeneous nuclear RNA genes by DRB is discussed.

Mechanism of action of DRB. III. Effect on specific in vitro initiation of transcription

5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole, an adenosine analogue, has been used previously as an inhibitor of heterogeneous nuclear and messenger RNA synthesis. In an in vitro transcriptional system, we have detected inhibition of synthesis of full-length runoff RNAs at concentrations at which in vivo mRNA synthesis is inhibited. By hybridization of RNA synthesized in vitro to single-stranded DNA and gel analysis, we were able to reduce the background of the transcription reaction, detect DRB-induced inhibition of full-length runoff RNAs and DRB-insensitive transcription of short RNAs. To establish further the effect of DRB on initiation of transcription, preincubation experiments with template, whole cell extract and two initial nucleotides of the transcript were performed. Elongation was then measured as discrete-sized RNAs transcribed from the truncated template after addition of the other triphosphates (one of them labeled), in the presence or absence of DRB. An effect on initiation but not on elongation or termination was detected. Fingerprint analysis of these runoff RNAs indicates that the labeling of U in the presence of DRB is uniform throughout the molecule. A model to explain a novel interpretation of the action of DRB is presented.

Characterization of the 5' termini of purified nascent simian virus 40 late transcripts

The primary transcripts of simian virus 40 are extensively processed in the nuclei of infected monkey cells before they are transported to the cytoplasm as mature mRNAs. To investigate the early steps in this process, in particular, to determine which events occur on nascent chains before the termination of transcription, we have developed a procedure for the purification of nascent viral transcripts. This technique involves the in vitro incorporation of mercurated residues into the growing 3' ends of pre-initiated nascent chains, allowing their specific purification by sulfhydrylcellulose affinity chromatography. We further selected viral specific transcripts by hybridization to simian virus 40 DNA-cellulose. We describe here our analysis of the 5' termini of purified nascent simian virus 40 transcripts. This analysis revealed various cap structures, providing direct evidence that primary viral transcripts are capped before chain completion. The various cap structures exhibited a full range of methylation states. Completely unmethylated GpppA cap cores were identified, as well as caps methylated at the penultimate position only. The presence of GpppAm and GpppmAm caps indicates that, in BSC-1 cells, the penultimate nucleotide can be methylated before 7-methyl-G formation. Furthermore, the proportions of the various intermediates suggest that, in contrast to the viral capping enzymes of vaccinia virus and reovirus, the cellular enzymes methylate in the following order: GpppA leads to GpppAm leads to GpppmAm leads to 7mGpppmAm. In addition to capped ends, we also detected some unprocessed pppA ends. To our knowledge, this is the first time uncapped termini have been identified on RNAs known to be polymerase II products.

Separation and properties of two kinds of simian virus 40 late transcription complexes

Simian virus 40 (SV40) transcription complexes were labeled in cells with 3-min pulses of [(3)H]uridine 48 h after infection and were extracted from nuclei in isotonic buffer or in a buffer containing Sarkosyl. In sucrose gradients, the labeled complexes sedimented faster than both free RNA and most SV40 nucleoproteins. Most of the pulse-labeled nascent RNA hybridized to the entire late region of SV40, remained bound to viral DNA in Cs(2)SO(4) gradients, and ranged in size from a few nucleotides to about 5,000 nucleotides, with a peak at about 700. In contrast, the SV40-associated RNA polymerase activity in the same preparations sedimented near the major peak of SV40 nucleoproteins and was clearly separated from the transcription complexes bearing pulse-labeled nascent RNA. The two kinds of transcription complexes were released from isolated nuclei at different rates. Complexes bearing pulse-labeled RNA were released immediately when the nuclei were agitated in a Dounce homogenizer in isotonic buffer, whereas most of the complexes bearing RNA polymerase active in vitro were released more slowly, during subsequent incubation of the nuclei at 0 degrees C. Since the complexes bearing pulse-labeled nascent RNA were virtually inactive in vitro, the blocked complexes described by Laub et al. (Proc. Natl. Acad. Sci. U.S.A. 77:3297-3301, 1980) probably account for almost all the SV40-associated RNA polymerase activity studied previously by many investigators. New procedures must be developed to preserve the activity of the pulse-labeled complexes if the many advantages of the SV40 system for studying transcription by nucleoprotein complexes in vitro are to be realized fully.

Evidence for simian virus 40 late transcriptional control: mixed infections of wild-type simian virus 40 and a late leader deletion mutant exhibit trans effects on late viral RNA synthesis

Mixed infections involving equal multiplicities of wild-type simian virus 40 and viable deletion mutant dl861 resulted in decreased cytoplasmic levels of wild-type-derived male mRNA, as well as very low to undetectable levels of mutant-derived late mRNA, as compared with individual infections. The dl861 deletion removes 16 to 25 base pairs from the late leader region. This deletion was shown to be the direct cause of the mixed-infection effect; replacement of the deletion with wild-type sequences restored normal levels of late mRNAs in mixed infections. Other viral functions, e.g., early gene expression and replication, were found to be unaffected by the dl861 deletion. Further examination of the mixed-infection effect showed that the levels of unspliced nuclear precursors of late mRNA, derived from both the mutant and wild-type genomes, were decreased or undetectable, in accord with the cytoplasmic results. Thus, the effect appears to be occurring at the transcriptional level. These data demonstrate a trans-acting effect on late transcription, which is detectable due to the presence of the dl861 mutant in the mixed infection. This finding is indicative of a diffusible factor which exerts a control on simian virus 40 late gene expression at the transcriptional level. A model for positive control of simian virus 40 late gene expression is presented.

Site of premature termination of late transcription of simian virus 40 DNA: enhancement by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole

Sedimentation analysis of pulse-labeled RNA synthesized in nuclei isolated from simian virus 40-infected cells revealed an abundance of short cellular and viral RNAs. The relative amount of the short chains is increased in nuclei isolated from cells treated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). The short viral RNAs were purified by hybridization to and elution from simian virus 40 DNA on filters, and their sizes were determined by gel electrophoresis. A major band of 93- to 95-nucleotide-long RNA was observed along with additional minor bands. Identical bands were revealed when the viral RNA was purified from nuclei of cells pretreated with DRB. The major band was identified as an aborted transcript of a RNA that initiated at the major initiation site (nucleotide 243). We have found that the DNA region where the RNA stops is A+T rich and is immediately preceded by a G+C-rich region that exhibits dyad symmetry, resembling the termination signal in prokaryotes. These observations show that RNA polymerase II responds to the same termination signal as the prokaryotic enzyme and suggest that a mechanism of attenuation regulates simian virus 40 late transcription.

Mechanism of action of dichloro-beta-D-ribofuranosylbenzimidazole: effect on in vitro transcription

The adenosine analog 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) and its mono- and triphosphate derivatives inhibit RNA polymerase II-specific transcription in an extract of whole HeLa cells. The analog does not inhibit RNA polymerase III-specific adenovirus VA RNA transcription in the whole cell extract. With purified RNA polymerase II under nonspecific transcription conditions, no effect on DRB could be detected. DRB is equally effective in inhibiting in vitro transcription from several of the adenovirus promoters and the human epsilon-globin gene. The inhibitory effects are in the order DRB greater than DRB monophosphate greater than DRB triphosphate. Thus DRB acts in vitro presumably on systems in which specific RNA polymerase II initiation of transcription occurs and with no detectable effect on premature termination. This will provide a suitable model for study of the molecular mechanism of action of DRB on transcription.

Induction of premature termination of transcription of the mouse beta-globin gene by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB)

Hybridization of pulse-labeled RNA from DRB-treated Friend cells to mouse beta-globin cDNA revealed that the appearance of beta-globin mRNA in the cytoplasm was inhibited by greater than 87%. To examine the effect of DRB (125 microM) on HnRNA synthesis, nuclear RNA was electrophoresed in methyl mercuric hydroxide gels, transferred to nitrocellulose, and hybridized with beta-globin specific probes. Full-length nuclear transcripts, while present in untreated cells, were not detected in DRB-treated cells. Using restriction enzymes, the cloned beta-globin gene was divided into fragments proceeding from the 5' gene region to the 3' gene region. RNA labeled in vitro by transcription in nuclei isolated from DRB-treated cells hybridized only to the promoter proximal DNA fragment. Transcripts hybridizing to fragments from both the 5' and 3' regions of the gene were produced in nuclei from untreated cells. Together these results indicate that DRB causes premature termination of transcription within the beta-globin gene.

Clustering of RNA polymerase B molecules in the 5' moiety of the adult beta-globin gene of hen erythrocytes

Nuclei were prepared from mature and immature hen erythrocytes and incubated for RNA synthesis in the absence or in the presence of Sarkosyl. The in vitro labelled synthesized RNA was hybridized to specific 5' and 3' fragments of the chicken adult beta-globin gene to investigate the possible presence of RNA polymerase molecules bound to this gene in the form of transcriptional complexes. Surprisingly, such RNA polymerase B molecules were found located preferentially in the 5' end moiety of the beta-globin genes of mature erythrocytes, although they are apparently evenly distributed along the beta-globin genes of immature polychromatic erythrocytes. The significance of these observations with respect to (1) preferential DNaseI sensitivity of "genes which have been transcribed" and (2) control of transcription in eukaryotic cells is discussed.

Two deletions within genes for simian virus 40 structural proteins VP2 and VP3 lead to formation of abnormal transcriptional complexes

The procedure developed by R. M. Fernandez-Muñoz et al. (J. Virol. 29:612-623, 1979) for isolating simian virus 40 (SV 40) chromatin free of disrupted previrions was optimized for preparing late transcriptional complexes, and these complexes were partially characterized. Transcriptional complexes derived from wild-type virus and from several deletion and temperature-sensitive mutants could be activated more than five-fold either by the anionic detergent Sarkosyl or by 300 mM ammonium sulfate, in agreement with the properties of SV40 transcriptional complexes prepared by other procedures. In contrast, complexes from cells infected with deletion mutants dl1261 or dl1262 were not activated at all by a high salt concentration, even though the extent of their activation by Sarkosyl was normal. Mutants dl1261 and dl1262 carry deletions of 54 and 36 base pairs, respectively, at an approximate map position of 0.91, which is within the overlapping genes for the virion proteins VP2 and VP3. The effects of these deletions on transcription in vitro indicate that VP2 or VP3 or both are bound to late transcriptional complexes in a way that affects the progress of initiated RNA polymerase. The properties of late transcriptional complexes derived from wild-type SV40 can be explained by the presence of the following two different kinds of complexes: (i) a minority class (about 20%), which is free of VP2 or VP3, active at low concentrations of ammonium sulfate in vitro, and responsible for late transcription in vivo, and (ii) a majority class (about 80%) with VP2 or VP3 bound, which is inactive at low salt concentrations both in vitro and in vivo but capable of being activated by high salt concentrations or by Sarkosyl. We propose that mutant VP2 and VP3 proteins from dl1261 and dl1262 bind to the majority class of late transcriptional complexes in a way that can be reversed by Sarkosyl but not by a high salt concentration.

Quantitation of transcribing native simian virus 40 minichromosomes extracted from CV1 cells late in infection

Simian virus 40 transcriptional complexes could be extracted from CV1 cells late in infection and separated from the bulk of inactive viral chromatin. Sucrose gradient sedimentation, cesium sulfate equilibrium density gradient centrifugation, and electron microscopy indicated that the viral transcriptional complexes corresponded to at least 0.5 to 1% of the viral minichromosomes extracted, about 5,000 copies per cell.

Escherichia coli RNA polymerase in vitro mimics simian virus 40 in vivo transcription when the template is viral nucleoprotein

We have used a low-salt detergent-free extraction procedure on cells infected with simian virus 40 to obtain viral nucleoprotein late after infection. Addition of EScherichia coli RNA polymerase and ribonucleotide triphosphates to the viral minichromosomes permitted transcription of RNA from viral templates. This synthesis was initiated predominantly within a fragment of DNA spanning 0.67 to 0.76 map unit on the genome. The synthesis from this region proceeded primarily along the "late" strand in a clockwise direction. These results were in contrast to the synthesis obtained with naked viral DNA in which initiation occurred on other regions of the genome and from which transcription proceeded counterclockwise along the early strand. These findings indicate that the nucleoprotein template or factors tightly associated with it may be responsible for site(s) and strand selection in transcription of simian virus 40.