Adenovirus stimulation of transcription by RNA polymerase III: evidence for an E1A-dependent increase in transcription factor IIIC concentration

Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler

Alu retrotransposons, which form the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase, EP400 chromatin remodeler and YAP1 and FOS transcription factors. The physical interaction of e1a with EP400 was critical for Alu derepression, which was abrogated upon EP400 ablation. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, which requires EP400 and is mediated by the e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenoviruses.

"Transfer" of power: The intersection of DNA virus infection and tRNA biology

Transfer RNAs (tRNAs) are at the heart of the molecular biology central dogma, functioning to decode messenger RNAs into proteins. As obligate intracellular parasites, viruses depend on the host translation machinery, including host tRNAs. Thus, the ability of a virus to fine-tune tRNA expression elicits the power to impact the outcome of infection. DNA viruses commonly upregulate the output of RNA polymerase III (Pol III)-dependent transcripts, including tRNAs. Decades after these initial discoveries we know very little about how mature tRNA pools change during viral infection, as tRNA sequencing methodology has only recently reached proficiency. Here, we review perturbation of tRNA biogenesis by DNA virus infection, including an emerging player called tRNA-derived fragments (tRFs). We discuss how tRNA dysregulation shifts the power landscape between the host and virus, highlighting the potential for tRNA-based antivirals as a future therapeutic.

Old and new functions for the adenovirus virus-associated RNAs

Adenovirus type 5 encodes two short, highly structured noncoding RNAs, the virus-associated (VA) RNAI and VA RNAII. These RNAs are expressed in large amounts late during a lytic infection. Early studies established an important role for VA RNAI in maintaining efficient translation in late virus-infected cells by blocking activation of the key interferon-induced PKR protein kinase. More recent studies have demonstrated that the VA RNAs also target the RNAi/miRNA pathway. Collectively, available data suggest that the VA RNAs are multifunctional RNAs suppressing the activity of three dsRNA-sensing enzyme systems in human cells. Here, the known functions of the VA RNAs are summarized and the interplay between VA RNA expression and the activity of the interferon and RNAi pathways are discussed in more detail.

Cell growth- and differentiation-dependent regulation of RNA polymerase III transcription

RNA polymerase III transcribes small untranslated RNAs that fulfill essential cellular functions in regulating transcription, RNA processing, translation and protein translocation. RNA polymerase III transcription activity is tightly regulated during the cell cycle and coupled to growth control mechanisms. Furthermore, there are reports of changes in RNA polymerase III transcription activity during cellular differentiation, including the discovery of a novel isoform of human RNA polymerase III that has been shown to be specifically expressed in undifferentiated human H1 embryonic stem cells. Here, we review major regulatory mechanisms of RNA polymerase III transcription during the cell cycle, cell growth and cell differentiation.

RNA polymerase III transcription and cancer

RNA polymerase (pol) III synthesizes a range of essential products, including tRNA, 5S rRNA and 7SL RNA, which are required for protein synthesis and trafficking. High rates of pol III transcription are necessary for cells to sustain growth. A wide range of transformed and tumour cell types have been shown to express elevated levels of pol III products. This review will summarize what is known about the mechanisms responsible for this deregulation. Some transforming agents have been shown to stimulate expression of the pol III-specific transcription factors TFIIIB or TFIIIC2. In addition, TFIIIB is bound and activated by several oncogenic proteins, including c-Myc. Conversely, TFIIIB interacts in healthy cells with the tumour suppressors RB and p53. Indeed, the ability to limit pol III transcription through TFIIIB may contribute to their growth-suppression capacities. The function of p53 and/or RB is compromised in most if not all transformed cells; the resultant derepression of TFIIIB may provide an almost universal route to deregulate pol III transcription in cancers. In addition to effects on protein synthesis and growth, there is a precedent for a pol III product having oncogenic activity.

Multiple mechanisms contribute to the activation of RNA polymerase III transcription in cells transformed by papovaviruses

RNA polymerase (pol) III transcription is abnormally active in fibroblasts transformed by polyomavirus (Py) or simian virus 40 (SV40). Several distinct mechanisms contribute to this effect. In untransformed fibroblasts, the basal pol III transcription factor (TF) IIIB is repressed through association with the retinoblastoma protein RB; this restraint is overcome by large T antigens of Py and SV40. Furthermore, cells transformed by these papovaviruses overexpress the BDP1 subunit of TFIIIB, at both the protein and mRNA levels. Despite the overexpression of BDP1, the abundance of the other TFIIIB components is unperturbed following papovavirus transformation. In contrast, mRNAs encoding all five subunits of the basal factor TFIIIC2 are found at elevated levels in fibroblasts transformed by Py or SV40. Thus, both papovaviruses stimulate pol III transcription by boosting production of selected components of the basal machinery. Py differs from SV40 in encoding a highly oncogenic middle T antigen that localizes outside the nucleus and activates several signal transduction pathways. Middle T can serve as a potent activator of a pol III reporter in transfected cells. Several distinct mechanisms therefore contribute to the high levels of pol III transcription that accompany transformation by Py and SV40.

Characterization of RNA polymerase III transcription factor TFIIIC from the mulberry silkworm, Bombyx mori

Fractionation of nuclear extracts from posterior silk glands of mulberry silkworm Bombyx mori, resolved the transcription factor TFIIIC into two components (designated here as TFIIIC and TFIIIC1) as in HeLa cell nuclear extracts. The reconstituted transcription of tRNA genes required the presence of both components. The affinity purified TFIIIC is a heteromeric complex comprising of five subunits ranging from 44 to 240 kDa. Of these, the 51-kDa subunit could be specifically crosslinked to the B box of tRNA1Gly. Purified swTFIIIC binds to the B box sequences with an affinity in the same range as of yTFIIIC or hTFIIIC2. Although an histone acetyl transferase (HAT) activity was associated with the TFIIIC fractions during the initial stages of purification, the HAT activity, unlike the human TFIIIC preparations, was separated at the final DNA affinity step. The tRNA transcription from DNA template was independent of HAT activity but the repressed transcription from chromatin template could be partially restored by external supplementation of the dissociated HAT activity. This is the first report on the purification and characterization of TFIIIC from insect systems.

RNA polymerase III transcription factor TFIIIC2 is overexpressed in ovarian tumors

Most transformed cells display abnormally high levels of RNA polymerase (pol) III transcripts. Although the full significance of this is unclear, it may be fundamental because healthy cells use two key tumor suppressors to restrain pol III activity. We present the first evidence that a pol III transcription factor is overexpressed in tumors. This factor, TFIIIC2, is a histone acetyltransferase that is required for synthesis of most pol III products, including tRNA and 5S rRNA. TFIIIC2 is a complex of five polypeptides, and mRNAs encoding each of these subunits are overexpressed in human ovarian carcinomas; this may explain the elevated TFIIIC2 activity that is found consistently in the tumors. Deregulation in these cancers is unlikely to be a secondary response to rapid proliferation, because there is little or no change in TFIIIC2 mRNA levels when actively cycling cells are compared with growth-arrested cells in culture. Using purified factors, we show that raising the level of TFIIIC2 is sufficient to stimulate pol III transcription in ovarian cell extracts. The data suggest that overexpression of TFIIIC2 contributes to the abnormal abundance of pol III transcripts in ovarian tumors.

Activation of RNA polymerase III transcription in cells transformed by simian virus 40

RNA polymerase (Pol) III transcription is abnormally active in fibroblasts that have been transformed by simian virus 40 (SV40). This report presents evidence that two separate components of the general Pol III transcription apparatus, TFIIIB and TFIIIC2, are deregulated following SV40 transformation. TFIIIC2 subunits are expressed at abnormally high levels in SV40-transformed cells, an effect which is observed at both protein and mRNA levels. In untransformed fibroblasts, TFIIIB is subject to repression through association with the retinoblastoma protein RB. The interaction between RB and TFIIIB is compromised following SV40 transformation. Furthermore, the large T antigen of SV40 is shown to relieve repression by RB. The E7 oncoprotein of human papillomavirus can also activate Pol III transcription, an effect that is dependent on its ability to bind to RB. The data provide evidence that both TFIIIB and TFIIIC2 are targets for activation by DNA tumor viruses.

A novel human DNA-binding protein with sequence similarity to a subfamily of redox proteins which is able to repress RNA-polymerase-III-driven transcription of the Alu-family retroposons in vitro

In this study we identified a novel protein which may contribute to the transcriptional inactivity of Alu retroposons in vivo. A human cDNA clone encoding this protein (ACR1) was isolated from a human expression library using South-western screening with an Alu subfragment, implicated in the regulation of Alu in vitro transcription and interacting with a HeLa nuclear protein down-regulated in adenovirus-infected cells. Bacterially expressed ACR1 is demonstrated to inhibit RNA polymerase III (Pol III)-dependent Alu transcription in vitro but showed no repression of transcription of a tRNA gene or of a reporter gene under control of a Pol II promoter. ACR1 mRNA is also found to be down-regulated in adenovirus-infected HeLa cells, consistent with a possible repressor function of the protein in vivo. ACR1 is mainly (but not exclusively) located in cytoplasm and appears to be a member of a weakly characterized redox protein family having a central, highly conserved sequence motif, PGAFTPXCXXXXLP. One member of the family identified earlier as peroxisomal membrane protein (PMP)20 is known to interact in a sequence-specific manner with a yeast homolog of mammalian cyclosporin-A-binding protein cyclophilin, and mammalian cyclophilin A (an abundant ubiquitously expressed protein) is known to interact with human transcriptional repressor YY1, which is a major sequence-specific Alu-binding protein in human cells. It appears, therefore, that transcriptional silencing of Alu in vivo is a result of complex interactions of many proteins which bind to its Pol III promoter.

Control of genes by mammalian retroposons

Available data on possible genetic impacts of mammalian retroposons are reviewed. Most important is the growing number of established examples showing the involvement of retroposons in modulation of expression of protein-coding genes transcribed by RNA polymerase II (Pol II). Retroposons contain conserved blocks of nucleotide sequence for binding of some important Pol II transcription factors as well as sequences involved in regulation of stability of mRNA. Moreover, these mobile genes provide short regions of sequence homology for illegitimate recombinations, leading to diverse genome rearrangements during evolution. Therefore, mammalian retroposons representing a significant fraction of noncoding DNA cannot be considered at present as junk DNA but as important genetic symbionts driving the evolution of regulatory networks controlling gene expression.

A tandem array of minimal U1 small nuclear RNA genes is sufficient to generate a new adenovirus type 12-inducible chromosome fragile site

Infection of human cells with adenovirus serotype 12 (Ad12) induces metaphase fragility of four, and apparently only four, chromosomal loci. Surprisingly, each of these four loci corresponds to a cluster of genes encoding a small abundant structural RNA: the RNU1 and RNU2 loci contain tandemly repeated genes encoding U1 and U2 small nuclear RNAs (snRNAs), respectively; the PSU1 locus is a cluster of degenerate U1 genes; and the RN5S locus contains the tandemly repeated genes encoding 5S rRNA. These observations suggested that high local levels of transcription, in combination with Ad12 early functions, can interfere with metaphase chromatin packing. In support of this hypothesis, we and others found that an artificial tandem array of transcriptionally active, but not inactive, U2 snRNA genes would generate a novel Ad12-inducible fragile site. Although U1 and U2 snRNA are both transcribed by RNA polymerase II and share similar enhancer, promoter, and terminator signals, the human U1 promoter is clearly more complex than that of U2. In addition, the natural U1 tandem repeat unit exceeds 45 kb, whereas the U2 tandem repeat unit is only 6.1 kb. We therefore asked whether an artificial array of minimal U1 genes would also generate a novel Ad12-inducible fragile site. The exogenous U1 genes were marked by an innocuous U72C point mutation within the U1 coding region so that steady-state levels of U1 snRNA derived from the artificial array could be quantified by a simple primer extension assay. We found that the minimal U1 genes were efficiently expressed and were as effective as minimal U2 genes in generating a novel Ad12-inducible fragile site. Thus, despite significant differences in promoter architecture and overall gene organization, the active U1 transcription units suffice to generate a new virally inducible fragile site.

Viral transactivating proteins

Many viruses utilize the cellular transcription apparatus to express their genomes, and they encode transcriptional regulatory proteins that modulate the process. Here we review the current understanding of three viral regulatory proteins. The adenovirus E1A protein acts within the nucleus to regulate transcription through its ability to bind to other proteins. The herpes simplex type 1 virus VP16 protein acts within the nucleus to control transcription by binding to DNA in conjunction with cellular proteins. The human T-cell leukemia virus Tax protein influences transcription through interactions with cellular proteins in the nucleus as well as the cytoplasm.

Human T-cell leukemia virus type I Tax protein transactivates RNA polymerase III promoter in vitro and in vivo

Tax protein of the human T-cell lymphotropic virus type 1 (HTLV-I) is critical for viral replication and is a potent transcriptional activator of viral and cellular polymerase II (pol II) genes. We report here that Tax is able to transactivate a classical pol III promoter, VA-I. In cotransfection experiments, Tax is shown to increase transcription of the VA-I promoter approximately 25-fold. Moreover, Tax is able to activate VA-I transcription when added exogenously to an in vitro transcription reaction. Using Tax affinity column chromatography, we demonstrate that Tax is able to deplete a HeLa cell extract for components required for transcription of VA-I. The transcriptional activity of the Tax-depleted extract can be restored by the 0.6 phosphocellulose fraction. Interestingly, a consensus binding site for cAMP-responsive element binding protein (CREB) is located upstream of the VA-I promoter, and deletion of this element results in the loss of Tax responsiveness. When this CREB binding site is replaced by a Gal-4 binding site, the VA-I promoter can be transactivated by a Gal4-Tax fusion protein. Taken together, these results suggest that Tax may activate pol III and pol II promoter through a similar mechanism involving the CREB activation pathway. It is also possible that Tax affects pol III transcription by direct interaction with a component of the pol III transcriptional machinery.

A human B-box-binding protein downregulated in adenovirus 5-transformed human cells

Internal promoters of some genes transcribed by RNA polymerase III (e.g. tRNA genes, adenovirus VA1 RNA gene, human retroposons of the Alu family) contain a conserved sequence element, B-box, interacting with basal transcription factor TFIIIC2 which initiates assembly of the full transcription complex on the genes, and which represents the major determinant of the efficiency of their expression. In this study we have identified in human nuclear extracts a protein which interacts with VA1 B-box DNA and forms a high-affinity complex which is very stable after the addition of a large excess of competitor DNA. Unlike TFIIIC2, the B-box-binding activity of the B-box-binding protein is found to be decreased in adenovirus 5-transformed human cells. In these cells (line 293) increased transcription of VA1 and tRNA genes in vivo and in vitro was previously detected by other workers. Our results suggest that besides TFIIIC2, an additional B-box-binding protein factor may be involved in the regulation of expression of the RNA polymerase III-transcribed genes.

Deregulation of protein synthesis as a mechanism of neoplastic transformation

Early research on the cell cycle revealed correlations between protein accumulation and cell proliferation. In this review, I describe the data showing that abnormality of cell growth and tumor development are dependent upon oncogene-induced increases in the levels and activity of factors that determine the rate of protein synthesis. It is proposed that the establishment of a vicious circle, namely oncoproteins-->increase in translation-->oncoproteins, is a major biological mechanism that fuels neoplastic growth. The constitutively high rates of protein synthesis and accumulation of proteins, including those necessary for DNA replication and mitosis, would drive cells to excessive proliferation.

Evidence for a regulatory protein complex on RNA polymerase III promoter of human retroposons of Alu family

Abundant human retroposons of the Alu family produce few RNA polymerase III (RPIII)-dependent transcripts in vivo. This suggests that either the bulk of the repeats has no proper promoter elements or that transcription of Alu by RPIII is repressed. In this study, we analyzed complexes formed by human nuclear proteins with the Alu B-box and with an adjacent downstream sequence (DB-sequence). Four complexes (C1-C4) were detected and two of them (C2 and C3) were found to be induced by different proteins. C3 formation was found to be sensitive to minor sequence variation within the Alu DB-sequence. The C2 complex is specifically repressed by the competing VA1 B-box oligonucleotide and was found to be very stable. In addition, it is downregulated in human cells transformed by adenovirus 5. This is consistent with a view that the C2 complex is formed by a protein (designated as ACR1) that is different from TFIIIC2. The ACR1 protein may be involved in the modulation of Alu transcription in vivo by interfering or cooperating with TFIIIC2. A similar complex is detected with the efficiently transcribed adenovirus VA1 RNA gene B-box. We compared the affinity of complexes formed by ACR1 with Alu and VA1 B-boxes. It was found that both B-boxes bind ACR1 with equal affinity with a dissociation constant of about 2 nM. However, DB-sequences in Alu and VA1 promoters are non-homologous, and C3/C4 complexes are found to be formed with Alu DB, but not formed with VA1 DB sequences. The Alu-specific protein forming C3 (named as ACR2) may cooperate with ACR1 in selective repression of RPIII-dependent Alu transcription in vivo.

Cloning and characterization of a TFIIIC2 subunit (TFIIIC beta) whose presence correlates with activation of RNA polymerase III-mediated transcription by adenovirus E1A expression and serum factors

TFIIIC2 is a general factor essential for transcription of 5S RNA, tRNA, and VA RNA genes by mammalian RNA polymerase III and consists of two forms designated TFIIIC2a and TFIIIC2b. TFIIIC2a and TFIIIC2b share common subunits of 220, 102, 90, and 63 kD but differ with respect to transcription activity and the presence of a presumptive 110-kD subunit in the active form (TFIIIC2a). Because both forms can bind the promoter directly, a selective role for the 110-kD subunit in the regulation of RNA polymerase III activity has been suggested. To investigate this possibility, we have cloned and expressed a cDNA encoding the 110-kD subunit (TFIIIC beta). Immunoprecipitation studies with anti-TFIIIC beta antibodies have confirmed that TFIIIC beta is a bona fide subunit present only in TFIIIC2a, that TFIIIC2a and the general factor TFIIIC1 are associated in unfractionated extracts, and that previously undetected polypeptides (potential TFIIIC1 subunits) can be isolated in association with TFIIIC2a. Previous studies have shown that increases in RNA polymerase III activity during infection of cells by adenovirus (with concomitant E1A expression) or during cell growth at high serum concentration results from an increased activity in the TFIIIC fraction. Studies with antibodies to TFIIIC beta have shown that this is strongly correlated with a selective increase in the cellular concentration of the TFIIIC beta 110-kD subunit and a concomitant rise in the ratio of the active-to-inactive forms of TFIIIC2.

Mechanism of TATA-binding protein recruitment to a TATA-less class III promoter

The TATA-binding protein (TBP) is required for transcription by RNA polymerase III (pol III), even though many pol III templates, such as the adenovirus VA1 gene, lack a consensus TATA box. We show that TBP alone does not form a stable, productive interaction with VA1 DNA. However, it can be incorporated into an initiation complex if the other class III basal factors, TFIIIB and TFIIIC, are also present. TFIIIB can associate with the evolutionarily conserved C-terminal domain of TBP in the absence of DNA or TFIIIC, suggesting that TFIIIB exists in solution as a complex with TBP. The stable association of TBP with an essential component of the pol III transcription apparatus may account for the ability of TATA-less class III genes to recruit TBP.

Trans-activation of H-1 parvovirus P38 promoter is correlated with increased binding of cellular protein(s) to the trans-activation responsive element (tar)

The parvovirus H-1 P38 promoter contains a trans-activation responsive element (tar). It was previously shown that the parvovirus H-1 nonstructural protein NS1 positively regulates the expression of the P38 promoter for the viral capsid protein gene via the tar (Rhode and Richard, 1987, J. Virol. 61, 2807-2515). To characterize the mechanism of trans-activation by the tar, we used gel shift assays to demonstrate that there exist proteins in virus-infected cellular extracts which have higher binding activity than that found in mock-infected extracts. These observations in vitro are consistent with the expression by P38 constructs with the wild-type promoter linked to a reporter gene, chloramphenicol acetyl transferase (cat), in vivo. We also provide evidence that the protein(s)-tar complex has a molecular mass of approximately 75 kDa in an SDS-polyacrylamide gel, which is less than NS1, and this complex cannot be precipitated by NS1 antibody, which suggests that NS1 mediates the trans-activation by inducing an alteration in the binding activity of some cellular protein(s) in an indirect manner. These data support our previous hypothesis for the activation of the P38 promoter, in which the trans-activator(s) interacts with the tar effectively in the presence of NS1, leading to the formation of the transcription initiation complex by protein-protein associations (Gu, Chen, and Rhode, 1992, Virology 187, 10-17).

RNA polymerase III transcription

Remarkable progress has been made in defining the functional significance of the protein-DNA interactions involved in transcription complex formation on yeast tRNA and 5S RNA genes. This new information leads to a re-evaluation of how the class III gene transcription machinery operates.

Distinct DNA targets for trans-activation by HTLV-1 tax and adenovirus E1A

The HTLV-1 LTR is trans-activated by both the HTLV-1 tax (p40x) and adenovirus E1A gene products. Previous experiments have localized tax-responsive cis-elements to three 21-bp repeat units within the promoter, as well as a fourth region located between the middle and proximal repeats. A sequence TGACG, resembling the ATF/CREB recognition element, is located at the center of each of these repeat units. Mutation of this ATF/CREB site in the 21-bp repeats impairs both tax and E1A-dependent trans-activation. However, assays of a variety of promoter mutants demonstrate that sequences required for E1A and tax induction differ, suggesting that these two viral trans-activators target different factors. In addition, although the adenovirus E4 promoter also contains three ATF/CREB sites involved in E1A activation, tax does not activate this promoter. Finally, we also find that the TATAA element of the HTLV-1 LTR contributes to E1A-dependent activation but not tax activation. We concluded that although both trans-activators exhibit similarities in their activation properties, the targets for activation must differ.

Adenovirus E1A proteins can dissociate heteromeric complexes involving the E2F transcription factor: a novel mechanism for E1A trans-activation

Adenovirus infection activates the E2F transcription factor, in part through the formation of a heteromeric protein complex involving a 19 kd E4 gene product that then allows cooperative and stable promoter binding. We now find that cellular factors are complexed to E2F in extracts of several uninfected cell lines. E1A proteins can dissociate these complexes, releasing free E2F. This activity of E1A is independent of conserved domain 3 but is dependent on conserved domain 2 sequence. The E1A-mediated dissociation of the complexes allows the E4 protein to interact with E2F, generating a stable DNA-protein complex with the E2 promoter and a stimulation of transcription. These experiments demonstrate a function for E1A in mediating a dissociation of transcription factor complexes, allowing new interactions to form and thus changing the transcriptional specificity.

Adenovirus terminal protein mediates both nuclear matrix association and efficient transcription of adenovirus DNA

Adenovirus DNA is tightly bound to the nuclear matrix throughout the course of infection. Analysis of adenovirus DNA from infected HeLa cell nuclei after extraction with lithium diiodosalicylate and digestion with restriction enzymes demonstrated that the sites of tightest attachment occur in the terminal fragments of the linear viral chromosome. Analysis of viruses mutated in the precursor terminal protein coding sequence demonstrated that the terminal protein, which is covalently attached to the 5' end of each DNA strand, mediates the tight binding. Virions containing chromosomes with mutant terminal proteins were unpackaged and viral DNA accumulated in the nucleus at a normal rate and competed for the limiting component during transcription complex formation, but their early genes were transcribed at reduced efficiency by both RNA polymerases II and III. The transcriptional defects were not complemented by coinfection with a wild-type virus. We propose that the adenovirus chromosome may exist as a single chromatin domain during infection and that binding of DNA to the nuclear matrix may play a critical role in adenovirus transcription.

Adenovirus early region 3 promoter regulation by E1A/E1B is independent of alterations in DNA binding and gene activation of CREB/ATF and AP1

Transcription of the adenovirus early region 3 promoter is strongly induced by the adenovirus E1A protein. Previous DNase I footprinting has indicated that four regions in this promoter serve as binding sites for HeLa nuclear proteins. These include binding sites for NF-1 (site IV), AP1 (site III), CREB/activating transcription factor (ATF) (site II), and TATA (site I). To determine the relative importance of these sites in both the in vivo and in vitro transcriptional regulation of the E3 promoter, oligonucleotide-directed mutagenesis of these sites was performed. Each of these constructs was assayed by transfection onto HeLa cells in the presence of either dl434, an E1A/E1B deletion mutant, or wild-type adenovirus. Mutations of either the ATF- or AP1-binding sites but not the TATA- and NF1-binding sites resulted in severe decreases in both basal and E1A/E1B-induced transcriptional levels. These constructs were also assayed in in vitro transcription assays with cellular extracts prepared from dl434-infected or wild-type-adenovirus-infected HeLa cells. The wild-type E3 promoter was transcribed approximately 30 times more efficiently in extracts containing the E1A/E1B proteins compared with extracts lacking these proteins. Mutations of either the TATA element, the ATF site, or the AP1-binding site decreased both basal and E1A/E1B-induced transcriptional levels. Gel retardation analysis using these extracts indicated that the binding to ATF, AP1, or NF1 oligonucleotides was not altered in the presence of the E1A/E1B proteins compared with extracts lacking these proteins. Northern (RNA) blot analysis of c-jun and CREB RNA prepared from wild-type adenovirus and dl434-infected cells indicated that the levels of these RNAs were not altered by the E1A/E1B proteins. Immunoprecipitation of AP1 and CREB from both dl434- and wild-type-adenovirus-infected cells indicated that the amounts of these proteins were not significantly altered. These results suggest that E1A/E1B-induced activation of the E3 promoter does not involve activation of transcription factor genes nor a change in the DNA binding activity of important promoter-binding components. Our results are consistent with a model in which the E1A/E1B proteins either directly or indirectly alter the interactions of factors that bind to the basal E3 promoter transcription complex, thereby inducing transcription.

Sarkosyl defines three intermediate steps in transcription initiation by RNA polymerase III: application to stimulation of transcription by E1A

We used Sarkosyl to analyze steps along the pathway of transcription initiation by RNA polymerase III. Sarkosyl (0.015%) inhibited transcription when present prior to incubation of RNA polymerase III, TFIIIB, and TFIIIC with the VAI gene, whereas it had no detectable effect on initiation or reinitiation of transcription when added subsequently. The formation of the corresponding 0.015% Sarkosyl-resistant complex required the presence of TFIIIC, TFIIIB, and RNA polymerase III but not nucleoside triphosphates. The addition of 0.05% Sarkosyl after this early step selectively inhibited a later step in the preinitiation pathway, allowing a single round of transcription after nucleoside triphosphate addition but blocking subsequent rounds of initiation. This step occurred prior to initiation because nucleoside triphosphates were not required for the formation of the corresponding 0.05% Sarkosyl-resistant complex. These observations provided a means to distinguish effects of regulatory factors on different steps in promoter activation and function. Using 0.05% Sarkosyl to limit reinitiation, we determined that the E1A-mediated stimulation of transcription by RNA polymerase III resulted from an increase in the number of active transcription complexes.

The hepatitis B virus X-gene product trans-activates both RNA polymerase II and III promoters

The transcriptional regulatory activity of the human hepatitis B virus (HBV) X-gene product was investigated. We demonstrate a new property for the HBV X-gene, the strong transcriptional trans-activation of promoters for class III genes. The stimulation of RNA polymerase III (pol III) as well as pol II promoters is shown in cells transiently transfected with the X-gene, and after its stable integration into hepatocytes. We demonstrate that X-gene containing cells stimulate the frequency of pol III transcription initiation by 20- to 40-fold, and accelerate the rate of formation of stable pol III initiation complexes in a manner indistinguishable from that of adenovirus E1a protein. Since the transcription factor TFIIIC has been shown to be limiting in the formation of stable pol III initiation complexes, template commitment experiments were performed which titrate the level of this factor in extracts. We show that X-protein containing extracts are far more efficient in forming stable pol III preinitiation complexes that cannot be competed away upon addition of a second template, indicating that TFIIIC is very probably a target of the X-protein. Thus, the HBV X-protein is apparently a member of a family of trans-activators capable of stimulating both pol II and III promoters, which includes the adenovirus E1a-protein and SV40 t antigen.

Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins

The cloning of genes encoding mammalian DNA binding transcription factors for RNA polymerase II has provided the opportunity to analyze the structure and function of these proteins. This review summarizes recent studies that define structural domains for DNA binding and transcriptional activation functions in sequence-specific transcription factors. The mechanisms by which these factors may activate transcriptional initiation and by which they may be regulated to achieve differential gene expression are also discussed.

DNA-binding activity of the adenovirus-induced E4F transcription factor is regulated by phosphorylation

Previous experiments have identified E4F, an inducible cellular factor that binds to sequences in the adenovirus E4 promoter that are critical for E1A-dependent transcriptional activation. The E4F factor has been purified and shown to stimulate transcription in vitro from the E4 promoter. Analysis of the affinity-purified factor identifies a single polypeptide of 50 kD that has E4F-specific binding activity. E4F binding activity is also regulated during F9 cell differentiation and can be activated in differentiated F9 cells by viral infection. Furthermore, the activation process appears to involve a phosphorylation event, because treatment of E4F with alkaline phosphatase abolishes activity and incubation of the phosphatase-inactivated factor with an extract from virus infected cells restores activity.

Regulation of cellular genes transduced by herpes simplex virus

Previous studies demonstrated that the rabbit beta-globin gene is transcribed from its own promoter and regulated as a herpes simplex virus (HSV) early gene following insertion into the early HSV thymidine kinase gene in the intact viral genome (J. R. Smiley, C. Smibert, and R. D. Everrett, J. Virol. 61:2368-2377, 1987). We report here that the beta-globin promoter remained under early control after insertion into the late HSV gene encoding glycoprotein C. On the basis of these findings, we concluded that the beta-globin promoter is functionally equivalent to an HSV early-control region. We found that a transduced human alpha-globin gene was also regulated as an early HSV gene, while two linked Alu elements mimicked the behavior of HSV late genes. These results demonstrate that certain aspects of HSV temporal regulation can be duplicated by cellular elements and provide strong support for the hypothesis that the regulation of HSV gene expression can occur through mechanisms that do not rely on recognition of virus-specific temporal control signals.

Cis- and trans-acting factors for transcription of the adenovirus 12 E1A gene

Cis- and trans-acting factors were analyzed for transcription of the adenovirus 12 E1A gene possessing two sites for transcription initiation. These sites are located at nucleotide positions 306 and 445 with respect to the left end of the viral genome as position 1. The template activity of DNAs with various deletions at the 5'-upstream region of the E1A gene was examined in a cell-free system using a nuclear extract of Ehrlich ascites tumor cells. A DNA region specifically stimulating transcription initiated at the site distal to the E1A coding sequence was found located between positions 1 and 166. No DNA sequence affecting transcription from a proximal start-site appeared to be present in the region between positions 1 and 378. DNaseI-footprinting indicated that factors present in the extract bind to two distinct DNA segments, both of which are located within a region stimulating distal transcription. Two footprints were observed, one between positions 19 and 55 and the other between 77 and 94. The former footprint was inhibited by synthetic oligonucleotides containing a sequence recognized by nuclear factor I and the latter contained a sequence similar to one present in the B-enhancer of polyoma virus. Competition of in vitro transcription with synthetic oligonucleotides indicated (a) nuclear factor(s) bound to the region between positions 19 and 55 to be responsible for stimulating distal transcription of the adenovirus 12 E1A gene.

Transcriptional activation by the pseudorabies virus immediate early protein requires the TATA box element in the adenovirus 2 E1B promoter

The adenovirus E1A protein and immediately early (IE) protein of pseudorabies virus stimulate transcription from many promoters. It has been postulated that these proteins function via cellular intermediates. We analyzed the transcription of adenovirus E1B promoter mutants in response to the stimulatory effect of IE protein in comparison with E1A. Far upstream deletions and precise Sp1 and TATA box substitution mutations were examined. Only mutations affecting the TATA box element interfered with transactivation by IE protein. This result is similar to observations for E1A transactivation (L. Wu et al. Nature (London) 326, 512-515, 1987), suggesting that both E1A and IE proteins mediate transactivation of the E1B promoter through a common cellular intermediate which interacts with the TATA box.

Cell-line specific activation of SV40 transcriptional enhancer by p40tax of HTLV-1

A transcriptional trans-activator p40tax of HTLV-1 was reported to activate HTLV-1 enhancer, but not SV40 or Rous sarcoma virus enhancer. However, in certain cell lines, we found that SV40 enhancer was activated by p40tax. These cell lines were mostly T cells, where the SV40 enhancer showed only low activity without p40tax. Since p40tax-mediated activation of the LTR is not cell line-specific, the activation of enhancers by p40tax depends on the combination of enhancer and cell type used for the test. Thus, apparent activation by p40tax depends on variable cellular components involved in transcriptional regulation.

Activation of transcription factor IIIC by the adenovirus E1A protein

The factor(s) responsible for the adenovirus E1A-stimulated transcription of RNA polymerase III genes was localized previously in a chromatographic fraction containing transcription factor IIIC (TFIIIC). In further studies, two distinct forms of TFIIIC, which were chromatographically separable, generated VA gene-protein complexes that were distinguished by gel shift assays. The form of TFIIIC that generated the more slowly migrating promoter complex had greater transcriptional activity in vitro, associated more rapidly with the promoter, and formed a more salt-resistant complex. Greater amounts of this more active form of TFIIIC resulted from either E1A expression during infection or growth of the cells in a higher concentration of serum, whereas template commitment assays indicated that overall TFIIIC concentrations remained unchanged during viral infection. The in vitro interconversion of the two forms of TFIIIC by phosphatase treatment suggests that transcriptional activation of RNA polymerase III genes can be mediated by phosphorylation of TFIIIC.