The sequence motifs that are involved in SV40 enhancer function also control SV40 late promoter activity

Directed Nucleosome Sliding during the Formation of the Simian Virus 40 Particle Exposes DNA Sequences Required for Early Transcription

Simian virus 40 (SV40) exists as chromatin throughout its life cycle and undergoes typical epigenetic regulation mediated by changes in nucleosome location and associated histone modifications. In order to investigate the role of epigenetic regulation during the encapsidation of late-stage minichromosomes into virions, we mapped the locations of nucleosomes containing acetylated or methylated lysines in the histone tails of H3 and H4 present in the chromatin from 48-h-postinfection minichromosomes and disrupted virions. In minichromosomes obtained late in infection, nucleosomes were found carrying various histone modifications primarily in the regulatory region, with a major nucleosome located within the enhancer and other nucleosomes at the early and late transcriptional start sites. The nucleosome found in the enhancer would be expected to repress early transcription by blocking access to part of the SP1 binding sites and the left side of the enhancer in late-stage minichromosomes while also allowing late transcription. In chromatin from virions, the principal nucleosome located in the enhancer was shifted ∼70 bases in the late direction from what was found in minichromosomes, and the level of modified histones was increased throughout the genome. The shifting of the enhancer-associated nucleosome to the late side would effectively serve as a switch to relieve the repression of early transcription found in late minichromosomes while likely also repressing late transcription by blocking access to necessary regulatory sequences. This epigenetic switch appeared to occur during the final stage of virion formation.IMPORTANCE For a virus to complete infection, it must produce a new virus particle in which the genome is able to support a new infection. This is particularly important for viruses like simian virus 40 (SV40), which exist as chromatin throughout their life cycles, since chromatin structure plays a major role in the regulation of the life cycle. In order to determine the role of SV40 chromatin structure late in infection, we mapped the locations of nucleosomes and their histone tail modifications in SV40 minichromosomes and in the SV40 chromatin found in virions using chromatin immunoprecipitation-DNA sequencing (ChIP-Seq). We have identified a novel viral transcriptional control mechanism in which a nucleosome found in the regulatory region of the SV40 minichromosome is directed to slide during the formation of the virus particle, exposing transcription factor binding sites required for early transcription that were previously blocked by the presence of the nucleosome.

Chromatin structure and factor site occupancies in an in vivo-assembled transcription elongation complex

The chromatin structure specific to the SV40 late transcription elongation complex as well as the occupancy of several sites that bind transcription factors have been examined. These features have been determined by assessing blockage to restriction enzyme digestion. Cleavage specific to the elongation complex has been quantified using ternary complex analysis. This method involves radioactively labeling the complex by in vitro transcription followed by determining the extent of linearization by electrophoresis in an agarose gel. It was found that not only is the origin region devoid of nucleosomes, but there is also no stable factor occupancy at the BglI, SphI, KpnI and MspI restriction enzyme sites within this region. Thus these sites were cleaved to a high degree, meaning that the binding sites for a number of transcription factors, including OBP/TEF-1, TBP, DAP, as well as a proposed positioned nucleosome, are unoccupied in the native viral transcription elongation complex. The absence of these trans-acting factors from their respective binding sites in the elongation complex indicates that they bind only transiently, possibly cycling on and off during the transcription cycle. This finding implies that various forms of transcription complex are assembled and disassembled during transcription and thus supports a 'hit-and-run' model of factor function.

Interaction between T antigen and TEA domain of the factor TEF-1 derepresses simian virus 40 late promoter in vitro: identification of T-antigen domains important for transcription control

The large tumor antigen (TAg) of simian virus 40 regulates transcription of the viral genes. The early promoter is repressed when TAg binds to the origin and DNA replication begins, whereas the late promoter is activated by TAg through both replication-dependent and -independent mechanisms. Previously it was shown that activation is diminished when a site in the viral enhancer to which the factor TEF-1 binds is disrupted. We show here that the NH2-terminal region of TAg binds to the TEA domain of TEF-1, a DNA binding domain also found in the Drosophila scalloped and the Saccharomyces cerevisiae TEC1 proteins. The interaction inhibits DNA binding by TEF-1 and activates transcription in vitro from a subset of naturally occurring late start sites. These sites are also activated by mutations in the DNA motifs to which TEF-1 binds. Therefore, TEF-1 appears to function as a repressor of late transcription, and its involvement in the early-to-late shift in viral transcription is discussed. The mutation of Ser-189 in TAg, which reduces transformation efficiency in certain assays, disrupts the interaction with TEF-1. Thus, TEF-1 might also regulate genes involved in growth control.

A cell-specific factor represses stimulation of transcription in vitro by transcriptional enhancer factor 1

Transcription in HeLa cell extracts in vitro was stimulated 8- to 10-fold by a recombinant chimera, GAL-TEF-1, consisting of the DNA-binding domain of GAL4 and the activation function of the HeLa cell activator TEF-1. In contrast, only a 2- to 3-fold stimulation was obtained with GAL-TEF-1 in extracts from BJA-B lymphoid cells. Stimulation by GAL-TEF-1 in BJA-B extracts was dramatically increased by the addition of immunopurified HeLa cell TFIID, suggesting that BJA-B TFIID lacks or contains lower quantities of a TATA-binding-protein-associated factor(s) required for the activity of the TEF-1 activation function. However, chromatography, immunopurification, and transcriptional reconstitution experiments indicated that BJA-B extracts did not lack the previously identified TATA-binding-protein-associated factors required for TEF-1 activity but rather contained a negatively acting factor(s) which inhibited transactivation by GAL-TEF-1. These results indicate that the relative lack of activity of the TEF-1 activation function in vitro in BJA-B cell extracts does not result from the absence of positively acting factors from the presence of a cell-specific negatively acting factor(s).

A cell-specific factor represses stimulation of transcription in vitro by transcriptional enhancer factor 1

Transcription in HeLa cell extracts in vitro was stimulated 8- to 10-fold by a recombinant chimera, GAL-TEF-1, consisting of the DNA-binding domain of GAL4 and the activation function of the HeLa cell activator TEF-1. In contrast, only a 2- to 3-fold stimulation was obtained with GAL-TEF-1 in extracts from BJA-B lymphoid cells. Stimulation by GAL-TEF-1 in BJA-B extracts was dramatically increased by the addition of immunopurified HeLa cell TFIID, suggesting that BJA-B TFIID lacks or contains lower quantities of a TATA-binding-protein-associated factor(s) required for the activity of the TEF-1 activation function. However, chromatography, immunopurification, and transcriptional reconstitution experiments indicated that BJA-B extracts did not lack the previously identified TATA-binding-protein-associated factors required for TEF-1 activity but rather contained a negatively acting factor(s) which inhibited transactivation by GAL-TEF-1. These results indicate that the relative lack of activity of the TEF-1 activation function in vitro in BJA-B cell extracts does not result from the absence of positively acting factors from the presence of a cell-specific negatively acting factor(s).

Transcriptional activation by simian virus 40 large T antigen: requirements for simple promoter structures containing either TATA or initiator elements with variable upstream factor binding sites

The simian virus 40 large T antigen is a promiscuous transcriptional activator of many viral and cellular promoters. We show that the promoter structure necessary for T antigen-mediated transcriptional activation is very simple. A TATA or initiator element is required, in addition to an upstream factor-binding site, which can be quite variable. We found that promoters containing an SP1-, ATF-, AP1-, or TEF-I-binding site, in conjunction with a TATA element, can all be activated in the presence of T antigen. In addition, preference for specific TATA elements was indicated. Promoters containing the HSP70 TATA element functioned better than those with the adenovirus E2 TATA element, while promoters containing the simian virus 40 (SV40) early TATA element failed to be activated. In addition, simple promoters containing the initiator element from the terminal deoxynucleotidyltransferase gene could be activated by T antigen. The SV40 late promoter, a primary target for T antigen transcriptional activation, conforms to this simple promoter structure. The region from which most late transcripts initiate contains a cluster of initiator-like elements (SV40 nucleotides [nt] 250 to 335) forming an initiator region (IR). This lies downstream of the previously described octamer-TEF element (SV40 nt 199 to 218) which contains the TEF-I-binding sites shown to be necessary for T antigen-mediated transcriptional activation of the late promoter. We show that a simple late promoter made up of IR sequences and octamer-TEF element-containing sequences is transcriptionally activated by T antigen. These experiments also showed that specific sequences in the IR, SV40 nt 272 to 294, are particularly important for late promoter activation. Previous findings (M. C. Gruda, J. M. Zablotny, J. H. Xiao, I. Davidson, and J. C. Alwine, Mol. Cell. Biol. 13:961-969, 1993) suggested that T antigen could mediate transcriptional activation through interaction with the TATA-binding protein, as well as upstream bound transcription factors. Our present data are predicted by this model and suggest that at least one mechanism by which the T antigen manifests promiscuous transcriptional activation is its ability to interact with numerous transcription factors in a simple promoter context.

Efficient transcriptional activation of many simple modular promoters by simian virus 40 large T antigen

Simian virus 40 (SV40) large T antigen is a multifunctional protein which plays central roles during both lytic and transforming infections by SV40. It is a potent transcriptional activator and increases expression from the SV40 late promoter and from several cellular promoters. To understand better the transcriptional activation activity of large T antigen, we examined its ability to transactivate a set of simple modular promoters containing one of four upstream activation sequences coupled with one of three different TATA box sequences originally constructed and studied by Taylor and Kingston (Mol. Cell. Biol. 10:165-175, 1990). Large T antigen activated transcription from all of these simple promoters. The identity of the TATA box was a more important determinant of the final level of gene expression than was the identity of the upstream activating sequence element. We also determined the ability of a set of mutant SV40 large T antigens to activate a subset of these promoters. Several mutant SV40 large T antigens which had reduced ability to activate the complex SV40 late and Rous sarcoma virus long terminal repeat promoters showed reduced transcriptional activation activity on all of the modular promoters tested. We used a set of promoter derivatives of the human U6 small nuclear RNA promoter containing different TATA boxes and found that wild-type large T antigen could activate transcription from all of them, although to widely different levels of expression.

Simian virus 40 T antigen activates the late promoter by modulating the activity of negative regulatory elements

Late promoter activity measured before viral DNA replication results from a complex involvement of negative and positive cis-acting elements located both in the enhancer and in the 21-bp repeats. GC motifs located within the 21-bp repeats act in cooperation with sequences overlapping the early TATA box to down-regulate the late promoter activity. Analysis of insertion mutants indicates that the late promoter might be negatively regulated at least partially by the early promoter machinery. The GTI motif located within the enhancer as well as the GC motifs lose the ability to down-regulate the late promoter in the presence of T antigen. Results obtained with tsA58 protein indicate that two different domains of T antigen are involved in the negative autoregulation of the early promoter activity and in the release of the down-regulation of the late promoter by the GC motifs.

Role of the SV40 enhancer in the early to late shift in viral transcription

Simian virus 40 large tumor antigen is a multifunctional protein, with two of its roles being the promotion of viral DNA replication and replication-independent activation of viral transcription. Replication leads to a shift in transcription from the early-early to the late and late-early cap sites, through mechanisms poorly understood. The viral transcription enhancer contains sequences important for both early and late transcription, and we therefore have carried out experiments to evaluate its role in these events. We find that the ability of replication to lead to a shift diminishes when early-early transcription is made increasingly stronger by multimerizing the enhancer, and suggest that replication might lead to the shift by interfering with the ability of the enhancer to direct initiation to those sites. The natural situation in the virus of having two copies of this element might represent a compromise between maximizing both T antigen expression early in infection and late gene expression after replication begins. We also show that replication-independent transcription activation by T antigen is bidirectional and involves at least in part elements to which the factor TEF-1 binds.

trans activation of the simian virus 40 late promoter by large T antigen requires binding sites for the cellular transcription factor TEF-1

Simian virus 40 (SV40) T antigen stimulates the level of transcription from several RNA polymerase II promoters, including the SV40 late promoter. The mechanism of trans activation appears to be indirect since binding of T antigen to specific DNA sequences is not required. However, specific promoter elements that respond to T antigen have not previously been defined. We identified DNA sequences from the SV40 late promoter whose ability to stimulate transcription is induced by the expression of T antigen. In particular, the Sph I + II motifs of the SV40 enhancer can confer T-antigen inducibility to the normally uninducible herpes simplex virus thymidine kinase gene promoter when multiple copies of the sequence are inserted 5' of the transcription initiation site and TATA sequence. Binding sites for the cellular transcription factor TEF-1 and octamer binding proteins are contained within the Sph I + II motifs, as well as at other positions in the SV40 promoter. To study the role of individual protein-binding sites in trans activation by T antigen, mutations were constructed in various TEF-1 and octamer protein-binding sites of the SV40 late promoter. These mutations did not significantly affect basal promoter activity. However, mutation of all three TEF-1 sites prevented detectable activation by T antigen. DNase I footprinting of the mutated promoters with purified proteins demonstrated that inducibility by T antigen correlated with binding affinity of TEF-1 for the DNA and not with binding affinity of an octamer binding protein.

SV40 activates transcription from the transferrin receptor promoter by inducing a factor which binds to the CRE/AP-1 recognition sequence

During the course of lytic infection by simian virus 40 (SV40), expression of both the viral late genes and certain host cellular genes is induced. The promoter of the cellular transferrin receptor (TR) gene contains a DNA sequence which is similar to the AP-1- and AP-4-binding region in SV40 which has been implicated in the control of the viral late promoter. Expression of TR is needed for cells to enter S-phase and is therefore expected to be important for the SV40 lytic cycle. Here we show that the level of TR mRNA in vivo was increased by SV40 infection. A factor which activates transcription from the TR promoter in vitro was specifically induced in SV40-infected cells. Gel mobility shift assays with an oligonucleotide comprising this part of the TR promoter showed three nucleoprotein complexes to be formed with proteins from CV-1 cells. Following SV40 infection, one of the complexes was increased ten-fold. Formation of this complex was specifically reduced by competition with the phorbol ester-responsive element of the collagenase gene, implying that the factor is a member of the AP-1/Jun/Fos family. Cross-linking of the complex by ultraviolet light showed major DNA-binding components to be proteins of about 55 kD and 47 kD. Removal of this factor by adding the oligonucleotide to in vitro transcription reactions with the TR promoter, abolished the activation of TR transcription. The factor which binds to the TR promoter co-sedimented with SV40 chromosomes extracted late in infection. This suggests that similar transcriptional regulatory proteins are involved in controlling transcription from both the SV40 and the TR promoters, and that the virus can use a common mechanism to induce viral and host cellular transcription.

Simian virus 40 (SV40) T-antigen transcriptional activation mediated through the Oct/SPH region of the SV40 late promoter

Simian virus 40 (SV40) large T antigen is a promiscuous transcriptional activator of many viral and cellular promoters. The SV40 late promoter, a primary target for T-antigen transcriptional activation, contains a previously described T-antigen-activatable binding site (SV40 nucleotides 186 to 225). The T-antigen-activatable binding site element contains overlapping octamer (Oct)- and SPH (TEF-1)-binding sites (Oct/SPH site). Using this Oct/SPH site as an upstream element in a simple promoter, we show that the SPH sites are necessary for transcriptional activation by T antigen. In addition, we show that when Oct 1 is overproduced, it can eliminate T-antigen-mediated transcriptional activation, as well as basal activity, from the simple Oct/SPH promoter as well as the intact SV40 late promoter. This suggests that one function of T antigen in transcriptional activation of the late promoter is to alter factor binding at the Oct/SPH region to favor binding of factors to the SPH sites.

Characterization of SV40 enhancer motifs involved in positive and negative regulation of the constitutive late promoter activity; effect of T-antigen

By analyzing the late promoter activity of a series of nonreplicative recombinants mutated within the different enhancer motifs of SV40 we identified both positive and negative regulatory elements. In the absence of T-antigen, the motifs Sph and/or octamer, and to a lesser extent the motifs GTI and P, account for the constitutive expression of the late promoter. The motif GTII overlaps elements that negatively regulate the expression of the late promoter. These results indicate that the late promoter is down-regulated not only at the level of the GC motifs but also at the enhancer level. Moreover, we showed that T-antigen interacts with both positive and negative regulatory elements.

Stable growth of simian virus 40 recombinants containing multimerized enhancers

Multiple copies of each of three genetically defined simian virus 40 protoenhancers, A, B, and C, were able to substitute for the wild-type simian virus 40 enhancer. Although the recombinant viruses grew poorly, they could be propagated without the accumulation of enhancer rearrangements that might improve viability. Mutations that inactivate the multimerized B and C protoenhancers abolished virus growth, but, unexpectedly, a mutation that inactivates the octamer-enhanson within the B protoenhancer increased virus viability. This positive effect may reflect loss of repression of the B protoenhancer by the ubiquitous octamer-motif-binding protein Oct-1.

Sequence requirements for activation of replication by the SV40 transcriptional promoter or enhancer elements

Previous studies have demonstrated that the 21- or the 72-bp repeat transcriptional control elements enhance the efficiency of SV40 DNA replication in vivo, provided either of these repeats is located near the end of the core replication origin containing the 17-bp A + T-containing sequence. Using two sets of point mutants we have investigated the contributions of the various sequence motifs present in the 21- or the 72-bp repeats toward activation of replication. Regarding the contribution of the six GC motif components of the 21-bp repeats, we find that GC motif I, located closest to the core origin, is dispensable for activation of replication. A mutation in GC-I in fact causes an increase in replication efficiency. We also find that GC motifs I and II present in the nontandem copy of the 21-bp repeats are not sufficient to activate replication. Our present study indicates that a combination of three GC motifs such as II, III, and IV (including one of the two perfect, tandem copies of the 21-bp repeats) is important for activation of replication. Regarding the 72-bp repeat transcriptional enhancer region, we find mutations in a number of its individual motifs to have a negative consequence on replication, with mutations in the GT-I*/TC-II and Sph-II/octamer motifs exhibiting the most negative effects. Overall, we find that the replication activation effects of the 21- and the 72-bp repeats require the participation of multiple motifs present in them. Cellular factors binding to these motifs are expected to mediate their replication activation effects. For the most part, the motifs required for activation of replication are the same as those reported in earlier studies to be important for efficient early and late viral mRNA transcription.

Activity of simian DNA-binding factors is altered in the presence of simian virus 40 (SV40) early proteins: characterization of factors binding to elements involved in activation of the SV40 late promoter

The early proteins of simian virus 40 (SV40) large T and small t antigen (T/t antigen) can each cause the transcriptional activation of a variety of cellular and viral promoters. We showed previously that simian cellular DNA-binding factors (the Band A factors) bind to sequences within the SV40 late promoter which are important for transcriptional activation in the presence of the SV40 early proteins. Band A factors isolated from simian cells which produce T/t antigen (COS cells or SV40-infected CV-1 cells) have altered binding properties in comparison with the factors from normal simian cells (CV-1). This suggests that the transcriptional activation mediated by T/t antigen may be due to either modification of existing factors or induction of new members of a family of factors. We have purified the Band A factors from both COS and CV-1 cells and have determined the binding site by methylation interference and DNase protection footprinting. The COS cell factors have altered chromatographic properties on ion-exchange columns and have higher-molecular-weight forms than the CV-1 cell factors. Major forms of the CV-1 factors migrate between 20 and 24 kilodaltons, while the COS factors migrate between 20 and 28 kilodaltons. The binding sites for the factors from CV-1 and COS cells are similar, covering a rather broad region within the 72-base-pair repeat comprising the AP-1 site and the two-octamer binding protein (OBP100/Oct 1) sites, OBP I and OBP II. Specific binding competition analyses indicate that the two general regions within the binding site (the AP-1-OBP II site and the OBP I site) each retain partial binding ability; however, the factors bind best when the two regions are adjacent in a relatively specific spatial arrangement. The binding site for the Band A factors corresponds very well to sequences necessary for the activation of the late promoter as defined by deletion and base substitution mutagenesis studies (J. M. Keller and J. C. Alwine, Mol. Cell. Biol. 5:1859-1869, 1985; E. May, F. Omilli, M. Emoult-Lange, M. Zenke, and P. Chambon, Nucleic Acids Res. 15:2445-2461, 1987). These data, in combination with the data showing that the Band A factors are modified or induced in the presence of T/t antigen, strongly suggest that T/t antigen mediates its transcriptional activation function, at least in part, through the Band A factors.

Control elements situated downstream of the major transcriptional start site are sufficient for highly efficient polyomavirus late transcription

In a transient expression assay in mouse fibroblasts in which neither replication nor T-antigen synthesis occurred, the polyomavirus late promoter functioned faithfully and even more efficiently than the simian virus 40 early promoter. Surprisingly, the DNA sequences upstream of the main transcriptional start sites were not required to obtain the high mRNA level observed. It appeared to result from the combined action of a basal promoter element within the A enhancer domain and of a more downstream element, located in the VP3 intron and abutting the late splice donor. We also show that although an enhancer region was required, enhancer function per se was not. Instead, it appeared that only a defined subset of the DNA-protein interactions necessary for enhancer function was involved in late promoter activity.

Characterization of a minimal simian virus 40 late promoter: enhancer elements in the 72-base-pair repeat not required

A 272-base-pair (bp) portion of the simian virus 40 regulatory region containing the replication origin, Sp1-binding region, and part of the 72-bp direct repeats makes up a minimal late promoter that is able to direct late-direction RNA synthesis in vivo and in vitro. Fourteen linker-scan mutants within this region were characterized. Mutations in the Sp1-binding region decreased late expression both in vivo and in vitro. By contrast, mutations that eliminate genetically defined elements of the early transcriptional enhancer or that prevent binding of the transcription factors AP-1, AP-2, and AP-3 in the 72-bp repeat region had little or no effect on late-direction expression. These results argue that, at least under certain circumstances, the early transcriptional enhancer sequences are not required for simian virus 40 late gene expression.

Unidirectional deletion and linker scan analysis of the late promoter of the human papovavirus BK

We have previously shown that the late promoter of the human papovavirus BK (prototype) is contained within the three 68-bp repeats and a 66-bp region to the late side of the repeats which together constitute the early promoter enhancer. We have now carried out unidirectional deletion and linker scan analyses of these sequences to identify the major elements of the late promoter in human and monkey cells. Several important sequence motifs involved in late promoter function are found throughout this region. The most active ones correspond to previously defined binding sites for the transcription factors NF1 and Sp1 and a GC-rich region known to be important for early promoter function. The NF1 sequences may also be involved in negative regulation in some situations.

The late promoter of the human papovavirus BK is contained within the early promoter enhancer region

We have analyzed the sequences necessary for late promoter function and mapped the late mRNA start sites of the human papovavirus BK (prototype). Our results show that, under both replicating and nonreplicating conditions, the BKV late promoter is contained within the same region defined as the enhancer for the early promoter. This region consists of three 68-bp repeats (the middle one of which has an 18-bp deletion) and a 66-bp region containing an enhancer element denoted as c, located to the late side of the 68-bp repeats. Deletions within the early enhancer domain indicate that elements of the late promoter are found throughout the entire region.

Capturing nuclear sequence-specific DNA-binding proteins by using simian virus 40-derived minichromosomes

We have used recombinant simian virus 40 (SV40) minichromosomes to retrieve sequence-specific DNA-binding proteins derived from the cell nucleus of COS-7 cells. We showed that the transcription factors AP-1 and Sp1 are stably bound to the SV40 DNA late in viral infection. Under similar conditions, minichromosomes carrying the rat insulin (rINS1) enhancer, which is under negative regulation in COS-7 cells, bound two proteins which mapped to distinct regions of the rINS1 enhancer. The SV40 P element competed for one of these proteins which bound to the region from -198 to -230. This factor may be related to AP-1. The other factor selectively bound a regulatory element in the region from -92 to -124 of the insulin enhancer. These proteins may play a role in regulating the rINS1 enhancer function.

Enhancer binding factors AP-4 and AP-1 act in concert to activate SV40 late transcription in vitro

The simian virus 40 (SV40) transcriptional enhancer is composed of multiple cis-acting DNA sequence motifs, each individually having a two- to fourfold effect on the efficiency of transcription. When various distinct cis-elements act in combination, however, a dramatic enhancement of transcription initiation often results. SV40-enhancer A-domain sequences were previously shown to be important for early and late transcription in vivo. Here we report the isolation of the enhancer binding factor AP-4, which recognizes a motif in this domain. Purified AP-4 activates SV40 late transcription in vitro, and this stimulation is augmented by the addition of transcription factor AP-1 which binds to adjacent sequences in the A-domain, suggesting coordinate action of the two factors for transcriptional enhancement. AP-1 also represses late transcription from a major in vitro start site which is poorly used in vivo, indicating that AP-1 can act as both a positive and negative regulator of SV40 late transcription. Thus by manipulating the levels of different trans-acting factors in vitro, we can recreate the pattern of SV40 late initiation observed during the viral lytic cycle in vivo.

Functional anatomy of the simian virus 40 late promoter

We have examined the control sequences for the late promoter function of simian virus 40 (SV40) in COS-1 cells which produce SV40 T antigen constitutively. Plasmids were constructed by cloning mutant late promoter segments upstream from sequences coding for the bacterial chloramphenicol acetyltransferase (CAT) gene, and were converted to "double-origin" type by inserting functional replication origin segments downstream from the CAT gene for replicative competence when necessary. The late promoter activity was determined by transient expression assay of the CAT mRNA and enzyme activity levels following DNA-mediated gene transfer into COS-1 cells. We find that the minimal replication origin and the 21-bp repeat containing T antigen and transcription factor Sp1 binding sites, respectively, are dispensable for late promoter function provided that one copy of the 72-bp repeat enhancer is present. We have mapped within the 72-bp repeat the major late promoter component in a 68-bp fragment (located between nucleotides 205 and 272), and found an overlapping 55-bp fragment (located between nucleotides 179 and 234) to have about one-fifth of the late promoter activity. Both the 68- and 55-bp fragments lack some of the core sequence elements required of the 72-bp repeat for transcriptional enhancer activity, and lack the ability to enhance the activity of the SV40 early promoter. The results suggest that the organization of functional units of the 72-bp repeat required for transcriptional enhancement of the early promoter is different from that required for late promoter function. The 21-bp repeat was found to have some late promoter activity located within the origin-distal copy in the absence of the 72-bp repeat. In association with the 21-bp repeat, the otherwise dispensable origin-proximal 22-bp of the 72-bp repeat containing activator protein AP-1 binding site augmented late promoter activity by three- to fourfold.

Capturing nuclear sequence-specific DNA-binding proteins by using simian virus 40-derived minichromosomes

We have used recombinant simian virus 40 (SV40) minichromosomes to retrieve sequence-specific DNA-binding proteins derived from the cell nucleus of COS-7 cells. We showed that the transcription factors AP-1 and Sp1 are stably bound to the SV40 DNA late in viral infection. Under similar conditions, minichromosomes carrying the rat insulin (rINS1) enhancer, which is under negative regulation in COS-7 cells, bound two proteins which mapped to distinct regions of the rINS1 enhancer. The SV40 P element competed for one of these proteins which bound to the region from -198 to -230. This factor may be related to AP-1. The other factor selectively bound a regulatory element in the region from -92 to -124 of the insulin enhancer. These proteins may play a role in regulating the rINS1 enhancer function.

Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes

The promoter for eukaryotic genes transcribed by RNA polymerase B can be divided into the TATA box (located at -30) and startsite (+1), the upstream element (situated between -40 and about -110), and the enhancer (no fixed position relative to the startsite). Trans-acting factors, which bind to these elements, have been identified and at least partially purified. The role of the TATA box is to bind factors which focus the transcription machinery to initiate at the startsite. The upstream element and the enhancer somehow modulate this interaction, possibly through direct protein-protein interactions. Another class of transcription factors, typified by viral proteins such as the adenovirus EIA products, do not appear to require binding to a particular DNA sequence to regulate transcription. The latest findings in these various subjects are discussed.

Organization of the transcriptional control region of the E1b gene of adenovirus type 5

Genetic analysis of the transcriptional control sequences of the E1b gene of adenovirus type 5 identified two regions that stimulated specific transcription by whole cell extracts from uninfected cells. The first region, located within 50 nucleotides (position -50) 5' to the transcription initiation (cap) site, contains a G+C-rich consensus-binding site (GC box) for the transcription factor Sp1 and a TATA box. Unambiguous stimulatory activity of the second region, between positions -358 and -127, was observed only in the absence of the GC box. DNase I protection experiments (footprinting) with crude nuclear extracts from uninfected cells revealed multiple DNA-protein interactions at the control region. Proximal to the initiation site, both the GC box and the cap site were protected; however, protection of the TATA box was not observed. In the distal region, four protein-binding sites, designated I through IV, were located between positions -250 and -120. Three of the four mapped in protein-coding sequences of the adjacent E1a gene. Sites I and II were 5' to position -218 whereas sites III and IV were 3' to position -218. This finding was consistent with results of the transcriptional analysis indicating that subsets of the distal region were sufficient for stimulation of transcription in vitro in the absence of the GC box. Within the boundaries of site I, a 10-base-pair protected sequence was similar to one located 5' to the adenovirus E1a, E2a, E3, E4, E2 late, and polypeptide IX transcription initiation sites. Sequences within the boundaries of the other three sites were similar to those within other viral and cellular enhancers.

Contribution of different GC-motifs to the control of simian virus 40 late promoter activity

During the course of lytic infection the 21-bp repeat region regulates differentially the late gene expression; a mutant deleted for this region expresses late genes either to a higher level in the absence of T antigen or to a lower level in the late phase of infection as compared to wild type (23). By analysing a series of clustered point mutations generated within the GC-motifs we show that i) mutations within motifs I and II stimulate late transcription two to three-fold, suggesting that competition for transcription machinery between early-early and late promoters is mediated by these two motifs, ii) after viral replication, simultaneous mutations within motifs IV, V and VI decrease to 23% the efficiency of late transcription, indicating that these motifs are elements of the late promoter. Moreover comparison of results presented in this paper with results published by Barrera-Saldana et al. strongly suggest that late-early and late promoters are regulated in a similar manner.