In vitro transcription of adenovirus

Characterization of adeno-associated virus rep protein inhibition of adenovirus E2a gene expression

Adeno-associated virus (AAV) replication (Rep) proteins are pleiotropic effectors of viral DNA replication, RNA transcription, and site-specific integration into chromosome 19. In addition to regulating AAV gene expression, the Rep proteins modulate expression of a variety of cellular and viral genes. In this report we investigate Rep-mediated effects on expression of the adenovirus (Ad) E2a gene and the Ad major late promoter. We have found that all four Rep proteins repress E2a expression at the protein level, with Rep40 showing the weakest repression. Mutations in the purine nucleotide binding (PNB) site weakened each of the protein's abilities to repress expression. Analysis of steady-state E2a mRNA showed that Rep proteins decreased mRNA levels, but to a lesser extent than E2a protein levels. Analysis of mRNA stability demonstrated that neither Rep78 nor Rep52 affected E2a mRNA stability, suggesting that the decrease in mRNA is due to Rep-mediated inhibition of Ad E2a transcription. To determine if Rep68 proteins could directly inhibit RNA transcription, we performed in vitro transcription assays using HeLa nuclear extracts supplemented with Rep68 and Rep68PNB. We demonstrate that Rep68, but not mutant Rep68PNB, blocked in vitro transcription of a template containing the Ad major late promoter. These results provide insight into how AAV and its encoded Rep proteins interact with Ad and provide a model system for the study of AAV and host-cell interactions.

Evidence that USF can interact with only a single general transcription complex at one time

By in vitro analysis, the major late promoter (MLP) of adenovirus has been shown to be a simple promoter requiring two elements for efficient transcription: a minimal promoter element (MPE), where the general transcription factor-polymerase II complex binds, and a single functional upstream promoter element (UPE) which interacts with USF. Two hundred bases upstream of the MLP cap site and divergently oriented is the IVa2 promoter. This promoter has its own MPE but shares the MLP UPE, suggesting the possibility that these promoters are coordinately regulated. To determine mechanistically how this might function, we replaced the weak IVa2 minimal promoter with a strong MPE (from the viral E1A gene) and observed mutual inhibition of both promoters and unstable transcription factor binding. Only by duplication of the UPE could this inhibition be relieved. When tested independently, both promoters were shown to require the USF site for maximal activity. These results are compatible with a model in which USF can stably interact with only one transcription complex at a time. When two divergently oriented general transcription complexes compete efficiently for binding of USF, transcription is reduced to the same levels as if the USF site were absent.

Evidence that USF can interact with only a single general transcription complex at one time

By in vitro analysis, the major late promoter (MLP) of adenovirus has been shown to be a simple promoter requiring two elements for efficient transcription: a minimal promoter element (MPE), where the general transcription factor-polymerase II complex binds, and a single functional upstream promoter element (UPE) which interacts with USF. Two hundred bases upstream of the MLP cap site and divergently oriented is the IVa2 promoter. This promoter has its own MPE but shares the MLP UPE, suggesting the possibility that these promoters are coordinately regulated. To determine mechanistically how this might function, we replaced the weak IVa2 minimal promoter with a strong MPE (from the viral E1A gene) and observed mutual inhibition of both promoters and unstable transcription factor binding. Only by duplication of the UPE could this inhibition be relieved. When tested independently, both promoters were shown to require the USF site for maximal activity. These results are compatible with a model in which USF can stably interact with only one transcription complex at a time. When two divergently oriented general transcription complexes compete efficiently for binding of USF, transcription is reduced to the same levels as if the USF site were absent.

A potent GAL4 derivative activates transcription at a distance in vitro

Transcription of a typical eukaryotic gene by RNA polymerase II is activated by proteins bound to sites found near the beginning of the gene as well as to sites, called enhancers, located a great distance from the gene. According to one view, the primary difference between an activator that can work at a large distance and one that cannot is that the former bears a particularly strong activating region; the stronger the activating region, the more readily the activator interacts with its target bound near the transcriptional start site, with the intervening DNA looping out to accommodate the reaction. One alternative view is that the effect of proteins bound to enhancers might require some special aspect of cellular or chromosome structure. Consistent with the first view, an activator bearing an unusually potent activating region can stimulate transcription of a mammalian gene in a HeLa nuclear extract when bound as far as 1.3 kilobase pairs upstream or 320 base pairs downstream of the transcriptional start site.

Sp1 activates transcription without enhancing DNA-binding activity of the TATA box factor

We have studied the interactions of the Sp1 and IID transcription factors with a simple RNA polymerase II promoter. The adenovirus E1B core promoter consists essentially of a GC box and a TATA box, binding sites for the Sp1 and IID transcription factors, respectively. The E1B promoter is accurately transcribed in vitro using a mammalian transcription system. Sp1 activates E1B transcription in vitro in reactions using IID factor isolated from either human or yeast cells. In DNase I footprinting studies, Sp1 bound rapidly to its recognition sequence even at 0 degrees C (t1/2 less than 1 min). In contrast, yeast IID bound more slowly (t1/2 approximately 6 min at 25 degrees C) and required thermal energy for stable binding to the TATA box sequence. Dissociation rates were measured by the addition of specific oligonucleotide competitors to preformed DNA-protein complexes. Sp1 dissociates rapidly (t1/2 less than 1 min) at 25 degrees C, while yeast IID dissociates with an estimated t1/2 of 1 h at 25 degrees C. Sp1 and yeast IID bound to the E1B promoter simultaneously but independently. The rates of binding and dissociation of these factors were not significantly affected by the presence of the other factor. Bound Sp1 factor did not alter or enhance the yeast IID footprint. Oligonucleotide challenge of in vitro transcription reactions indicated that Sp1 also did not enhance the binding of the human IID factor to the E1B promoter. Thus the Sp1 factor activates transcription of the E1B gene by a mechanism that does not enhance the DNA-binding activity of the IID factor. Sp1 factor activates E1B transcription by 5- to 10-fold in vitro. Under these in vitro transcription conditions, transcripts due to reinitiation from an individual promoter complex contribute only a small portion of the total yield of E1B transcripts. Thus Sp1 cannot activate transcription by increasing the rate of initiation events per complex. Instead it appears that Sp1 acts by increasing the number of productive transcription complexes formed in vitro.

NF-kappa B-mediated activation of the human immunodeficiency virus enhancer: site of transcriptional initiation is independent of the TATA box

The activation of the human immunodeficiency virus (HIV) enhancer in T cells can occur through multiple independent pathways. This enhancer is stimulated by NF-kappa B or through alternative mechanisms, including E1A transactivation, which is dependent on the TATA box. In this report, the role of the TATA box in activation by NF-kappa B is examined. E1A stimulation of the HIV enhancer requires the presence of the TATA sequence in the sense orientation. Analysis of mutant HIV enhancer plasmids shows that basal mRNA levels are reduced when the TATA sequence is altered but that inducibility of NF-kappa B and the site of transcriptional initiation are unchanged. These data suggest that transcriptional initiation in this class II promoter is determined by an initiator factor which does not require binding to the TATA sequence. Because kappa B is found in a variety of viruses, this mechanism may be relevant to the activation of other viral enhancers.

Sp1 activates transcription without enhancing DNA-binding activity of the TATA box factor

We have studied the interactions of the Sp1 and IID transcription factors with a simple RNA polymerase II promoter. The adenovirus E1B core promoter consists essentially of a GC box and a TATA box, binding sites for the Sp1 and IID transcription factors, respectively. The E1B promoter is accurately transcribed in vitro using a mammalian transcription system. Sp1 activates E1B transcription in vitro in reactions using IID factor isolated from either human or yeast cells. In DNase I footprinting studies, Sp1 bound rapidly to its recognition sequence even at 0 degrees C (t1/2 less than 1 min). In contrast, yeast IID bound more slowly (t1/2 approximately 6 min at 25 degrees C) and required thermal energy for stable binding to the TATA box sequence. Dissociation rates were measured by the addition of specific oligonucleotide competitors to preformed DNA-protein complexes. Sp1 dissociates rapidly (t1/2 less than 1 min) at 25 degrees C, while yeast IID dissociates with an estimated t1/2 of 1 h at 25 degrees C. Sp1 and yeast IID bound to the E1B promoter simultaneously but independently. The rates of binding and dissociation of these factors were not significantly affected by the presence of the other factor. Bound Sp1 factor did not alter or enhance the yeast IID footprint. Oligonucleotide challenge of in vitro transcription reactions indicated that Sp1 also did not enhance the binding of the human IID factor to the E1B promoter. Thus the Sp1 factor activates transcription of the E1B gene by a mechanism that does not enhance the DNA-binding activity of the IID factor. Sp1 factor activates E1B transcription by 5- to 10-fold in vitro. Under these in vitro transcription conditions, transcripts due to reinitiation from an individual promoter complex contribute only a small portion of the total yield of E1B transcripts. Thus Sp1 cannot activate transcription by increasing the rate of initiation events per complex. Instead it appears that Sp1 acts by increasing the number of productive transcription complexes formed in vitro.

Promoters of bovine papillomavirus type 1: in vitro activity and utilization

Five of six bovine papillomavirus type 1 (BPV-1) promoters which were previously mapped by determining the 5' termini of viral mRNAs from bovine fibropapillomas and BPV-1-transformed cells were found to be active under in vitro transcription conditions. Transcription initiation at each of these promoters was accurate at the nucleotide level as determined by primer extension analysis. The most active promoter in vitro was P89, a typical RNA polymerase II promoter with both TATA and CAAT boxes. The promoters P7185 and P2443 also have TATA-like boxes, but none of the other promoters contain these typical regulatory elements.

Delineation of DNA sequences that are important for in vitro transcription from the adenovirus EIIa late promoter

Late in infection, transcription of the EIIa gene is initiated primarily at map unit 72 of the adenovirus genome. A cell-free nuclear extract system was used to determine sequence elements important for the function of this late promoter. In such a system, the transcriptional activity of a circular template was found to be much higher (5- to 10-fold) than that of a linear template. The effect of template topology appeared to be dependent on two distal upstream elements with 5' boundaries located near -265 to -223 and -147 to -133 (in relation to the initiation site), since deletions of these regions reduced transcription of the circular template, in a stepwise fashion, to a level similar to that observed with the linear template. Further deletions revealed an element in the -116 region that appeared to be more important for transcription of the circular template (10-fold reduction) than for transcription of the linear template (3-fold reduction). Lastly, deletion of the TACAAA sequence in the -29 region resulted in further reduction in transcription, indicating that this element functions as a promoter in vitro.

Identification of two transcription factors that bind to specific elements in the promoter of the adenovirus early-region 4

Two kinds of trans-acting factors that regulate transcription from the promoter of the adenovirus early-region 4 (E4) have been identified by reconstituting nuclear extracts of HeLa cells. They were designated E4TF1 and E4TF3 for E4 transcription factors. These factors were responsible for efficient and accurate transcription in vitro from the E4 promoter, as were another transcription factor, designated E4TF2, and a crude fraction containing endogenous RNA polymerase II. E4TF1 stimulated transcription from the E4 promoter but not from the major late promoter or the E4 mutant promoter lacking the E4TF1-binding site. Footprint analysis of E4TF1 revealed that it binds to a specific region, residing between 132 and 152 base pairs upstream from the initiation site of the E4 mRNA. E4TF3 also regulated transcription from the E4 promoter. E4TF3 protected four ca. 20-base-pair regions in a DNase I footprinting assay. They were located around 40, 160, 230, and 260 base pairs upstream from the initiation site of E4 mRNA. Specific inhibition of E4 transcription was observed by addition of DNA fragments covering one of the E4TF1- and E4TF3-binding sites to in vitro transcription assays. These results suggest that both E4TF1 and E4TF3 regulate E4 transcription by binding to the specific upstream elements in the E4 promoter. These factors may be involved in the E1A transactivation of E4 transcription.

Delineation of DNA sequences that are important for in vitro transcription from the adenovirus EIIa late promoter

Late in infection, transcription of the EIIa gene is initiated primarily at map unit 72 of the adenovirus genome. A cell-free nuclear extract system was used to determine sequence elements important for the function of this late promoter. In such a system, the transcriptional activity of a circular template was found to be much higher (5- to 10-fold) than that of a linear template. The effect of template topology appeared to be dependent on two distal upstream elements with 5' boundaries located near -265 to -223 and -147 to -133 (in relation to the initiation site), since deletions of these regions reduced transcription of the circular template, in a stepwise fashion, to a level similar to that observed with the linear template. Further deletions revealed an element in the -116 region that appeared to be more important for transcription of the circular template (10-fold reduction) than for transcription of the linear template (3-fold reduction). Lastly, deletion of the TACAAA sequence in the -29 region resulted in further reduction in transcription, indicating that this element functions as a promoter in vitro.

Human CCAAT-binding proteins have heterologous subunits

We have characterized three distinct proteins present in HeLa cell extracts that specifically recognize different subsets of transcriptional elements containing the pentanucleotide sequence CCAAT. One of these CCAAT-binding proteins, CP1, binds with high affinity to CCAAT elements present in the human alpha-globin promoter and the adenovirus major late promoter (MLP). A second protein, CP2, binds with high affinity to a CCAAT element present in the rat gamma-fibrinogen promoter. Finally, the third CCAAT-binding protein is nuclear factor I (NF-I), a cellular DNA-binding protein that binds to the adenovirus origin of replication and is required for the initiation of adenoviral replication. CP1, CP2, and NF-I are distinct activities in that each binds to its own recognition site with an affinity that is at least three orders of magnitude higher than that with which it binds to the recognition sites of the other two proteins. Surprisingly, CP1, CP2, and NF-I each appear to recognize their binding site with highest affinity as a multisubunit complex composed of heterologous subunits. In the case of CP1, two different types of subunits form a stable complex in the absence of a DNA-binding site. Moreover, both subunits are present in the CP1-DNA complex. We thus propose the existence of a family of related multisubunit CCAAT-binding proteins that are composed of heterologous subunits.

Alternative mechanisms for activation of human immunodeficiency virus enhancer in T cells

The expression of human immunodeficiency virus (HIV) after T cell activation is regulated by NF-kappa B, an inducible DNA-binding protein that stimulates transcription. Proteins encoded by a variety of DNA viruses are also able to activate expression from the HIV enhancer. To determine how this activation occurs, specific genes from herpes simplex virus type 1 and adenovirus that activate HIV in T lymphoma cells have been identified. The cis-acting regulatory sequences in the HIV enhancer that mediate their effect have also been characterized. The relevant genes are those for ICP0-an immediate-early product of herpes simplex virus type 1-and the form of E1A encoded by the 13S messenger RNA of adenovirus. Activation of HIV by adenovirus E1A was found to depend on the TATA box, whereas herpesvirus ICP0 did not work through a single defined cis-acting element. These findings suggest multiple pathways that can be used to bypass normal cellular activation of HIV, and they raise the possibility that infection by herpes simplex virus or adenovirus may directly contribute to the activation of HIV in acquired immunodeficiency syndrome by mechanisms independent of antigenic stimulation in T cells.

Identification of two transcription factors that bind to specific elements in the promoter of the adenovirus early-region 4

Two kinds of trans-acting factors that regulate transcription from the promoter of the adenovirus early-region 4 (E4) have been identified by reconstituting nuclear extracts of HeLa cells. They were designated E4TF1 and E4TF3 for E4 transcription factors. These factors were responsible for efficient and accurate transcription in vitro from the E4 promoter, as were another transcription factor, designated E4TF2, and a crude fraction containing endogenous RNA polymerase II. E4TF1 stimulated transcription from the E4 promoter but not from the major late promoter or the E4 mutant promoter lacking the E4TF1-binding site. Footprint analysis of E4TF1 revealed that it binds to a specific region, residing between 132 and 152 base pairs upstream from the initiation site of the E4 mRNA. E4TF3 also regulated transcription from the E4 promoter. E4TF3 protected four ca. 20-base-pair regions in a DNase I footprinting assay. They were located around 40, 160, 230, and 260 base pairs upstream from the initiation site of E4 mRNA. Specific inhibition of E4 transcription was observed by addition of DNA fragments covering one of the E4TF1- and E4TF3-binding sites to in vitro transcription assays. These results suggest that both E4TF1 and E4TF3 regulate E4 transcription by binding to the specific upstream elements in the E4 promoter. These factors may be involved in the E1A transactivation of E4 transcription.

Regulation of in vitro and in vivo transcription of early-region IV of adenovirus type 5 by multiple cis-acting elements

A series of deletion mutants spanning the promoter of the adenovirus early-region IV (EIV) gene were tested for transcriptional activity, using both in vitro and in vivo assays. Four distinct domains had additive effects on efficient transcription from the EIV promoter in HeLa whole-cell extracts. The first resided 20 to 27 bases upstream of the initiation site and included the TATA box. Deletion of the TATA box drastically reduced the transcriptional activity in vitro but had a lesser effect in vivo. The second region extended from -32 to -177 and contained two 17-base-pair inverted repeats, centered around -40 and -162. Sequences lying between -140 and -173 were important for efficient transcription since deletion of this region reduced the activity fourfold. Deletion of either one of the two inverted repeats or insertion of DNA fragments between them resulted in the synthesis of extra transcripts that initiated at sites upstream from the EIV site. The third region was located between -198 and -250 and contains three guanosine-plus-cytosine-rich sequences, present around -212 (GGGCGG), -233 (GGGCGG), and -251 (CGCGGG). The fourth, most upstream region was located between -260 and -307. Deletion of this region, which contains the NF-1 factor-binding site, slightly reduced transcriptional activity both in vivo and in vitro. The data indicate that multiple cis-acting elements are required for efficient transcription from the EIV promoter in both in vitro and in vivo systems.

Activation of adenovirus promoters by the adenovirus E1A protein in cell-free extracts

The primary product of the adenovirus E1A gene is a protein that is sufficient for controlling host-cell proliferation and immortalizing primary rodent cells. The mechanism by which the protein induces these cellular effects is poorly understood, but might be linked to its ability to regulate RNA transcription from a number of viral and cellular genes. The mechanism of E1A's transcriptional-activation (trans-activation) was studied here by monitoring the protein's effect on specific adenovirus promoters in two types of transcriptional systems in vitro. One of these systems consisted of extracts from transformed cells constitutively expressing E1A, and the other consisted of extracts of HeLa cells supplemented with a plasmid-encoded E1A protein purified from Escherichia coli. The results show that the E1A protein specifically stimulates transcription from adenovirus promoters; thus, the induction of cellular transcription factors is not necessary to explain the stimulation of transcription by E1A.

The requirement for the A block promoter element in tRNA gene transcription in vitro depends on the ionic environment

When yeast cell extracts that faithfully transcribe class III genes are provided with different electrolyte ions, the pattern of transcripts changes. A transcription unit in pBR322, silent with 0.1M potassium chloride, becomes active in the presence of 0.1M potassium acetate. This pseudogene depends on transcription factors B and C and RNA polymerase III like a tRNA gene. The transcribed region contains the only sequence in pBR322 homologous to the modified B block consensus sequence GTTCRDNNC found in normal tRNA genes. The presence of a block A sequence is less evident. When a block A deleted tRNA(GLU) gene was constructed, it behaved similarly: poorly transcribed with 0.1M potassium chloride, well transcribed with 0.1M potassium acetate. In fact, the deletion of the A block promoter element from the tRNA(GLU) gene did not dramatically lower its transcription when tested with potassium acetate, while it had a strong negative effect when tested with potassium chloride. Consequently the requirement for this promoter element is not constant but is a function of the electrolyte composition.

Regulation of in vitro and in vivo transcription of early-region IV of adenovirus type 5 by multiple cis-acting elements

A series of deletion mutants spanning the promoter of the adenovirus early-region IV (EIV) gene were tested for transcriptional activity, using both in vitro and in vivo assays. Four distinct domains had additive effects on efficient transcription from the EIV promoter in HeLa whole-cell extracts. The first resided 20 to 27 bases upstream of the initiation site and included the TATA box. Deletion of the TATA box drastically reduced the transcriptional activity in vitro but had a lesser effect in vivo. The second region extended from -32 to -177 and contained two 17-base-pair inverted repeats, centered around -40 and -162. Sequences lying between -140 and -173 were important for efficient transcription since deletion of this region reduced the activity fourfold. Deletion of either one of the two inverted repeats or insertion of DNA fragments between them resulted in the synthesis of extra transcripts that initiated at sites upstream from the EIV site. The third region was located between -198 and -250 and contains three guanosine-plus-cytosine-rich sequences, present around -212 (GGGCGG), -233 (GGGCGG), and -251 (CGCGGG). The fourth, most upstream region was located between -260 and -307. Deletion of this region, which contains the NF-1 factor-binding site, slightly reduced transcriptional activity both in vivo and in vitro. The data indicate that multiple cis-acting elements are required for efficient transcription from the EIV promoter in both in vitro and in vivo systems.

Identification of a transcription factor which interacts with the distal domain of the adenovirus IVa2 promoter

For efficient in vitro transcription from the adenovirus IVa2 promoter, two upstream control regions, one proximal to the RNA initiation site at nucleotide position (np) -39 to -48 and the other a distal domain between np -152 and -179, are necessary. By using the band competition assay of Strauss and Varshavsky (Cell 37:889, 1984), we identified a factor which binds to the IVa2 promoter. Competition studies with various deletion mutants demonstrated that the region present 152 to 160 base pairs upstream of the IVa2 transcription start site was necessary for binding of this factor. DNase I footprinting assays demonstrated directly that this factor interacted with the distal domain of the IVa2 promoter. This factor was necessary for efficient transcription from the IVa2 promoter, as evidenced by the ability of a DNA fragment containing the binding site for this factor to inhibit transcription. Its role in bidirectional activation of transcription from major late and IVa2 promoters is discussed.

In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene

We have developed an in vitro transcription system for the murine dihydrofolate reductase gene. Although transcription in vitro from a linearized template was initiated at the same start sites as in vivo, the correct ratios were more closely approximated when a supercoiled template was used. In addition, whereas the dihydrofolate reductase promoter functions bidirectionally in vivo, the initiation signals directed unidirectional transcription in this in vitro system. The dihydrofolate reductase gene does not have a typical TATA box, but has four GGGCGG hexanucleotides within 300 base pairs 5' of the AUG codon. Deletion analysis suggested that, although sequences surrounding each of the GC boxes could specify initiation approximately 40 to 50 nucleotides downstream, three of the four GC boxes could be removed without changing the accuracy or efficiency of initiation at the major in vivo site. The dihydrofolate reductase promoter initiated transcription very rapidly in vitro, with transcripts visible by 1 min and almost maximal by 2 min at 30 degrees C with no preincubation. Nuclear extracts prepared from cells blocked in the S phase by aphidicolin or from adenovirus-infected cells at 16 h postinfection had enhanced dihydrofolate reductase transcriptional activity. This increased in vitro transcription mimicked the increase in dihydrofolate reductase mRNA seen in S-phase cells and suggested the presence of a cell-cycle-specific factor(s) which stimulated transcription from the dihydrofolate reductase gene.

The promoter for the late gene encoding Vp5 of herpes simplex virus type 1 is recognized by cell extracts derived from uninfected cells

The ability of whole-cell extracts from uninfected HeLa cells to recognize the promoter for the herpes simplex virus type 1 late gene encoding the major capsid protein Vp5 was investigated by using both in vitro transcriptional and S1 nuclease protection analysis. This gene promoter was recognized by the cell extracts and produced abundant amounts of transcript in the absence of any other virus-encoded factors. This transcript was shown to arise, in vitro, from specific initiation at or very near the physiological mRNA start site. Thus, it appears that cell extracts from uninfected HeLa cells can efficiently recognize both early- and late-gene promoters.

Adenovirus early region 1A protein increases the number of template molecules transcribed in cell-free extracts

Protein encoded by adenovirus early region 1A (E1A) stimulates transcription from adenovirus promoters in vivo. Here we show that this effect can be observed in vitro. In a run-off transcription assay from the adenovirus serotype 2 (Ad2) major late promoter, extracts prepared 20 hr postinfection were 5-15 times more active than mock-infected-cell extracts prepared in parallel. Similar results were observed for in vitro transcription from the protein IX and E3 adenovirus promoters, whereas a 2-fold increase was observed for the human beta-globin promoter. The increased activities of infected-cell extracts did not depend on the expression of viral late proteins or the small E1A-encoded proteins but did require expression of the large E1A protein. These results are consistent with the large E1A protein stimulating transcription in vitro as it does in vivo. By limiting in vitro transcription to one initiation per template, we found that the higher activity of an infected-cell extract was due to an increase in the number of templates transcribed. These results suggest that the large E1A protein either increases the number of active transcription factors in infected cells or facilitates the interaction of cellular transcription factors with promoter DNA.

In vitro transcription and delimitation of promoter elements of the murine dihydrofolate reductase gene

We have developed an in vitro transcription system for the murine dihydrofolate reductase gene. Although transcription in vitro from a linearized template was initiated at the same start sites as in vivo, the correct ratios were more closely approximated when a supercoiled template was used. In addition, whereas the dihydrofolate reductase promoter functions bidirectionally in vivo, the initiation signals directed unidirectional transcription in this in vitro system. The dihydrofolate reductase gene does not have a typical TATA box, but has four GGGCGG hexanucleotides within 300 base pairs 5' of the AUG codon. Deletion analysis suggested that, although sequences surrounding each of the GC boxes could specify initiation approximately 40 to 50 nucleotides downstream, three of the four GC boxes could be removed without changing the accuracy or efficiency of initiation at the major in vivo site. The dihydrofolate reductase promoter initiated transcription very rapidly in vitro, with transcripts visible by 1 min and almost maximal by 2 min at 30 degrees C with no preincubation. Nuclear extracts prepared from cells blocked in the S phase by aphidicolin or from adenovirus-infected cells at 16 h postinfection had enhanced dihydrofolate reductase transcriptional activity. This increased in vitro transcription mimicked the increase in dihydrofolate reductase mRNA seen in S-phase cells and suggested the presence of a cell-cycle-specific factor(s) which stimulated transcription from the dihydrofolate reductase gene.

Human U2 small nuclear RNA genes contain an upstream enhancer

The human U1 and U2 snRNA genes lack an obvious TATA box, but are extremely powerful RNA polymerase II transcription units capable of accurately initiating at least one transcript per gene every 2-4 s. We have investigated the location of cis-acting regulatory elements within the flanking sequences of human U2 and U1 genes. By introducing marked human U2 genes into HeLa cells on SV40- and pUC13-based vectors, we found that transient expression of the marked U2 gene did not require the SV40 enhancer. The U2 promoter element responsible for SV40 enhancer-independent U2 expression was localized within the 5'-flanking sequence of the gene, and shown to stimulate transcription from the U2 basal promoter in an orientation- and position-independent fashion. In addition, the U2 element could be functionally replaced by either the SV40 enhancer or by distal sequences from the human U1 promoter. We conclude that the human U2 and U1 genes contain functionally equivalent enhancer elements. Moreover, since the human U2 enhancer sequences resemble the Xenopus U2 enhancer-like element, enhancers appear to be a general feature of vertebrate snRNA promoter structure.

Identification of a cellular transcription factor involved in E1A trans-activation

We have employed a gel assay to detect a transcription factor in nuclear extracts of adenovirus-infected cells that interacts with the adenovirus E2 promoter, an E1A inducible promoter. Binding of the factor to the promoter protected sequences between -33 and -74 from DNAase cleavage in a footprint assay. This region was also protected from exonuclease III digestion. These sequences coincide with those previously shown to be essential for promoter activity and E1A stimulation. The factor could be detected in extracts of uninfected cells, although at greatly reduced levels. The increased level of factor in infected cells required a functional E1A gene. These results suggest that the E2 binding activity is a cellular transcriptional factor, the concentration or binding activity of which increases as a result of the action of the E1A gene product.

An RNA polymerase II transcription factor binds to an upstream element in the adenovirus major late promoter

A gel electrophoresis DNA binding assay has been used to identify proteins in HeLa cell extracts that specifically bind to the major late promoter of adenovirus. A major late promoter transcription factor MLTF has been detected as a discrete protein-DNA complex. MLTF binds specifically and with high affinity to sequences upstream of the TATA box of the major late promoter. This factor protects a 17 bp (-50 to -66) region in a DNAase I footprinting assay. The same region has been shown to be important for efficient transcription from the major late promoter both in vivo and in vitro. MLTF stimulates in vitro transcription only from a template containing this upstream region. The binding, footprinting, and transcription-stimulatory activities of MLTF cofractionate through two chromatographic steps. These results suggest that direct binding of MLTF to an upstream element activates transcription from the major late promoter.

Specific transcription of preformed nucleoprotein complexes, containing the adenovirus major late promoter, with a chromatographic fraction containing RNA polymerase II

Incubation in a HeLa whole-cell extract converted a plasmid DNA containing the adenovirus type 2 major late promoter into ordered nucleoprotein complexes similar to those described for simian virus DNA [Sinha, S. N., Hellwig, R. J., Allison, D. P. & Niyogi, S. K. (1982) Nucleic Acids Res. 10, 5533-5552]. Purified nucleoprotein complexes containing the plasmid DNA were able to serve as template for accurate transcription in vitro. Use of such nucleoprotein complexes eliminated the need for addition of nontemplate DNA (poly[d(I-C)]) to transcription reaction mixtures with template concentrations too low to yield a detectable specific-transcription signal from "naked" DNA. Of the four fractions resulting from phosphocellulose column chromatography of the whole cell extract, only the fraction that contained the RNA polymerase II activity was needed to accurately transcribe these nucleoprotein complexes in the presence of human placental ribonuclease inhibitor. In contrast, specific transcription of naked template DNA under these conditions required at least one additional fraction containing specificity factors. These results show that the nucleoprotein complexes contain factor(s) needed for specific initiation of transcription and that these complexes may be useful in the purification and analysis of these factors.

Positive and negative control sequences within the distal domain of the adenovirus IVa2 promoter overlap with the major late promoter

The RNA initiation sites of the adenovirus IVa2 and major late promoters (MLP) are separated by 210 base pairs and transcribed from opposite DNA strands. We had previously shown that they contained overlapping promoter sequences (V. Natarajan, M. J. Madden, and N. P. Salzman, Proc. Natl. Acad. Sci. U.S.A. 81:6290-6294, 1984). The transcription efficiencies of these two promoters were studied in vitro with templates of covalently closed circular DNAs that contained various deletion and point mutants. The distal control region of the IVa2 promoter that is located at nucleotide position (np) -152 to -242 from the RNA initiation site consists of at least two domains. The first distal domain, present between np -152 and -179, is necessary for efficient transcription of the IVa2 promoter, and it overlaps with sequences that have been shown to be necessary for efficient transcription of MLP. This region may serve as the entry site for the transcription machinery. The second distal domain consists of sequences present between np -211 and -242. These sequences are contained at the 5' end in the MLP transcript, and they inhibit transcription from the IVa2 promoter. However, these sequences are not necessary for transcription of the MLP with a covalently closed template but are needed for transcription with a linear template. The TATA box that is located at np -180 to -186 between these two domains has a critical role for efficient transcription of the MLP. A point mutation that reduces transcription from MLP by more than 80% stimulates transcription from IVa2 promoter by 10-fold. This finding is consistent with the proposal that MLP and IVa2 promoters share an entry site for transcription machinery and compete for its use.

Cis and trans activation of adenovirus IVa2 gene transcription

The transcriptional control region of the adenovirus IVa2 promoter was analyzed by cloning this promoter in front of a gene coding for bacterial chloramphenicol acetyl transferase (CATase) and estimating levels of CATase and IVa2 promoter specific RNA synthesized after transfection. To produce detectable amounts of CATase with the IVa2 promoter, an enhancer has to be present in cis. In the absence of enhancer sequences, the adenovirus E1A gene can not stimulate CATase synthesis. When cells were transfected with plasmids containing enhancer sequences and various IVa2 mutant promoters upstream of the CAT gene, we observed that CATase activity was not reduced significantly even after deletion of all sequences upstream of the RNA initiation site. Synthesis of IVa2 specific RNA was dependent on plasmids containing an enhancer (SV40 72 bp repeat) that was present in cis. In the absence of enhancer sequences, co-transfection to provide the adenovirus E1A gene in trans also stimulated IVa2 RNA synthesis. When HeLa cells were transfected with various deletion mutants with an enhancer in cis it was seen that sequences -38 to -64 base pairs upstream of the RNA initiation site are necessary for efficient transcription. The E1A gene in trans and an enhancer in cis have an additive effect on RNA synthesis from both IVa2 and major late promoters. The basis for the conflicting results between transcription and CATase synthesis is discussed.

Characterization of a surrogate TATA box promoter that regulates in vitro transcription of the simian virus 40 major late gene

The presence of a surrogate TATA box sequence located ca. 30 nucleotides upstream of the major late RNA start site at nucleotide position (np) 325 (Brady et al., Cell 31:625-633, 1982) has been confirmed, and its structural specificity has been determined by the generation of additional base substitution mutations at the KpnI restriction site (np 294) in cloned simian virus 40 DNA. Two mutants generated new RNA initiation sites upstream of the np 325 start site and continued to utilize the authentic start site, but with decreased efficiency. The replacement of either one or both cytosines by thymines at np 298 and np 299 specifically enhanced in vitro transcription from the np 325 start site by 430 and 800%, respectively. This enhancement was due to conversion of the simian virus 40 late promoter present in the wild-type virus to a sequence that is similar to the TATA box present in the simian virus 40 early promoter.

The expression of the SV40 early region in the transformed human cell line SV80

The one complete copy of the SV40 early region present in human cells of the transformed line SV80 carries a duplication of the 5' portion of the early region, including its transcriptional control region and splicing signals (W. Gish and M. Botchan, personal communication). Novel SV40-specific RNA species of sufficiently large size, 3.8 and 4.2 kb, to be expressed from the duplicated early transcriptional control region were detected in SV80 cytoplasmic and nuclear RNA preparations by blot hybridization. The results of transcription in a cell-free system of a plasmid, pSV80-04, representing this SV80 cell SV40 DNA integrate (W. Gish and M. Botchan, personal communication) and of nuclease protection experiments with end-labelled pSV80-04 DNA fragments support the conclusion that the duplicated early sequences are transcribed in SV80 cells. It has also been established that the duplicated early splicing signals are functional in SV80 cells. These results are discussed in relation to the large amounts of SV40 early mRNA and T-antigen synthesized in cells of the SV80 line.

Sequences upstream of c-mos(rat) that block RNA accumulation in mouse cells do not inhibit in vitro transcription

An unusual feature of the c-mos oncogene is the lack of expression in mouse tissues. Recombinant plasmids that contain the strong adenovirus late promoter and different amounts of cellular DNA 5' to c-mos(rat) were constructed and tested in transfection and transcription assays. The cellular sequences inhibit RNA accumulation in mouse but not human cells and do not inhibit in vitro transcription of the plasmid DNAs.

Both trans-acting factors and chromatin structure are involved in the regulation of transcription from the early and late promoters in simian virus 40 chromosomes

We isolated simian virus 40 (SV40) chromosomes from lytically infected CV-1 cells at various times during the late phase and transcribed them in vitro with either whole-cell or nuclear extracts of HeLa cells. The late promoter was 3- to 10-fold more active than the early promoter. With bare SV40 DNA templates, the early promoter was up to 10-fold stronger than the late promoter. The relative strengths of the early and late promoters on SV40 chromosomes were essentially independent of template concentration or length of the replicative phase of the infection. When monoclonal antibodies or antisera against T antigen (T Ag) were added to SV40 chromosomes or when T Ag, both free and chromatin bound, was removed by immunoprecipitation with anti-T, the activity of the late promoter remained essentially unchanged. Washing with 0.4 M NaCl removed T Ag from more than 90% of the mature chromosomes associated with T Ag. Transcription from the late promoter still predominated in the salt-washed T Ag-depleted chromosomes, even though there was a marked increase in early promoter activity. The depression of the early promoter could be reversed by adding the T Ag-containing extract back to the depleted chromosomes. Extraction of SV40 chromosomes with 1.5 M NaCl resulted in a decrease in the activity of the late promoter and a further increase in the activity of the early promoter so that the relative amounts of early and late RNA synthesized were similar to those for bare SV40 DNA templates. Late RNA synthesis from bare SV40 DNA templates was stimulated by high-speed supernatants prepared from nuclear extracts of SV40-infected cells but not from those of uninfected cells. Pretreatment of the supernatants with anti-T did not alter the result. Our findings indicate that the activity of the early and late SV40 promoters is regulated by at least two different mechanisms at the chromosomal level. One is mediated by a subclass of T Ag bound to SV40 chromosomes which represses early SV40 transcription but has no effect on late transcription. A second level of regulation, involving a tightly bound trans-acting chromosomal factor and a stable nucleoprotein structure, favors the late promoter over the early promoter by up to 10-fold.

Characterization of a surrogate TATA box promoter that regulates in vitro transcription of the simian virus 40 major late gene

The presence of a surrogate TATA box sequence located ca. 30 nucleotides upstream of the major late RNA start site at nucleotide position (np) 325 (Brady et al., Cell 31:625-633, 1982) has been confirmed, and its structural specificity has been determined by the generation of additional base substitution mutations at the KpnI restriction site (np 294) in cloned simian virus 40 DNA. Two mutants generated new RNA initiation sites upstream of the np 325 start site and continued to utilize the authentic start site, but with decreased efficiency. The replacement of either one or both cytosines by thymines at np 298 and np 299 specifically enhanced in vitro transcription from the np 325 start site by 430 and 800%, respectively. This enhancement was due to conversion of the simian virus 40 late promoter present in the wild-type virus to a sequence that is similar to the TATA box present in the simian virus 40 early promoter.

Sequences upstream of c-mos(rat) that block RNA accumulation in mouse cells do not inhibit in vitro transcription

An unusual feature of the c-mos oncogene is the lack of expression in mouse tissues. Recombinant plasmids that contain the strong adenovirus late promoter and different amounts of cellular DNA 5' to c-mos(rat) were constructed and tested in transfection and transcription assays. The cellular sequences inhibit RNA accumulation in mouse but not human cells and do not inhibit in vitro transcription of the plasmid DNAs.

Generation and functional analyses for base-substitution mutants of the adenovirus 2 major late promoter

The function of guanosine residues surrounding the TATA box of the adenovirus 2 major late promoter (MLP) in promoting efficient transcription initiation and in selecting a specific transcription start site in vitro has been examined. Multiple and single base substitutions (G----A) were generated in this region (from -63 to +25 relative to the cap site, +1) of the MLP. The promoter activities of the wild type and 21 mutants were assayed in an in vitro transcription system using whole cell extract (WCE) prepared from HeLa cells. The results suggest that the strings of G residues immediately adjacent to the TATA box are not required for full promoter activity in vitro. These G residues also appear not to be involved in the selection of a specific transcription start site by RNA polymerase II in vitro, since the identical cap site was used by wild-type and mutated MLP's. However, two G residues (-55 and -57) were identified as part of an upstream promoter element: a G----A transition at either -55 or -57 resulted in a 2.6 fold reduction in promoter activity. However, neither single nor double G----A transitions at -62 and -63 had an effect on promoter activity.

Unusual heterogeneity of the 5'-termini of human adenovirus type 2 early region E2 mRNA

The 5'-terminal structures of human adenovirus type 2 (Ad2) early region 2 (E2) mRNA were investigated. The E2 transcription unit has several interesting properties, including the presence of a TATA-like box that matches the consensus sequence poorly, delayed transcription during early stages of infection, and a switch in promoter recognition late after infection. E2-specific RNA, 5'-labeled in vitro to high specific activity was analyzed. Purified E2 mRNA was digested with RNase A or RNase T1 and the resulting oligonucleotides were resolved by two dimensional paper electrophoresis-homochromatography. Remarkably, as many as sixteen 5'-terminal RNase A oligonucleotides were identified and their sequences were deduced. The most common 5'-termini in the RNase A digest were p(m6)AmCp, p(m6)AmA(m)Cp, pGmA(m)Cp, and p(m6)AmG(m)Cp. Two RNase A oligonucleotides originated from the E4 promoter region, consistent with electron microscopic observations. The sequence encoding these potential initiation sites covered about 90 nucleotides. Eleven of the sequences of the 5'-terminal RNase A oligonucleotides were aligned with the Ad2 DNA sequence in the Ad2 E2 promoter region. If the heterogeneous termini in the E2 promoter region were generated by a process of transcription initiation, their existence cannot be explained by stuttering of RNA polymerase II. This suggests that the transcription of Ad early region 2 has features which differ from those of other Ad2 early gene transcription units. Perhaps this is due to the absence of a conventional TATA box which is believed to position the initiation site. Alternatively, it is conceivable that the E2 promoter represents an alternate class of RNA polymerase II promoters containing different signals with different requirements for activation and/or that an E1A gene product modifies transcription initiation.

Transcription of adenovirus cores in vitro

Transcription in whole HeLa cell extracts of the nucleoprotein core complexes released from adenovirus type 2 or type 5 virions has been examined. The average length of transcripts from deproteinized DNA templates increased steadily during a 90-min reaction in vitro, exhibiting an elongation rate of approximately 70 nucleotides per minute. On the other hand, transcripts made from viral core templates were restricted to a length of less than 2000 nucleotides. Accordingly, efficient transcription of cores (50 nucleotides elongated/min) ceased after 10-20 min of incubation in whole-cell extracts. Deproteinized viral DNA and viral nucleoprotein complexes appeared to support the initiation of a similar number of transcripts per template molecule, but the rate of initiation was faster when cores were provided as templates. Deproteinized viral DNA supported the synthesis of VA-RNA and of transcripts that hybridized to the region of the viral genome containing the 5' portion of the major late transcriptional. Viral cores also directed the synthesis of RNA products which hybridized to fragments of the viral genome containing E1A, E1B, and E4 regions. The results of nuclease protection experiments indicated that the presence of core proteins did not preclude accurate initiation of transcription from the E4 region.

Proximal and distal domains that control in vitro transcription of the adenovirus IVa2 gene

The adenovirus IVa2 gene, which is expressed at an intermediate time in the viral infectious cycle, is separated from the adenovirus major late promoter (MLP) 5' start site by 210 base pairs and is transcribed from the opposite strand. In contrast to the MLP, the IVa2 gene does not contain a "TATA" box upstream from its 5' start sites. By using a series of deletion mutants, two upstream control regions that are rich in cytidine residues, one proximal to the cap site at nucleotide positions -39 to -48 and a distal domain between nucleotide positions -152 and -242 have been identified as essential for IVa2 transcription (IVa2 cap site is nucleotide position + 1). Transcription efficiency is decreased by 70-90% after the deletion of a proximal C-rich domain when either linear or supercoiled DNAs were used as template. However, distal sequences functioned as transcriptional control domains only with covalently closed DNA templates. The deletion of both the proximal and distal regions from covalently closed DNA templates reduces the levels of IVa2 transcription by a factor of 100-150. When the plasmid pAd242 that contains the 5' start sites of adenovirus MLP and IVa2 is transcribed, there is essentially a complete suppression of transcription of the adenovirus IVa2 gene. The transcription efficiency of IVa2 is increased 10-fold after deletion of the MLP cap site. A model based on a shared entry site for RNA polymerase II and competition between major late and IVa2 promoters is proposed to explain the in vitro transcriptional results.

Requirement for distal upstream sequences for maximal transcription in vitro of early region IV of adenovirus

A series of deletion mutants spanning the adenovirus early region IV (EIV) promoter were tested for transcription activity in vitro. At least three elements were found to be important for maximal transcription in HeLa whole-cell extracts. Deletion of the TATA box drastically reduced the transcription activity from the EIV promoter. Sequences between nucleotides -58 and -44 are also important for efficient transcription since deletion of this region reduced activity by 50%. More importantly, sequences residing upstream from -140 critically influence the level of EIV transcription. Deletion of sequences between nucleotides -325 (the right terminus of adenovirus genome) and -140 reduced the level of transcription more than 10-fold. It is possible that a specific cellular factor stimulates EIV transcription by recognition of these upstream sequences. The dependence of transcription from the EIV promoter on a distal upstream element may explain some aspects of the regulation of this promoter.

Requirement for distal upstream sequences for maximal transcription in vitro of early region IV of adenovirus

A series of deletion mutants spanning the adenovirus early region IV (EIV) promoter were tested for transcription activity in vitro. At least three elements were found to be important for maximal transcription in HeLa whole-cell extracts. Deletion of the TATA box drastically reduced the transcription activity from the EIV promoter. Sequences between nucleotides -58 and -44 are also important for efficient transcription since deletion of this region reduced activity by 50%. More importantly, sequences residing upstream from -140 critically influence the level of EIV transcription. Deletion of sequences between nucleotides -325 (the right terminus of adenovirus genome) and -140 reduced the level of transcription more than 10-fold. It is possible that a specific cellular factor stimulates EIV transcription by recognition of these upstream sequences. The dependence of transcription from the EIV promoter on a distal upstream element may explain some aspects of the regulation of this promoter.

Homologous globin cell-free transcription system with comparison of heterologous factors

Mouse erythroleukemia (MEL) cells provide a useful model system to examine the regulation of globin gene expression. MEL cells ordinarily do not express globin genes, but in the presence of inducers, such as dimethyl sulfoxide or hexamethylene bisacetamide, they mimic erythroid differentiation. We have developed a cell-free transcription system from uninduced MEL cells to determine the requirements for mRNA synthesis. The MEL system directs accurate transcription of adenovirus type 2 major late DNA and mouse betamaj-globin with an efficiency comparable to those of HeLa and KB cell extracts. Using the procedure of Matsui et al. (T. Matsui, J. Segall, P.A. Weil, and R.G. Roeder, J. Biol. Chem. 255:11992-11996, 1980), we have isolated three active fractions from both MEL and HeLa cell extracts which are required for accurate transcription and have shown that equivalent fractions from MEL and HeLa cell extracts are interchangeable. Our findings suggest that the components required for initiation of transcription are similar in different cell types, at least to the extent that they can be assayed in these in vitro systems.