Far upstream initiation sites for adenovirus early region 1A transcription are utilized after the onset of viral DNA replication

The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs

We have used the Nanopore long-read sequencing platform to demonstrate how amazingly complex the human adenovirus type 2 (Ad2) transcriptome is with a flexible splicing machinery producing a range of novel mRNAs both from the early and late transcription units. In total we report more than 900 alternatively spliced mRNAs produced from the Ad2 transcriptome whereof more than 850 are novel mRNAs. A surprising finding was that more than 50% of all E1A transcripts extended upstream of the previously defined transcriptional start site. The novel start sites mapped close to the inverted terminal repeat (ITR) and within the E1A enhancer region. We speculate that novel promoters or enhancer driven transcription, so-called eRNA transcription, is responsible for producing these novel mRNAs. Their existence was verified by a peptide in the Ad2 proteome that was unique for the E1A ITR mRNA. Although we show a high complexity of alternative splicing from most early and late regions, the E3 region was by far the most complex when expressed at late times of infection. More than 400 alternatively spliced mRNAs were observed in this region alone. These mRNAs included extended L4 mRNAs containing E3 and L5 sequences and readthrough mRNAs combining E3 and L5 sequences. Our findings demonstrate that the virus has a remarkable capacity to produce novel exon combinations, which will offer the virus an evolutionary advantage to change the gene expression repertoire and protein production in an evolving environment.IMPORTANCE Work in the adenovirus system led to the groundbreaking discovery of RNA splicing and alternative RNA splicing in 1977. These mechanisms are essential in mammalian evolution by increasing the coding capacity of a genome. Here, we have used a long-read sequencing technology to characterize the complexity of human adenovirus pre-mRNA splicing in detail. It is mindboggling that the viral genome, which only houses around 36,000 bp, not being much larger than a single cellular gene, generates more than 900 alternatively spliced mRNAs. Recently, adenoviruses have been used as the backbone in several promising SARS-CoV-2 vaccines. Further improvement of adenovirus-based vaccines demands that the virus can be tamed into an innocent carrier of foreign genes. This requires a full understanding of the components that govern adenovirus replication and gene expression.

Oncolytic adenoviruses: A thorny path to glioma cure

Glioblastoma Multiforme (GBM) is a rapidly progressing brain tumor. Despite the relatively low percentage of cancer patients with glioma diagnoses, recent statistics indicate that the number of glioma patients may have increased over the past decade. Current therapeutic options for glioma patients include tumor resection, chemotherapy, and concomitant radiation therapy with an average survival of approximately 16 months. The rapid progression of gliomas has spurred the development of novel treatment options, such as cancer gene therapy and oncolytic virotherapy. Preclinical testing of oncolytic adenoviruses using glioma models revealed both positive and negative sides of the virotherapy approach. Here we present a detailed overview of the glioma virotherapy field and discuss auxiliary therapeutic strategies with the potential for augmenting clinical efficacy of GBM virotherapy treatment.

CRM1-dependent transport supports cytoplasmic accumulation of adenoviral early transcripts

The life cycle of adenoviruses is divided by convention into early and late phases, separated by the onset of viral genome replication. Early events include virus adsorption, transport of the genome into the nucleus, and the expression of early genes. After the onset of viral DNA replication, transcription of the major late transcription unit (MLTU) and thereby synthesis of late proteins is induced. These steps are controlled by an orchestra of regulatory processes and require import of the genome and numerous viral proteins into the nucleus, as well as active transport of viral transcripts and proteins from the nucleus to the cytoplasm. The latter is achieved by exploiting the shuttling functions of cellular transport receptors, which normally stimulate the nuclear export of cellular mRNA and protein cargos. A set of adenoviral early and late proteins contains a leucine-rich nuclear export signal of the HIV-1 Rev type, known to be recognized by the cellular export receptor CRM1. However, a role for CRM1-dependent export in supporting adenoviral replication has not been established. To address this issue in detail, we investigated the impact of two different CRM1 inhibitors on several steps of the adenoviral life cycle. Inhibition of CRM1 led to a reduction in viral early and late gene expression, viral genome replication, and progeny virus production. For the first time, our findings indicate that CRM1-dependent shuttling is required for the efficient export of adenoviral early mRNA.

Efficient virotherapy for osteosarcoma by telomerase-specific oncolytic adenovirus

PURPOSE

A telomerase-specific oncolytic adenovirus, Telomelysin, can selectively kill cancer cells, and be attenuated in normal cells. We herein describe the oncolytic effect of Telomelysin on human osteosarcoma both in vitro and in vivo.

METHODS

The anti-tumor effects of Telomelysin were evaluated on human osteosarcoma cell lines in vitro and in a mouse xenograft model of human osteosarcoma in vivo. The replication efficiencies of Telomelysin in human osteosarcoma cell lines and normal cell lines and in osteosarcoma xenografts were determined by the expression levels of E1 mRNA and E1A protein using real-time quantitative PCR, Western blot analysis and immunohistochemistry. The in vitro telomerase-specific replication and the viral infection rate were also confirmed by TelomeScan (Telomelysin-GFP), using fluorescent microscopy and flow cytometry, respectively. The cell viabilities were examined by XTT assay, and the tumor volumes were measured every 2 days. The induction of apoptosis was assessed by Western blot analysis, as well as by TUNEL assay.

RESULTS

TelomeScan and Telomelysin were efficiently replicated in human osteosarcoma cell lines and led to a dose- and time-dependent expression of GFP, E1 mRNA and E1A protein. Telomelysin infection induced marked cytolysis and apoptosis in osteosarcoma cell lines in vitro. Neither cytotoxicity nor apoptosis were induced in normal human cell lines. In the human osteosarcoma cell xenograft model, intratumoral injection of Telomelysin resulted in increased viral replication, significant tumor growth suppression and distinct apoptotic cell death.

CONCLUSIONS

This study indicated that virotherapy with Telomelysin may provide a promising strategy for the treatment of human osteosarcoma.

Selective replication of E1B55K-deleted adenoviruses depends on enhanced E1A expression in cancer cells

E1B55K-deleted dl1520 could selectively replicate in cancer cells and has been used in clinical trials as an antitumor agent. The mechanism of virus selective replication in cancer cells, including a possible role of p53, is unclear. Studies with established cancer cell lines have demonstrated that some cancer cells are resistant to dl1520 replication, regardless of the p53 status. Hep3B cells supported the E1b-deleted adenoviruses to replicate, whereas Saos2 cells were resistant to viral replication. We applied p53-null Hep3B and Saos2 cells as models to clarify the replication ability of E1B55K-deleted adenoviruses with different expression levels of E1a. We show that lower E1A expression in Saos2 may be the reason for the poor replication in some cancer cells due to the fact that E1a promoter was less activated in Saos2 than in Hep3B. We also demonstrate that the E1B55K protein can increase E1A expression in Saos2 cells for efficient virus replication. In addition, the upstream regions of the E1a promoter have transcriptional activity in Hep3B cells but not in Saos2 cells. The viral E1B55K protein may activate cancer cellular factor(s) that targets the upstream regions of the E1a gene to increase its expression. This is the first study demonstrating that E1B55K protein affects the E1A production levels that is related to cancer selective replication. Our studies have suggested that increase of E1A expression from E1b-deleted adenoviruses may enhance killing cancer cells that otherwise are resistant to viral replication.

Development of transcriptionally regulated oncolytic adenoviruses

Changes initiated at the cellular and systemic levels as a result of viral infection or neoplastic transformation share significant overlap. Therefore, the use of replicating viruses to treat tumors has long been postulated as a promising avenue for oncolytic therapy. Over the last 10 years, transcriptionally regulated adenoviruses have become a popular platform for the development of such oncolytic viruses. Placement of heterologous promoters in front of key adenoviral transcription units to achieve tumor- or tissue-specific viral replication is well documented. Various derivatives of this general strategy have led to considerable insight into its limitations, pitfalls, and potential. Although a general process can be described by which to develop transcriptionally regulated adenoviruses, it is apparent that few set rules can yet be defined as to what constitutes a safe, stable, and therapeutically effective vector. Clinical experiences to date suggest the short-term potential for this class of therapeutics lies in combination therapy regimens. Such lessons from the clinic suggest the next generation of transcriptionally regulated oncolytic adenoviruses take advantage of the ability of the platform to carry transgenes in order to deliver a multimodal therapy from a single agent. Beyond this 'arming' of the vectors lies the detargeting, retargeting, and coating of adenoviruses to improve the delivery of the agent to the treatment site(s). As a therapeutic platform, transcriptionally regulated adenoviruses are at an early stage of development with considerable opportunities for advancement.

An RNA polymerase III transcription unit located in the upstream control regions of the human proliferating-cell nucleolar protein p120 gene is transcribed in vitro and in vivo

An RNA polymerase III (Pol III) transcription unit containing homology to highly repeated Alu sequences was identified in the upstream flanking sequences of the gene for the human proliferating-cell nucleolar antigen p120. When transcribed in vitro, this Pol III unit produced three RNA transcripts, designated by nucleotide length as T150, T385 and T635; RNA transcript T635 was the most abundant accounting for over 90%. The transcription initiates at nucleotide -729 of the human p120 promoter and proceeds in the opposite orientation to the p120 gene transcription. Northern blot analysis and cDNA cloning followed by sequencing showed the presence of the T635 RNA in HeLa cells, indicating that this Pol III transcription unit is functional and transcribed in vivo. Disruption of this Pol III transcription unit by deletion of the Box A residues (-733 to -744) resulted in a sixfold reduction of the p120 gene transcription. A possible role for this Pol III transcription unit in p120 gene transcription is discussed.

Characterization of the promoter region of human steroid sulfatase: a gene which escapes X inactivation

The human X-linked steroid sulfatase gene (STS) was among the first genes shown to escape X inactivation. At least fourteen genes regulated in this fashion have now been recognized. They are dispersed into several regions of the X chromosome and may be controlled in a locus specific manner. Studies of the promoters of these genes could provide insights into the mechanism of X inactivation, however little information of this nature is currently available. For this reason we examined 5' flanking sequences of the human STS gene for promoter function. Four transcription start sites scattered over a 50bp region were identified. Functional domains of this TATA-less and GC poor promoter were identified by study of a series of terminal and internal deletions. A putative promoter sequence was identified which by itself exhibits little or no basal activity. However when combined with upstream regulatory elements, this segment showed weak but reproducible activity in a CAT (chloramphenicol acetyltransferase) reporter assay. Several regulatory domains acting as enhancers and repressors were subsequently identified. The relationship of this 5' sequence to the ability of the STS gene to escape X-inactivation is discussed.

The NFIII/OCT-1 binding site stimulates adenovirus DNA replication in vivo and is functionally redundant with adjacent sequences

The inverted terminal repeat (ITR) of adenovirus type 5 (Ad5) is 103 bp in length and contains the origin of DNA replication. Cellular transcription factors NFI/CTF and NFIII/OCT-1 bind to sites within the ITR and participate in the initiation of viral DNA replication in vitro. The ITR also contains multiple copies of two conserved sequence motifs that bind the cellular transcription factors SP1 and ATF. We have analyzed a series of viruses that carry deletions at the left terminus of Ad5. A virus carrying a deletion of the NFIII/OCT-1, SP1, and ATF sites within the ITR (mutant dl309-44/107) was wild type for virus growth. However, the deletion of these elements in addition to sequences immediately flanking the ITR (mutant dl309-44/195) resulted in a virus that grew poorly. The analysis of growth parameters of these and other mutants demonstrate that the NFIII/OCT-1 and adjacent SP1 sites augment the accumulation of viral DNA following infection. The function of these elements was most evident in coinfections with a wild-type virus, suggesting that these sites enhance the ability of a limiting trans-acting factor(s), that stimulates viral DNA replication, to interact with the ITR. The results of these analyses indicate functional redundancy between different transcription elements at the left terminus of the Ad5 genome and demonstrate that the NFIII/OCT-1 site and adjacent SP1 site, previously thought to be nonessential for adenovirus growth, play a role in viral DNA replication in vivo.

ICP22 homolog of equine herpesvirus 1: expression from early and late promoters

The complete nucleotide sequence of the short region, made up of a unique segment (Us; 6.5 kb) bracketed by a pair of inverted repeat sequences (IR; 12.8 kb each), of the equine herpesvirus 1 (EHV-1) genome has been determined recently in our laboratory. Analysis of the IR segment revealed a major open reading frame (ORF) designated IR4. The IR4 ORF exhibits significant homology to the immediate-early gene US1 (ICP22) of herpes simplex virus type 1 and to the ICP22 homologs of varicella-zoster virus (ORF63), pseudorabies virus (RSp40), and equine herpesvirus 4 (ORF4). The IR4 ORF is located entirely within each of the inverted repeat sequences (nucleotides [nt] 7918 to 9327) and has the potential to encode a polypeptide of 469 amino acids (49,890 Da). Within the IR4 ORF are two reiterated sequences: a 7-nt sequence tandemly repeated 17 times and a 25-nt sequence tandemly repeated 13 times. Nucleotide sequence analyses of IR4 also revealed several potential cis-regulatory sequences, two TATA sequences separated by 287 nt, an in-frame translation initiation codon following each TATA sequence, and a single polyadenylation site. To address the nature of the mRNA species encoded by IR4, we used Northern (RNA) blot and S1 nuclease analyses. RNA mapping data revealed that IR4 has two promoters that are regulated differentially during a lytic infection. A 1.4-kb mRNA appears initially at 2 h postinfection and is an early transcript since its synthesis is not affected by the presence of phosphonoacetic acid, an inhibitor of EHV-1 DNA replication. In contrast, a 1.7-kb mRNA appears at later times postinfection and is designated as a gamma-1 transcript, since its synthesis is significantly reduced by phosphonoacetic acid. These IR4-specific mRNAs are 3' coterminal, have unique 5' termini, and would code for in-frame, overlapping, carboxy-coterminal proteins of 293 and 469 amino acids, respectively. Interestingly, the site of homologous recombination to generate the genome of EHV-1 defective interfering particles that initiate persistent infection occurs between nt 3244 and 3251 of UL3 (ICP27 homolog) and nt 9027 and 9034 of IR4 (ICP22 homolog). Thus, this recombination event would generate a unique ORF that would encode a potential protein whose amino end was derived from the N-terminal 193 amino acids of the ICP22 homolog and whose carboxyl end was derived from the C-terminal 68 amino acids of the ICP27 homolog.

Redundant elements in the adenovirus type 5 inverted terminal repeat promote bidirectional transcription in vitro and are important for virus growth in vivo

The adenovirus inverted terminal repeat (ITR) contains a number of cis-acting elements that are involved in the initiation of viral DNA replication, as well as multiple binding motifs for the cellular transcription factors SP1 and ATF. In this study, we utilized a Hela cell transcription extract to demonstrate that the adenovirus type 5 ITR promotes bidirectional transcription in vitro. Primer extension analyses demonstrated that the ITR directed transcription at initiation sites both within the terminal repeat and at fixed distances outside of the ITR. The ITR also strongly stimulated transcription at the early region 1A (E1A) initiation site when it was situated immediately upstream of the E1A TATA box region. Deletion and point mutational analyses demonstrated that two distinct cis-acting elements were involved in these ITR-dependent transcriptional activities in vitro. Cellular transcription factors SP1 and ATF were previously shown to bind to these two regions. Analysis of viral mutants in vivo demonstrated that the NFIII/OCT-1 binding site and a conserved ATF motif were important for efficient viral growth. Regulatory elements in the ITR flanking region were found to functionally substitute for these sites.

An early gene maps within and is 3' coterminal with the immediate-early gene of equine herpesvirus 1

The immediate-early (IE) gene (IR1 gene) of equine herpesvirus 1 (EHV-1) encodes a single, spliced 6.0-kb mRNA during cytolytic infection. However, under early (in the presence of phosphonoacetic acid) and late (8 h postinfection; no metabolic inhibitors) conditions, in addition to the 6.0-kb IE mRNA, a 4.4-kb early (E) mRNA is transcribed from the IE gene region beginning at approximately 4 h postinfection. To map and characterize the 4.4-kb E mRNA and the protein product of this early gene (IR2 gene), Northern (RNA) blot hybridization, S1 nuclease, primer extension, and in vitro transcription and translation analyses were used. The data from RNA mapping analyses revealed that the 4.4-kb E IR2 mRNA (i) maps at nucleotides 4481 to 635 within each of the inverted repeats of the short region and thus is encoded by sequences that lie entirely within the IE gene, (ii) is transcribed in the same direction as the IE mRNA, initiating at nucleotide 4481, which lies 25 bp downstream of a putative TATA-like sequence and 1,548 bp downstream of the transcription initiation site of the IE mRNA, and (iii) is 3' coterminal with the IE mRNA which terminates at nucleotide 635 of the inverted repeats. The IR2 open reading frame was inserted into the transcription expression vector pGEM-3Z, and the RNA transcribed from this construct (pGEM44) was shown to be a 4.2-kb transcript that contained all IR2 sequences. In vitro translation of the 4.2-kb RNA yielded a major protein of approximately 130 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. This protein corresponds to the predicted IR2 product of 1,165 amino acids that would be in frame with the major IE polypeptide (IE1 = 200 kDa; 1,487 amino acids) and thus would be a 5'-truncated form of the IE1 polypeptide. The presence and potential role of the IR2 gene embedded within the IR1 gene increase the complexity of the regulation of the IE gene region during various stages of a productive infection.

Isolation and characterization of insertion mutants in E1A of adenovirus type 5

We have constructed a series of insertion mutations at 18 sites in the coding sequences of early region 1A (E1A) of human adenovirus type 5 (Ad5). At each site we have introduced three types of mutation: a 39-bp insertion specifying a 13-aa residue oligopeptide, a 39-bp insertion containing chain termination codons in all three reading frames, and a "collapsed" insert of 6-bp forming a conventional linker insertion mutation. All mutants were sequenced to determine the precise location, structure, and orientation of the inserts. The mutants were assayed for their abilities to trans-activate and to repress using transient expression assays in HeLa cells cotransfected with the E1A mutant plasmids and a reporter plasmid containing the bacterial beta-galactosidase (lac Z) gene under the control of Ad5 early promoters. The mutants were also tested for their ability to transform baby rat kidney cells in cooperation with either E1B or the ras oncogene. Each mutant was rescued into virus and infectivity was compared in HeLa and 293 cells. In addition, E1A protein synthesis was analyzed in cells infected with the mutant viruses and the insertions were found to have pronounced but unpredictable effects on electrophoretic mobility of E1A proteins in SDS-polyacrylamide gels. The results of functional assays indicated that only mutations mapping in, or deleting, the unique region of the 13 S mRNA product had any effect on ability to trans-activate and that a perfect correlation existed between ability of a mutant to trans-activate and to replicate efficiently in HeLa cells or to transform baby rat kidney cells in an E1A plus E1B mediated assay. In contrast, insertions near conserved region 2 of exon I and in the NH2-terminal portion of exon II significantly reduced repression activity but left transforming activity with E1B or with ras essentially unaffected suggesting that the repression function of E1A is separate from, or at least nonessential in, transformation.

Expression and interactions of human adenovirus oncoproteins

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Adenovirus E1A and E1B genes are regulated posttranscriptionally in human lymphoid cells

The interactions of adenovirus with differentiated human cells have been investigated in human myeloma cells. Relative to HeLa cells, the E1A and E1B genes, but not other viral genes, were markedly repressed by differential RNA stabilization, resulting in 20- to 50-fold less E1A and E1B mRNAs at steady state late in infection. The reduced E1A level corresponded to an approximately 200-fold-lower abundance of E1A polypeptides, which were nonetheless capable of efficient transactivation of E1A-dependent viral genes and were necessary for productive infection. The E1B gene was further regulated posttranscriptionally, yielding altered molar representation of alternatively spliced 22S and 13S mRNAs early in infection of myeloma cells. Taken together, these results suggested that repression and altered expression of E1A and E1B genes may provide a molecular basis of delayed kinetics of infection of lymphoid cells with adenovirus (D. Lavery, S. M. Fu, T. Lufkin, and S. Chen-Kiang, J. Virol. 61:1466-1472, 1987). The molecular mechanisms by which E1A and E1B are regulated and by which E1A transactivates viral genes in lymphoid cells are discussed.

Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development

DNA 5' to the human epsilon-globin gene exhibits unique patterns of DNase I-hypersensitive sites (DHS) in three human erythroleukemic cell lines which represent the embryonic (K562), fetal (HEL), and adult (KMOE) stages of erythroid development. We have mapped 10 epsilon-globin DHS in K562 cells, in which the epsilon-globin gene is maximally active. Major sites are located -11.7, -10.5, -6.5, -2.2 kilobase pairs (kbp) and -200 base pairs (bp) upstream of the gene and directly over the major cap site. Minor sites are located -5.5, -4.5, and -1.48 kbp and -900 bp upstream of the cap site. In HEL cells, in which the epsilon-globin gene is expressed at extremely low levels, the -11.7-, -10.5-, -5.5-, -4.5-, and -2.2-kbp DHS are no longer detectable; the -200-bp site is approximately 300-fold less sensitive to DNase I; and the -1.48-kbp, -900-bp, and major cap site DHS are 3- to 4-fold less sensitive. Only the DHS located -6.5 kbp relative to the major cap site is detectable at all three stages of erythroid development, including KMOE cells in which epsilon-globin synthesis is undetectable. We suggest that this site may be implicated in maintaining the entire beta-globin cluster in an active chromatin conformation. The five DHS downstream of the -6.5-kbp element possess associated promoters. Thus two distinct types of DHS exist--promoter positive and promoter negative. In HEL cells, all the upstream promoters are inactivated, although the -1.48-kbp and -900- and -200-bp DHS are still present. This suggests that the maintenance of DHS and regulation of their associated promoters occur by independent mechanisms. The inactivation of the upstream promoters in HEL cells while the major cap site remains active represents a unique pattern of expression and suggests that HEL cells possess regulatory factors which specifically down regulate the epsilon-globin upstream promoters.

Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element

The human epsilon-globin gene has a number of alternative transcription initiation sites which correspond with regions of DNase I hypersensitivity upstream of the canonical cap site. Transcripts originating from the promoters located -4.3/-4.5 and -1.48 kilobase pairs (kbp) and -900 and -200 base pairs (bp) upstream of the major epsilon-globin cap site can, at certain stages of erythroid differentiation, extend through the gene and are polyadenylated. The 350-bp PolIII transcripts, originating within the Alu repetitive element -2.2 kbp upstream of the cap site, extend in the opposite direction from the gene, are nonpolyadenylated, nucleus confined, and are detectable only in mature K562 cells or mature embryonic red blood cells where the epsilon-globin major cap site is maximally transcribed. Fragments containing the promoters located between -4.5 and -4.3 kbp upstream of the gene down regulate transcription from the epsilon-globin gene 20- to 30-fold in a transient expression assay in which both erythroid and nonerythroid cell lines were used. This occurs only when the direction of transcription from the -4.3/-4.5-kbp promoters is towards the gene, and we hypothesize that down regulation is caused by transcriptional interference. Fragments containing the Alu repetitive element -2.2 kbp upstream of the gene can overcome down regulation of the epsilon-globin gene by the -4.5-kbp element when interposed in the direct orientation between this element and the epsilon-globin gene.

Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element

The human epsilon-globin gene has a number of alternative transcription initiation sites which correspond with regions of DNase I hypersensitivity upstream of the canonical cap site. Transcripts originating from the promoters located -4.3/-4.5 and -1.48 kilobase pairs (kbp) and -900 and -200 base pairs (bp) upstream of the major epsilon-globin cap site can, at certain stages of erythroid differentiation, extend through the gene and are polyadenylated. The 350-bp PolIII transcripts, originating within the Alu repetitive element -2.2 kbp upstream of the cap site, extend in the opposite direction from the gene, are nonpolyadenylated, nucleus confined, and are detectable only in mature K562 cells or mature embryonic red blood cells where the epsilon-globin major cap site is maximally transcribed. Fragments containing the promoters located between -4.5 and -4.3 kbp upstream of the gene down regulate transcription from the epsilon-globin gene 20- to 30-fold in a transient expression assay in which both erythroid and nonerythroid cell lines were used. This occurs only when the direction of transcription from the -4.3/-4.5-kbp promoters is towards the gene, and we hypothesize that down regulation is caused by transcriptional interference. Fragments containing the Alu repetitive element -2.2 kbp upstream of the gene can overcome down regulation of the epsilon-globin gene by the -4.5-kbp element when interposed in the direct orientation between this element and the epsilon-globin gene.

Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development

DNA 5' to the human epsilon-globin gene exhibits unique patterns of DNase I-hypersensitive sites (DHS) in three human erythroleukemic cell lines which represent the embryonic (K562), fetal (HEL), and adult (KMOE) stages of erythroid development. We have mapped 10 epsilon-globin DHS in K562 cells, in which the epsilon-globin gene is maximally active. Major sites are located -11.7, -10.5, -6.5, -2.2 kilobase pairs (kbp) and -200 base pairs (bp) upstream of the gene and directly over the major cap site. Minor sites are located -5.5, -4.5, and -1.48 kbp and -900 bp upstream of the cap site. In HEL cells, in which the epsilon-globin gene is expressed at extremely low levels, the -11.7-, -10.5-, -5.5-, -4.5-, and -2.2-kbp DHS are no longer detectable; the -200-bp site is approximately 300-fold less sensitive to DNase I; and the -1.48-kbp, -900-bp, and major cap site DHS are 3- to 4-fold less sensitive. Only the DHS located -6.5 kbp relative to the major cap site is detectable at all three stages of erythroid development, including KMOE cells in which epsilon-globin synthesis is undetectable. We suggest that this site may be implicated in maintaining the entire beta-globin cluster in an active chromatin conformation. The five DHS downstream of the -6.5-kbp element possess associated promoters. Thus two distinct types of DHS exist--promoter positive and promoter negative. In HEL cells, all the upstream promoters are inactivated, although the -1.48-kbp and -900- and -200-bp DHS are still present. This suggests that the maintenance of DHS and regulation of their associated promoters occur by independent mechanisms. The inactivation of the upstream promoters in HEL cells while the major cap site remains active represents a unique pattern of expression and suggests that HEL cells possess regulatory factors which specifically down regulate the epsilon-globin upstream promoters.

Genome organization of mouse adenovirus type 1 early region 1: a novel transcription map

Mouse adenovirus type 1 (MAV-1) genomic DNA from 8.9 to 13.7 map units was sequenced and the early region 1 (E1) transcription map was determined by S1 nuclease, primer extension, and Northern analyses, and cDNA sequencing. The E1 transcription map of MAV-1 had marked dissimilarities from the conserved transcription maps of primate adenovirus E1s. One major E1A and two E1B mRNAs were identified in overlapping transcription units. The single E1A mRNA was composed of three exons; the last exon was coincident with the last exon of the E1B mRNAs. While human adenovirus type 2 (Ad2) utilizes alternate splice donors for the first E1A mRNA exon, MAV-1 does not. Thus, no protein is predicted that would correspond to the Ad2 243 amino acid protein, although MAV-1 can encode a protein similar to the Ad2 289 amino acid protein (A. O. Ball, M. E. Williams, and K. R. Spindler, 1988, J. Virol. 62, 3947-3957). Two spliced E1B mRNAs differed from each other in an intron near the 5' end of the smaller E1B mRNA. This smaller mRNA could encode only the 55K E1B protein, while the larger mRNA could encode both the 21K and 55K E1B proteins.

Regulation of cytomegalovirus late-gene expression: differential use of three start sites in the transcriptional activation of ICP36 gene expression

We have investigated the transcriptional regulation of the human cytomegalovirus gamma gene encoding the ICP36 family (p52, the major late DNA-binding protein). The ICP36 transcription unit initiates at three distinct sites which are separated by approximately 50 nucleotides and are differentially regulated during infection. At early times (8 h postinfection), only two of these start sites, the most proximal and distal site, were active whereas at late times (36 h postinfection), the middle start site was activated. Expression from this late start site was dependent upon DNA replication. Consensus TATA elements were located upstream of all three start sites, although the element upstream of the late start site was unusual in both sequence and position when compared with conventional TATA elements. Deletion analysis was used in conjunction with transient assays to define independent promoters in this region. The two early start sites and associated TATA elements functioned as separable independently regulated promoters. The region containing the late start site and TATA element but excluding either of the flanking TATA elements was inactive in transient assays. Our work establishes that the ICP36 gene is under complex early and late transcriptional regulation and that the sequences regulating transcriptional activation are temporally and spatially distinct.

A human cytomegalovirus early gene has three inducible promoters that are regulated differentially at various times after infection

The long inverted repeat and the adjacent sequences are major early transcription sites of the human cytomegalovirus genome (M. W. Wathen and M. F. Stinski, J. Virol. 41:462-477, 1982). An early transcription unit which flanks the large terminal repeat was analyzed by RNA mapping at various times after infection. Three unspliced, overlapping RNAs were transcribed from different initiation sites and terminated at the same 3' end. Individual promoters were isolated for all three transcripts. These promoters were activated in trans by viral immediate-early (IE) regulatory proteins after either infection with virus or cotransfection with IE2 alone or IE1 plus IE2 genes. DNA sequence analysis detected TATA and CAAT boxes plus multiple-dyad symmetries in the promoter-regulatory region. Deletion analyses showed that the maximum inducible promoter activity lay in a 230-base-pair region. When in the viral genome, the three promoters were regulated differentially during the course of infection. The upstream promoter was used only at late times after infection. Possible reasons for viral RNAs with multiple 5' ends at different times after infection and the recognition of the upstream promoter at only late times after infection are discussed.

Changes in minor transcripts from the alpha 1 and beta maj globin and glutathione peroxidase genes during erythropoiesis

We have analysed the transcriptional regulation of the murine alpha 1 and beta maj globin genes and the glutathione peroxidase (GSHPx) gene, which are all highly expressed during erythropoiesis. The levels of minor RNAs compared to the major message were monitored throughout differentiation within the erythroid lineage. For each gene, upstream transcripts arise from distinct clusters of sites which are regulated differently during differentiation: some occur only during early erythropoiesis, some occur early and persist to the terminal stages, while others accumulate later and roughly in parallel with the main RNA transcript. In addition, opposite strand transcripts from the GSHPx gene were found in increasing amounts during later stages of erythropoiesis. The initiation sites for specific subsets of these minor transcripts lie close to sequences known to be involved in globin gene regulation (i.e. the TATA, CAAT and the CACCCT boxes) or other conserved sequences; others lie close to developmentally regulated DNase I hypersensitive sites around the globin and GSHPx genes.

Alpha-amanitin insensitive transcription of the human epsilon-globin gene

In vitro transcription was used to show that RNA polymerase III is responsible for the initiation of transcription at a position 200 bp upstream from the epsilon-globin major cap site. High levels of -200 transcription interferes with the RNA polymerase II major cap site transcription. Using DNA mediated transient expression, the ratio of -200 to +1 transcription can be modulated by either the direction of replication or the presence of an enhancing element in the vector. We suggest that this heterogeneous usage of cap sites is not related to epsilon-globin gene transcription in vivo, but is instead the result of a combination of factors inherent to transient expression experiments.

Transcription control region within the protein-coding portion of adenovirus E1A genes

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

Transcription of the human adenovirus E1a gene in Saccharomyces cerevisiae

The early region 1a (E1a) and its flanking sequences of human adenovirus type 5 (Ad5) have been cloned in the yeast-Escherichia coli shuttle vector YEp13 and transferred into the yeast Saccharomyces cerevisiae. The E1a-specific RNAs were produced in the transformed yeast cells. The 5' ends of these transcripts were capped but were lacking 10 to 45 nucleotides from the 5' end of the proper E1a mRNA. These transcripts terminated approx. 1000 nucleotides downstream from the proper 3' end. No splicing of the E1a-specific RNA could be detected in the yeast cells.

Differential response of multiple epsilon-globin cap sites to cis- and trans-acting controls

The human epsilon-globin gene has a number of alternative transcription-initiation sites located upstream of the canonical mRNA cap site. In three nonerythroid cell lines, "leaky" epsilon-globin transcription occurs exclusively from one of these upstream sites, the -200 cap site. Using a transient expression assay, we have shown that transcription initiation from the -200 cap site and the major cap site can be independently regulated in response to plasmid replication, SV40 enhancer sequences in cis, and the adenovirus E1A gene in trans. The -200 cap site is located within a region of S1 hypersensitivity in the supercoiled plasmid, and in the absence of viral enhancer sequences it is the main initiation site following transfection into a number of cell lines. We suggest that the -200 cap site acts as a polymerase entry site by virtue of its accessible chromatin structure. The efficiency of polymerase binding at this site may be altered by trans-acting regulatory molecules.

Translation efficiency of adenovirus early region 1A mRNAs deleted in the 5' untranslated region

Adenovirus deletion mutants were studied to examine the influence of the 5' untranslated sequence on the translation of early region 1A mRNAs. Alterations of the 5' untranslated sequence, including complete deletion of the wild-type 5' untranslated sequence, did not significantly affect the rate of translation.

HMG CoA reductase: a negatively regulated gene with unusual promoter and 5' untranslated regions

The rate-limiting enzyme of cholesterol biosynthesis, HMG CoA reductase, is controlled by negative feedback regulation of transcription. We have isolated the reductase gene from a bacteriophage lambda genomic library prepared from hamster UT-1 cells. The 25 kilobase gene is split into 20 exons. The 5' untranslated and promoter regions differ from those of previously characterized genes. The 5' untranslated region encompasses as many as 670 nucleotides; contains up to eight AUG codons upstream of the codon used to initiate translation; and has multiple transcription initiation sites as determined by S1 nuclease mapping and primer extension analysis. The promoter region lacks a characteristic TATA box and CCAAT box; is rich in G + C residues (65%); and contains repeat sequences homologous to the 21 base pair repeats of the SV40 promoter. These unusual features may be relevant to the mechanism of expression of "housekeeping" genes, particularly those that are subject to negative feedback regulation.

Transcription control region within the protein-coding portion of adenovirus E1A genes

A single-base deletion within the protein-coding region of the adenovirus type 5 early region 1A (E1A) genes, 399 bases downstream from the transcription start site, depresses transcription to 2% of the wild-type rate. Complementation studies demonstrated that this was due to two effects of the mutation: first, inactivation of an E1A protein, causing a reduction by a factor of 5; second, a defect which acts in cis to depress E1A mRNA and nuclear RNA concentrations by a factor of 10. A larger deletion within the protein-coding region of E1A which overlaps the single-base deletion produces the same phenotype. In contrast, a linker insertion which results in a similar truncated E1A protein does not produce the cis-acting defect in E1A transcription. These results demonstrate that a critical cis-acting transcription control region occurs within the protein coding sequence in adenovirus type 5 E1A. The single-base deletion occurs in a sequence which shows extensive homology with a sequence from the enhancer regions of simian virus 40 and polyomavirus. This region is not required for E1A transcription during the late phase of infection.

Regulation of adenovirus transcription by an E1a gene in microinjected Xenopus laevis oocytes

The regulation of adenovirus type 5 gene expression by the E1a gene product was examined in microinjected Xenopus laevis oocytes. Chimeric genes were constructed which included the promoter region of early adenovirus type 5 gene 3 and the structural sequence which codes for the bacterial enzyme chloramphenicol-3-O-acetyltransferase (CAT). A plasmid containing this chimeric gene as well as plasmids containing the E1a gene were coinjected into oocyte nuclei. The presence of the E1a gene was shown to increase CAT activity by up to 8.5-fold over basal levels. Synthesis of the functional product from the E1a gene requires the removal of intron sequences by RNA splicing. The E1a gene and a derivative that precisely lacks the intron were equally effective in increasing CAT activity, suggesting that splicing of the primary E1a transcript is efficiently accomplished in the oocyte nucleus. This was confirmed by directly examining the E1a mRNAs by the S1 mapping procedure. A protein extract from adenovirus type 5-infected HeLa cells enriched for the E1a protein may supplant the E1a plasmid in enhancing CAT activity. Synthesis of the CAT enzyme after gene injection is invariant in oocytes from the same frog, but oocytes from different frogs show a high degree of variability in their ability to synthesize the CAT enzyme. Microinjected X. laevis oocytes appear to be an extremely useful system to study the effects of protein elements on transcription.

Adenovirus early region 1A protein activates transcription of a nonviral gene introduced into mammalian cells by infection or transfection

Transcription from all early adenovirus promoters is stimulated by a 289 amino acid phosphoprotein encoded in the pre-early transcription unit E1A. To determine if this protein could act on a nonviral gene placed on the viral chromosome, adenovirus recombinants were constructed in which the rat preproinsulin I gene, including its promoter region, was substituted in both orientations for E1A. Preproinsulin mRNA synthesis from these recombinants was greatly stimulated after infection of line 293 cells, which constitutively express E1A protein, compared to HeLa cells, which do not. Expression of the preproinsulin gene was also greatly stimulated when HeLa cells were coinfected with the recombinants and wild-type adenovirus or a mutant defective in a second E1A protein, but much less so by coinfection with a mutant defective in the 289 amino acid phosphoprotein. Much of the E1A-induced preproinsulin mRNA had a 5' end at the same position as the preproinsulin mRNA isolated from insulinoma cells, but a considerable fraction had 5' ends mapping heterogeneously within several hundred nucleotides of this site. Preproinsulin mRNA was also detected in 293 cells but not HeLa or HEK cells after transfection of a plasmid containing the preproinsulin gene with no adenovirus sequence. This indicates that there is no cis-acting adenovirus sequence required for E1A protein stimulation of preproinsulin transcription. Infection of rat cells with adenovirus did not induce detectable mRNA synthesis from the endogenous preproinsulin I gene. These results demonstrate that the E1A protein can induce expression of a nonviral gene when it is newly introduced into mammalian cells by viral infection or transfection, but it does not induce the endogenous cellular gene.

Analysis of adenovirus transforming proteins from early regions 1A and 1B with antisera to inducible fusion antigens produced in Escherichia coli

Plasmid vectors were constructed which expressed three adenovirus tumor antigens fused to a portion of the trpE protein of Escherichia coli. Insertion of adenovirus type 2 DNA from early region 1A (E1A) into such a plasmid led to a fusion protein which contained the C-terminal 266 amino acids of the 289-amino acid protein encoded by the viral 13S mRNA. Similarly, insertion of adenovirus type 5 DNA corresponding to the E1B 55- and 21-kilodalton proteins led to production of fusion proteins containing amino acid sequences from these proteins. After induction with indoleacrylic acid, fusion proteins accumulated stably in the E. coli cells. By using a simple extraction of insoluble protein, 1 to 10 mg of fusion protein per liter of culture was obtained. The fusion proteins were purified on preparative polyacrylamide gels and used to immunize rabbits. Specific antisera for the E1A 289- and closely related 243-amino acid proteins and the E1B 55- and 21-kilodalton proteins were obtained. These sera were used to immunoprecipitate the tumor antigens in cells infected with wild-type and various mutants of adenovirus or to analyze them by an immunoblotting procedure. Mutant E1A proteins in which the C-terminal 70 amino acids are deleted were phosphorylated to much lower extents than the wild-type E1A proteins. This indicates that the deleted region is important for the process of phosphorylation. The E1A proteins were extracted, sedimented in glycerol gradients, analyzed by immunoprecipitation, and found to sediment primarily as monomers.

Far upstream sequences are required for efficient transcription from the adenovirus-2 E1A transcription unit

We have investigated the requirement for sequences located upstream from the TATA box for efficient transcription from the Adenovirus-2 (Ad2) E1A promoter. A series of deletions located within the E1A promoter upstream sequences were introduced into recombinants which contain or do not contain the E1A structural sequences. The amount of E1A-specific RNA produced after transfection into HeLa cells was determined by quantitative S1 nuclease analysis. We demonstrate that sequences located more than 231 bp upstream from the E1A capsite are required for efficient transcription from the E1A promoter. However, the requirement for these stimulatory sequences is less pronounced in recombinants which contain the E1A structural sequences than in those in which these sequences have been deleted. We demonstrate also that these Ad2 stimulatory sequences activate transcription in cis when inserted upstream from the heterologous -34 to +33 Ad2 major late promoter (Ad2MLP) element which is otherwise inactive when transfected into HeLa cells. These results suggest that the 270 bp Ad2 left-terminal segment contains an enhancer-like element.

An enhancer element is located 340 base pairs upstream from the adenovirus-2 E1A capsite

A chimeric recombinant, containing the 270 bp left-terminal fragment of Adenovirus-2 (Ad2) inserted upstream from the -34 to +33 Ad2 major late promoter (Ad2MLP) element, has been used to characterize the transcription stimulatory element which is located at least 231 bp upstream from the E1A capsite in the left-end of Ad2 (Ref. 1). We demonstrate that this element, which acts in cis, possesses several properties characteristic of transcriptional enhancers. Firstly, it potentiates initiation of transcription from the capsite of the heterologous Ad2MLP and from "cryptic" sites often preceded by TATA box-like sequences. Secondly, although there is no critical distance requirement between the enhancer element and the Ad2MLP, the extent of stimulation decreases as the distance between the two element increases. However, in contrast to the other known viral or cellular enhancers which are bidirectional, the Ad2 enhancer is unidirectional, i.e. it potentiates the Ad2MLP element only when it is inserted in its "natural" orientation with respect to the direction of transcription. Using two convergent series of deletions, we have localized the Ad2 enhancer element within a 24 bp segment located at approximately 160 bp from the Ad2 left-end, i.e. 340 bp upstream from the E1A capsite. This 24 bp segment contains a sequence which exhibits a striking homology with the consensus sequence of several viral and cellular enhancers.

Regulation of adenovirus transcription by an E1a gene in microinjected Xenopus laevis oocytes

The regulation of adenovirus type 5 gene expression by the E1a gene product was examined in microinjected Xenopus laevis oocytes. Chimeric genes were constructed which included the promoter region of early adenovirus type 5 gene 3 and the structural sequence which codes for the bacterial enzyme chloramphenicol-3-O-acetyltransferase (CAT). A plasmid containing this chimeric gene as well as plasmids containing the E1a gene were coinjected into oocyte nuclei. The presence of the E1a gene was shown to increase CAT activity by up to 8.5-fold over basal levels. Synthesis of the functional product from the E1a gene requires the removal of intron sequences by RNA splicing. The E1a gene and a derivative that precisely lacks the intron were equally effective in increasing CAT activity, suggesting that splicing of the primary E1a transcript is efficiently accomplished in the oocyte nucleus. This was confirmed by directly examining the E1a mRNAs by the S1 mapping procedure. A protein extract from adenovirus type 5-infected HeLa cells enriched for the E1a protein may supplant the E1a plasmid in enhancing CAT activity. Synthesis of the CAT enzyme after gene injection is invariant in oocytes from the same frog, but oocytes from different frogs show a high degree of variability in their ability to synthesize the CAT enzyme. Microinjected X. laevis oocytes appear to be an extremely useful system to study the effects of protein elements on transcription.

Inhibition of RNA cleavage but not polyadenylation by a point mutation in mRNA 3' consensus sequence AAUAAA

A single U leads to G transversion in the 3' consensus sequence AAUAAA of the adenovirus early region 1A gene was constructed and the effect of this mutation on processing of the 3' end of the nuclear early region 1A RNAs was analysed. The results demonstrate that the intact AAUAAA is not required for RNA polyadenylation but is required for the cleavage step preceding polyadenylation to occur efficiently.