Activation of the adenovirus EIIa late promoter by a single-point mutation which enhances binding of transcription factor IID

The structure and function of the adenovirus major late promoter

The adenovirus major late promoter (MLP) has played a pre-eminent role in the analysis of transcription initiation in mammalian cells, and is an outstanding example of the ways in which the study of adenovirus has led to fundamental insights into general cellular processes. The aim of this chapter is to give a comprehensive review of the structure and function of this model mammalian promoter. After a brief description of late transcription in the adenovirus replication cycle, the experimental evidence for the current consensus on the genetic structure of the MLP, including a consideration of non-primate adenovirus MLPs, will be reviewed. Next, the functions of the MLP in the viral life cycle will be examined, and some of the problems that remain to be resolved will be addressed. The review ends with some ideas on how the knowledge of the structure and function of the MLP can be used in designing virus vectors for specific experimental purposes.

The TATA motif specifies the differential activation of minimal promoters by varicella zoster virus immediate-early regulatory protein IE62

The immediate-early IE62 protein of varicella zoster virus is an acidic transcriptional activator capable of up-regulating many viral and cellular promoters with varying efficiencies. We demonstrate that, in the context of a minimal promoter, a TATA element is both sufficient and essential for IE62-mediated transcriptional activation. Differential levels of activation by IE62 in this context were conferred by a panel of naturally occurring sequence variations within the TATA motif itself. TATA motif-specific, differential induction was not obtained when the IE62 acidic activation domain was targeted as a GAL4 fusion protein to the same panel. The prototype acidic transactivator, VP16 of herpes simplex virus, failed to discriminate between these different TATA motifs when they were placed into an appropriate responsive promoter context. Nonetheless, a chimeric IE62 polypeptide substituted with the VP16 activation domain retained the ability to differentially modulate minimal promoters with various TATA motifs. Taken together with its binding to TATA box-binding protein (TBP) and transcription factor IIB in vitro, we suggest that IE62 has the unusual ability to achieve differential levels of transcriptional activation through different TATA motifs, which may be accomplished either directly or indirectly by recognizing conformational variations in DNA-bound TBP, TBP-transcription factor IIA/B, or TBP-TATA-associated factor complexes.

Human acyl-CoA:cholesterol acyltransferase-1 (ACAT-1) gene organization and evidence that the 4.3-kilobase ACAT-1 mRNA is produced from two different chromosomes

Acyl-CoA:cholesterol acyltransferase (ACAT) plays important roles in cellular cholesterol homeostasis. Four human ACAT-1 mRNAs (7.0, 4.3, 3.6, and 2.8 kilobases (kb)) share the same short 5'-untranslated region (exon 1) and coding sequence (exons 2-15). The 4.3-kb mRNA contains an additional 5'-untranslated region (1289 nucleotides in length; exons Xa and Xb) immediately upstream from the exon 1 sequence. One ACAT-1 genomic DNA insert covers exons 1-16 and a promoter (the P1 promoter). A separate insert covers exon Xa (1277 base pairs) and a different promoter (the P7 promoter). Gene mapping shows that exons 1-16 and the P1 promoter sequences are located in chromosome 1, while exon Xa and the P7 promoter sequence are located in chromosome 7. RNase protection assays demonstrate three different protected fragments, corresponding to the 4.3-kb mRNA and the two other mRNAs transcribed from the two promoters. These results are consistent with the interpretation that the 4.3-kb mRNA is produced from two different chromosomes, by a novel RNA recombination mechanism involving trans-splicing of two discontinuous precursor RNAs.

Structure of the human beta2-glycoprotein I (apolipoprotein H) gene

The gene encoding the human plasma protein beta2-glycoprotein I or apolipoprotein H was cloned and its structure determined. The gene which consists of eight exons was shown to span 18 kb and was localized to chromosome 17q23-24. The transcriptional initiation site was assigned to a position 31 bp upstream of the start codon. Several consensus sequence elements relevant for regulation of transcription in liver were seen in the 5'-upstream region of the gene. Exon 1 contains the 5'-UTR together with the signal peptide coding sequences. Short consensus repeats (SCRs) 1, 3, 4, and 5 are encoded by single exons each while SCR2 is encoded by two exons. Exon 8 comprises the region encoding the C-terminal end of beta2-glycoprotein I (from His-310), the stop codon and the 3'-UTR.

Control of adenovirus early gene expression during the late phase of infection

The adenovirus gene regulatory program occurs in two distinct phases, as defined by the onset of DNA replication. During the early phase, the E1A, E1B, E2, E3, and E4 genes are maximally expressed, while the major late promoter (MLP) is minimally expressed and transcription is attenuated. After the onset of DNA replication, the IVa2 and pIX genes are expressed at high levels, transcription from the MLP is unattenuated and fully activated, and early gene expression is repressed. Although the cis elements and trans-acting factors responsible for the late-phase activation of the MLP have been identified and characterized and the role of DNA replication in activation has been established, the mechanism(s) underlying the commensurate decrease in early gene expression has yet to be elucidated. The results of this study demonstrate that this decrease depends on a fully functional MLP. Specifically, virus mutants with severely deficient transcription from the MLP exhibit a marked increase in expression of the E1A, E1B, and E2 early genes. These increases were observed at the level of transcription initiation, mRNA accumulation, and protein production. In addition, expression from the late gene pIX, which is not contained within the major late transcription unit (MLTU), is also markedly increased. To begin the analysis of the mechanisms underlying these late-phase effects, mixed-infection experiments with mutant and wild-type viruses were performed. The results show that the effects on early gene expression, as measured both at the protein and RNA levels, are mediated in trans and not in cis. These observations are consistent either with a model in which one or more late protein products encoded by the MLTU acts as a repressor of early gene expression or with one in which the wild-type MLP competes with early promoters for limiting transcription factors.

The interferon gamma (IFN-gamma) receptor: a paradigm for the multichain cytokine receptor

With the purification and cloning of the interferon gamma (IFN-gamma) receptor chains the mechanism of IFN-gamma action and the resultant signal transduction events were delineated in remarkable detail. The interferon gamma (IFN-gamma) receptor complex consists of two chains: IFN-gammaR1, the ligand-binding chain, and IFN-gammaR2, the accessory chain. Binding of IFN-gamma causes oligomerization of the two IFN-gamma receptor subunits, IFN-gammaR1 and IFN-gammaR2, which initiates the signal transduction events: activation of Jak1 and Jak2 receptor associated protein tyrosine kinases, phosphorylation of the IFN-gammaR1 intracellular domain on Tyr440 followed by phosphorylation and activation of Stat1alpha, the latent transcriptional factor. With all these steps established, the IFN-gamma receptor complex has provided the basic model for understanding the receptors for other members of the family of class II cytokine receptors.

Considerations of transcriptional control mechanisms: do TFIID-core promoter complexes recapitulate nucleosome-like functions?

The general transcription initiation factor TFIID was originally identified, purified, and characterized with a biochemical assay in which accurate transcription initiation is reconstituted with multiple, chromatographically separable activities. Biochemical analyses have demonstrated that TFIID is a multiprotein complex that directs preinitiation complex assembly on both TATA box-containing and TATA-less promoters, and some TFIID subunits have been shown to be molecular targets for activation domains in DNA-binding regulatory proteins. These findings have most commonly been interpreted to support the view that transcriptional activation by upstream factors is the result of enhanced TFIID recruitment to the core promoter. Recent insights into the architecture and cell-cycle regulation of the multiprotein TFIID complex prompt both a reassessment of the functional role of TFIID in gene activation and a review of some of the less well-appreciated literature on TFIID. We present a speculative model for diverse functional roles of TFIID in the cell, explore the merits of the model in the context of published data, and suggest experimental approaches to resolve unanswered questions. Finally, we point out how the proposed functional roles of TFIID in eukaryotic class II transcription fit into a model for promoter recognition and activation that applies to both eubacteria and eukaryotes.

Expression and regulation of the human and mouse aspartylglucosaminidase gene

Aspartylglucosaminidase (AGA) is a lysosomal enzyme that catalyzes one of the final steps in the degradation of N-linked glycoproteins. Here we have analyzed the tissue-specific expression and regulation of the human and mouse AGA genes. We isolated and characterized human and mouse AGA 5'-flanking sequences including the promoter regions. Primer extension assay revealed multiple transcription start sites in both genes, characteristic of a housekeeping gene. The cross-species comparison studies pinpointed an approximately 450-base pair (bp) homologous region in the distal promoter. In the functional analysis of human AGA 5' sequence, the critical promoter region was defined, and an additional upstream region of 181 bp exhibiting an inhibitory effect on transcription was identified. Footprinting and gel shift assays indicated protein binding to the core promoter region consisting of two Sp1 binding sites, which were sufficient to produce basal promoter activity in the functional studies. The results also suggested the binding of a previously uncharacterized transcription factor to a 23-bp stretch in the inhibitory region.

Expression of the 90K immunostimulator gene is controlled by a promoter with unique features

90K is a secreted glycoprotein with tumor suppressive functions, which is up-regulated in various types of cancer and in AIDS. In order to understand the regulation of its expression, the mouse 90K gene was isolated and analyzed. The gene spans about 8.8-kilobase pairs and consists of 6 exons and was localized on chromosome 11, region E. RNase protection identified one major transcription start site (+1) and three minor ones (-3, +32, +34). The mouse 90K gene was found to have a TATA-less promoter of unusual structure. The 2. 3-kilobase pair 5'-flanking region exhibited strong promoter activity in NIH 3T3 cells; however, it contained neither a TATA-box nor a SP1 site and was not GC-rich. No known initiator motif was found around the transcription start site. 5'- and 3'-deletions defined a minimal promoter of 51 base pairs (-66 --> -16), not including the start site, essential and sufficient for promoter activity. This minimal promoter showed increased activity after stimulation with interferon-gamma or poly(I.C), a substance mimicking viral infection. Essential for both inductions was the integrity of an interferon regulatory factor element within this sequence, a potential binding site for the anti-oncogenic transcription factor interferon regulatory factor-1.

The promoter region of the carbamoyl-phosphate synthetase III gene of Squalus acanthias

Carbamoyl-phosphate synthetase III (CPSase III) of Squalus acanthias (spiny dogfish) is a nuclear-encoded mitochondrial enzyme that catalyzes glutamine-dependent formation of carbamoyl phosphate for urea synthesis. In this paper we report the results of cloning a 10-kb segment of genomic DNA which includes the region flanking the 5' end of the spiny dogfish CPSase III gene. A total of 1,295 base pairs of sequence straddling the start codon was obtained. Primer extension experiments revealed that the transcription start site is the G located 114 residues upstream of the translation start codon ATG. The first exon has 240 base pairs, including the 5' untranslated region, the coding sequence for the signal peptide (38 amino acids), and the four N-terminal amino acids of the mature enzyme. The boundary of the first exon and the first intron of the CPSase III gene is concordant with that of rat and frog (Rana catesbeiana) CPSase I, which have been suggested to have evolved from CPSase III. The putative TATA box sequence, TACAAA, is located at position -31 with an uncommonly found C at the third position. Two C/EBP binding site sequences, ATTCTGCAAG (-405 to -397) and GTGCAGTAAG (-168 to -160), were identified in the promoter region, which suggests that spiny dogfish CPSase III might be subjected to transactivation of transcription by C/EBP-related proteins, as has been reported for rat CPSase I. The preparation and binding of a recombinant RcC/EBP-1 protein (the R. catesbeiana homolog of the mammalian C/EBP alpha) to the two spiny dogfish C/EBP binding sequences are described. Two putative heat-shock binding elements were also identified in the promoter region.

The structure of the gene for the second chain of the human interferon-gamma receptor

The gene for the second chain of the human interferon-gamma receptor was analyzed from cosmid DNA clones. The gene spans over 33 kilobases of DNA and contains seven exons. The signal peptide is encoded by exons 1 and 2, the extracellular domain by exons 2, 3, 4, 5, and by part of 6. Exon 6 also encodes the whole transmembrane domain and part of the intracellular domain. Exon 7 encodes the remainder of the intracellular domain and contains the 3'-untranslated region. The sequences at the exon/intron boundaries are well conserved with respect to canonical acceptor/donor sites (AG/GT). The 5'-flanking region was sequenced and analyzed for transcription factor binding sites. No TATA or CAAT boxes in the promoter region were identified. Consistent with the lack of a TATA box, analysis of the mRNAs by primer extension showed multiple transcription start sites. Promoter activity of the 5'-flanking region was investigated with a luciferase reporter gene and the cytomegalovirus minimal promoter. Segments of the 5' region with promoter activity were identified.

Analysis of intron 4 of the p53 gene in human cutaneous melanoma

DNA sequencing of intron 4 of the p53 gene from seven cutaneous melanoma cell lines showed an absence of mutations. However, both control and melanoma cell lines sequences were different from the reference source obtained from GenBank databank (accession No. X54156). Base pairs 101 and 689 were determined to be T (instead of A) and C (instead of G). Also, an additional C was not detected at position 371. Comparative analysis with p53 DNA-binding sequences, a sequence recognized by a p53 intron 4-binding protein and consensus sequences recognized by transcription factors demonstrated that intron 4 contains putative sequences for NF-kappa B, SP1, AP1 and TFIID binding. Binding of transcription factors could be one of the mechanisms by which intron 4 modulates human p53 expression.

The TATA motif is a target for efficient transcriptional activation and nerve growth factor induction of the peripherin gene

Three proximal elements, PER1, PER2, and PER3, have been implicated in the regulation of peripherin gene expression. PER1 contains the TATA motif and was identified as the principal mediator of neuronal specificity. Here, we demonstrate by transfection of constructs mutated in PER1 that the in vitro protein binding activity of PER1 is irrelevant to its function. However, mutations or substitutions in the TATA box decreased promoter activity by up to 80%. We have investigated this unusual preference for a particular TATA sequence in PC12 cells. In these cells, nerve growth factor induces neuronal differentiation, increasing peripherin gene expression 3-4-fold, while dexamethasone elicits chromaffin differentiation and a 3-fold decrease in peripherin mRNA. Experiments with stably transfected PC12 cells revealed that the specific TATA box of the peripherin gene was crucial for nerve growth factor response. However, it did not affect dexamethasone down-regulation. Therefore, nerve growth factor acts through an element essential for neuronal peripherin gene expression. The results predict that proteins interacting in the vicinity of the TATA box, by inference factors associated with the preinitiation complex, are important for peripherin gene regulation and provide new insights into the mechanisms underlying neuronal differentiation.

Southern hybridization analyses of somatic cell hybrids reveal that human BB1 is a member of a multigene family dispersed throughout the human genome and appears to be linked to the human G25K genes

The hBB1 RNA (2.3 kb in length) encodes a 57-amino-acid protein whose production is essential for cellular transit of G1 phase of the cell cycle (Moats-Staats et al., 1994). Homology searches of GenBank and EMBL revealed that bases 1-234 of the hBB1 cDNA were 97% homologous to the 3' terminal 234 bases of the g25K cDNA (bases 940-1,175, Shinjo et al., 1990) the human homolog of the yeast cdc42 cDNA. We have used the techniques of the long-range polymerase chain reaction (PCR) (Barnes, 1994) and Southern hybridization analyses of a somatic cell hybrid panel to investigate hBB1 gene structure and to determine whether the hBB1 gene(s) overlaps the g25K gene. These studies have demonstrated that the hBB1 RNA is encoded by a gene family composed of eight members that is dispersed throughout the human genome localizing under high-stringency conditions to chromosomes 1, 4, 7, 8, and 20. We have also determined that two hBB1 gene(s) and two g25K gene(s) map to similar-size Bam HI restriction fragments on chromosomes 4 and 7.

Cloning and partial characterization of the promoter for the human p55 tumor necrosis factor (TNF) receptor

An 809-bp region at the 5' flank of the human p55 tumor necrosis factor receptor (TNF-R)-encoding gene was found to be active in driving expression of the cat reporter gene, indicating that it contains a functional promoter. Deletion analysis showed that the promoter activity is present in the region between nucleotides (nt) -385 and -207; the sequence upstream from this region (nt -809 to -385) has an inhibitory effect. The promoter for the p55 TNF-R resembles housekeeping-type promoters in that it drives transcription from multiple start points (tsp) and lacks canonical TATA and CAAT box motifs. The cluster of tsp lies in a region which is particularly C+T rich. In this region, upstream from and near to the furthest upstream tsp, two closely located TCC repeat motifs were identified. These motifs also appear twice in the promoter for the epidermal growth factor receptor, where they were shown to be essential for promoter activity. The human p55 TNF-R promoter shows an overall resemblance, yet also some marked dissimilarities, to the recently described promoter for the mouse p55 TNF-R.

Establishment of de novo DNA methylation patterns. Transcription factor binding and deoxycytidine methylation at CpG and non-CpG sequences in an integrated adenovirus promoter

The establishment of de novo patterns of DNA methylation in mammalian genomes is characterized by the gradual spreading of methylation, which has been documented to occur across an entire integrated adenovirus genome as well as at the nucleotide level in the integrated late E2A promoter of adenovirus type 2. By applying the techniques of genomic sequencing and dimethylsulfate or DNase I genomic footprinting in vivo, we have now demonstrated that the spreading of methylation in cell lines that carry the late E2A promoter with three in vitro pre-methylated 5'-CCGG-3' sequences initially involves a DNA domain of this promoter that is devoid of bound proteins. Subsequently, methylation further spreads to neighboring regions, and the patterns of complexed transcription factors are altered. Evidence has been adduced that DNA methylation at sequences homologous to the AP-1 and octamer binding factor sites interferes with protein binding. In contrast, the methylation of sequences in the vicinity of but not involving sequences homologous to an AP-2 site still permits the binding of proteins to these sites. It is significant that during the spreading of methylation a few 5'-CG-3' sequences can remain hemimethylated for several cell generations, before they also become methylated in both complements. Moreover, in cell line HE2, the integrated, heavily methylated late E2A promoter has been shown by the genomic sequencing technique to contain 5-methyldeoxycytidine residues, not only in all 5'-CG-3' dinucleotides but also in a 5'CA-3' and a 5'-CT-3' dinucleotide sequence. Hence, 5-methyldeoxycytidine occurs in a silenced mammalian DNA sequence also in dinucleotides other than 5'-CG-3'. This finding raises the question of whether 5-methyldeoxycytidine in non-5'-CG-3' dinucleotides can be maintained in the methylated state during continuous cell propagation.

Functional heterogeneity of mammalian TATA-box sequences revealed by interaction with a cell-specific enhancer

A regulatory element upstream of the human myoglobin gene functions as a muscle-specific enhancer (MSE) in conjunction with core promoter elements of the myoglobin gene, but not in combination with the simian virus 40 (SV40) early promoter. These two promoters differ in the sequences of their 'TATA boxes': for the myoglobin gene, the sequence is TATAAAA, whereas for SV40, the sequence is TATTTAT. We have now tested the hypothesis that this sequence difference is responsible for the differential response of the promoters to the MSE. We found that when the TATA box sequence of the myoglobin promoter was changed to that of the SV40 promoter, responsiveness to the MSE was abolished; conversely, when the SV40 TATA box sequence was changed to that of the myoglobin promoter, the promoter became responsive to the MSE. We conclude that mammalian TATA-box elements are functionally heterogeneous, and suggest that this heterogeneity reflects differential interactions with distinctive TATA box-binding factors, only some of which can act cooperatively with MSE-binding proteins to generate an active transcriptional complex.