Simian virus 40 major late promoter: a novel tripartite structure that includes intragenic sequences

Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component

We have identified a component of the eukaryotic RNA polymerase II transcriptional machinery that is more heat-labile than TFIID. DHFR transcriptional activity was severely reduced in 40 degrees C heat-treated extracts in which TFIID was fully active. This heat-labile activity was required for the transcription of both TATA box and non-TATA box promoters that are activated by the transcription factor Sp1. Gel mobility shifts indicated that Sp1 DNA binding activity was heat-labile, and the addition of purified Sp1 to 40 degrees C heat-treated extracts fully restored DHFR transcriptional activity. In contrast, the addition of Sp1 to 47 degrees C heat-treated extract did not result in transcriptional activity from the DHFR promoter. We conclude that reduction in Sp1 DNA binding activity is partially responsible for the heat-sensitive loss of DHFR transcriptional activity, but that a second essential activity is also inactivated by 47 degrees C heat-treatment. The discovery of this heat-labile component of Sp1 activation has two important implications in the analysis of transcriptional regulation. First, it demonstrates that heat-treated extracts are not appropriate for examination of the involvement of TFIID in the transcription of Sp1-activated promoters. Second, it explains the previously reported low-temperature optima for transcription from the DHFR promoter and demonstrates that transcriptional studies of Sp1-activated promoters should not be performed at 30 degrees C.

Genome-wide survey of mRNA half-lives in Bacillus subtilis identifies extremely stable mRNAs

We have used DNA microarrays to survey rates of mRNA decay on a genomic scale in early stationary-phase cultures of Bacillus subtilis. The decay rates for mRNAs corresponding to about 1500 genes could be estimated. About 80% of these mRNAs had a half-life of less than 7 min. More than 30 mRNAs, including both mono- and polycistronic transcripts, were found to be extremely stable, i.e. to have a half-life of > or =15 min. Only two such transcripts were known previously in B. subtilis. The results provide the first overview of mRNA decay rates in a gram-positive bacterium and help to identify polycistronic operons. We could find no obvious correlation between the stability of an mRNA and the function of the encoded protein. We have also not found any general features in the 5' regions of mRNAs that distinguish stable from unstable transcripts. The identified set of extremely stable mRNAs may be useful in the construction of stable recombinant genes for the overproduction of biomolecules in Bacillus species.

Initiation site binding protein and the initiator-like promoter element of mouse mammary tumor virus

The mouse mammary tumor virus (MMTV) promoter contains an element near its transcription initiation site that is recognized by a protein termed initiation site binding protein (ISBP). Spacing between the TATA box and the ISBP site is important for MMTV promoter function, as altered spacing results in heterogeneity in start site selection in vitro and in vivo. The sequence of the ISBP site is related to initiator elements common in many RNA polymerase II promoters. However, binding of partially purified ISBP to several promoters that contain well-characterized initiator elements was not detected; these promoters included binding sites for a number of previously identified initiator-binding proteins. Partially purified ISBP did, however, bind with high affinity to sequences near the initiation sites of the SV40 major late and adenovirus 2 E1B promoters.

A 5' stem-loop and ribosome binding but not translation are important for the stability of Bacillus subtilis aprE leader mRNA

The Bacillus subtilis aprE leader is a determinant of extreme mRNA stability. The authors examined what properties of the aprE leader confer stability on an mRNA. The secondary structure of the aprE leader mRNA was analysed in vitro and in vivo, and mutations were introduced into different domains of an aprE leader-lacZ fusion. The half-lives of the corresponding transcripts were determined and beta-galactosidase activities were measured. Removal of a stem-loop structure at the 5' end or diminishing the strength of the RBS reduced the half-lives from more than 25 min to about 5 min. Interfering with translation by abolishing the start codon or creating an early stop codon had no or little effect on mRNA stability. The authors conclude that a 5' stem-loop and binding of ribosomes are necessary for the stability of aprE leader mRNA. The present results, together with a number of other data, suggest that translation of a B. subtilis mRNA is generally not important for its stability; the situation seems different in Escherichia coli. It is further concluded that the calculated strength of a B. subtilis RBS cannot be used to predict the stability of the corresponding transcript.

The aprE leader is a determinant of extreme mRNA stability in Bacillus subtilis

The Bacillus subtilis aprE gene encodes subtilisin, an extracellular proteolytic enzyme produced in stationary phase. The authors examined the stability of aprE mRNA and aprE leader-lacZ fusion mRNA. Both mRNAs were found to be unusually stable, with half-lives longer than 25 min, demonstrating that the aprE leader contains a determinant for extreme mRNA stability. The half-lives were the same in growing and stationary-phase cells. This contrasts with the findings of O. Resnekov et al. (1990) [Proc Natl Acad Sci USA 87, 8355-8359], which suggested a growth-phase-dependent mechanism for decay of aprE mRNA. The discrepancy is explained by the techniques used. Substitution of two bases or deletion of 25 nucleotides in the aprE leader led to a major difference in its predicted secondary structure and resulted in a fivefold reduction of the half-life of aprE mRNA. The authors also determined the half-life of amyE mRNA, which encodes alpha-amylase, another stationary-phase, excreted enzyme and found it to be around 5 min. This shows that extreme stability is not a general property of stationary-phase mRNAs encoding excreted enzymes.

Isolation and initial characterization of the BRCA2 promoter

The hereditary breast cancer susceptibility gene, BRCA2, is considered to be a tumor suppressor gene that may be involved in the cellular response to DNA damage. The transcript for this gene is cell cycle regulated with mRNA levels reaching a peak just before the onset of DNA synthesis. In order to define the mechanisms by which BRCA2 is transcriptionally regulated, we have begun to study upstream regulatory sequences. In this report, we define a minimal promoter region that has strong activity in human breast epithelial cells. Deletions of this sequence narrowed the strong basal activity to a region extending from -66 to +129 with respect to the BRCA2 transcriptional start site. This sequence demonstrated cell cycle regulated activity with kinetics similar to the endogenous transcript. Examination of the sequence revealed several consensus binding sites for transcription factors including an E-box, E2F and Ets recognition motifs. Electrohoretic mobility shift assays revealed specific protein binding to two sequences upstream of the start site; the palindromic E-box and an Ets/E2F site. Site-directed mutagenesis of either of these sites reduced both the basal activity in log phase cells and the cell cycle regulated activity of the promoter. Mutational inactivation of both sites within the same construct effectively eliminated promoter activity. Antibodies to candidate transcription factors used in super shift experiments revealed specific interactions between the BRCA2 promoter and the basic region/helix - loop - helix containing USF-1 and 2 proteins and Elf-1, an Ets domain protein. Binding of these factors depended upon the presence of intact recognition sequences. The USF factors were shown to bind predominantly as a heterodimeric complex of USF-1 and 2 while Elf-1 bound the promoter when it was not occupied by USF. Co-transfection studies with USF proteins and the varicella zoster IE62 protein provide evidence for the involvement of endogenous and exogenous USF in the activation of the BRCA2 promoter. We propose that interactions between USF-1, USF-2 and Elf-1 play an important role in the transcriptional regulation of the BRCA2 gene.

The adherence-associated lipoprotein P100, encoded by an opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis

Mycoplasma hominis, a cell-wall-less prokaryote, was shown to be cytoadherent by the participation of a 100-kDa membrane protein (P100). To identify the gene encoding P100, peptides of P100 were partially sequenced to enable the synthesis of P100-specific oligonucleotides suitable as probes for the detection of the P100 gene. With this strategy, we identified a genomic region of about 10. 4 kb in M. hominis FBG carrying the P100 gene. Analysis of the complete deduced protein sequence suggests that P100 is expressed as a pre-lipoprotein with a structure in the N-terminal region common to peptide-binding proteins and an ATP- or GTP-binding P-loop structure in the C-terminal region. Downstream of the P100 gene, an additional four open reading frames putatively encoding the four core domains of an active transport system, OppBCDF, were localized. The organization of the P100 gene and oppBCDF in a transcriptionally active operon structure was demonstrated in Northern blot and reverse transcription-PCR analyses, as all gene-specific probes detected a common RNA of 9.5 kb. Primer extension analysis revealed that the transcriptional initiation site was localized 323 nucleotides upstream of the methionine-encoding ATG of the P100 gene. The peptide-binding character of the P100 protein was confirmed by fluorescence spectroscopy and strongly suggests that the cytoadherence-mediating lipoprotein P100 represents OppA, the substrate-binding domain of a peptide transport system in M. hominis.

DNA sequences outside the simian virus 40 early region cause downregulation of T-antigen production in permissive simian cells

Using a series of modified wtSV40 and early region SV40 DNAs we assayed the effect of viral late region sequences on T-antigen production by the SV40 early region. We found that SV40 late region (L-SV40) DNA sequences reduced T-antigen (T-Ag) production by the SV40 early region (E-SV40) when both viral regions were linked as they are in wtSV40 DNA. This was demonstrated by Western analysis which showed that E-SV40 DNA produced 10 times more T-Ag than wtSV40 DNA L-SV40, with its own promoter but unlinked to E-SV40 DNA, also greatly inhibited T-Ag production when it was contrasfected with E-SV40. Therefore, L-SV40 DNA inhibited T-Ag production by E-SV40 DNA when present in cis or in trans. We have shown that expression of the SV40 late transcription unit dominated that of the early (T-Ag gene) transcription unit because late region RNA accumulated to much higher levels than early viral RNA. However, in contrasfected cells L-SV40 DNA did not replicate to higher levels than E-SV40 DNA. We offer a model for control of T-Ag expression in which a relatively small amount of T-Ag activates late transcription at the expense of T-Ag gene transcription and that this represents a switch from early to late viral gene expression. We suggest that when activation of the late transcription unit occurs at the late promoter, expression of the T-Ag gene is greatly reduced. The L-SV40 promoter may inhibit T-Ag gene transcription by sequestering cellular factors required for early transcription, factors which may be present in limited amounts. We suggest further that activation of late transcription allows for the necessary production of large amounts of capsomeres and virions and downregulation of early transcription prevents the early region from interfering with capsid synthesis. We tested the model using a construct with a wild-type T-Ag gene but with mutations in the SV40 major late promoter which prevent the promoter from being bound by cellular repressors of late transcription. We found that this construct, which overproduces late SV40 RNA, was defective for T-Ag production. This indicates that activation of the late promoter results in repression of T-Ag gene expression.

The gene encoding T protein of the glycine decarboxylase complex involved in the mitochondrial step of the photorespiratory pathway in plants exhibits features of light-induced genes

We have isolated and characterized a genomic clone encoding the 41 kDa monomer T-protein. This gene called gdcT spans approximately 3 kbp and is composed of four exons interrupted by three introns (321, 691 and 114 bp). The splice sites for donor and acceptor are in agreement with the canonical GT/AG rule. Primer extension strongly suggests the presence of two major transcription start sites. The first transcription start site around 43 bases downstream of a putative TATA box was assigned the +1 position. The second (+31) is not correlated with a putative TATA box, but revealed a pyrimidine-rich region which is very similar to the initiator element. Sequence analysis of the 5'-upstream region of the gene reveals three consensus regions found in the nuclear genes encoding the chloroplastic proteins of ribulose-1,5-bisphosphate carboxylase (rbcS) and the chlorophyll a/b-binding protein (cab) such as an AT-rich sequence localized at -539 to -530, a box II core sequence GGTTAA (-123 to -118) and between -364 and -354 a tandem GATA motif. These elements are known to be involved respectively in the regulation of light-responsiveness and cell-type specificity expression of plant genes. Gel shift assays indicate that the box II core sequence could bind protein nuclear factors similar to the trans-acting factor which interact with corresponding promoter region of rbcS gene.

Functional analysis of the promoter for the human CYP1B1 gene

Our laboratory has cloned the cDNA (Sutter, T. R., Tang, Y. M., Hayes, C. L., Wo, Y.-Y. P., Jabs, E. W., Li, X., Yin, H., Cody, C. W. , and Greenlee, W. F. (1994) J. Biol. Chem. 269, 13092-13099) and gene (Tang, Y. M., Wo, Y.-Y. P., Jabs, E. W., Stewart, J. C., Sutter, T. R., and Greenlee, W. F. (1996) J. Biol. Chem. 271, 28324-28330) for human CYP1B1, a new member of the cytochrome P450 superfamily. Here, we report on the mapping and function of the CYP1B1 promoter. The CYP1B1 promoter is fully functional, when it is uncoupled from upstream enhancer elements. Deletion analysis and site-directed mutagenesis identified four regulatory elements required for maximum promoter activity: two antisense Sp1 sites (-84 to -89 and -68 to -73), a TATA-like box (-34 to -29), and an initiator motif (-5 to +3). The initiator and the TATA-like elements are both required for basal promoter activity, with enhanced activity mediated by the two antisense Sp1 elements. The CYP1B1 initiator was demonstrated by in vitro transcription analysis to be a positioning element that maintained fidelity of transcription from a single site. Specific binding to a CYP1B1 initiator probe by human nuclear extract proteins was competed either by the highly homologous murine terminal deoxynucleotidyl transferase initiator or, to a lesser extent, by the adenovirus major late initiator. Taken together, these results indicate that the structure and function of the CYP1B1 promoter confers constitutive expression of the gene and assures fidelity of transcription initiation from a single site. The CYP1B1 promoter is distinct from the promoters of the closely related cytochrome P450s CYP1A1 and CYP1A2 and is structurally and functionally similar to the promoters of constitutively expressed genes and at least two viruses.

The major transcription initiation site of the SV40 late promoter is a potent thyroid hormone response element

Thyroid hormone receptors (TRs) are members of the nuclear hormone receptor superfamily, which act as transcription factors upon binding to specific DNA sequences called thyroid hormone (T3) response elements (TREs). Such elements are found in the upstream regulatory region of promoters as well as in intragenic sequences of T3-responsive genes. In this report, we demonstrate that SV40 late (SVL) promoter activity is strongly down-regulated by TR in the absence of ligand. Addition of T3 releases this repression, but does not further induce SVL promoter activity. Electrophoretic mobility shift analyses reveal a TR binding element that overlaps with the SV40 major late transcription initiation site. This element closely fits the consensus TRE, formed of two hexanucleotides organized in a tandem repeat separated by 4 nt, and is able to confer T3 responsiveness on a heterologous promoter. We further show that, although the presence of TR leads to quantitatively modified expression of an SVL-driven reporter gene, neither displacement of the site of transcription initiation nor modification of the splicing pattern of the primary transcripts occur.

Replication protein A is a component of a complex that binds the human metallothionein IIA gene transcription start site

Previous studies revealed that sequences surrounding the initiation sites in many mammalian and viral gene promoters, called initiator (Inr) elements, may be essential for promoter strength and for determining the actual transcription start sites. DNA sequences in the vicinity of the human metallothionein IIA (hMTIIA) gene transcription start site share homology with some of the previously identified Inr elements. However, in the present study we have found by in vitro transcription assays that the hMTIIA promoter does not contain a typical Inr. Electrophoretic mobility shift assays identified several DNA-protein complexes at the hMTIIA gene transcription start site. A partially purified protein fraction containing replication protein A (RPA) binds to the hMTIIA gene transcription start site and represses transcription from the hMTIIA promoter in vitro. In addition, overexpression of the human 70-kDa RPA-1 protein represses transcription of a reporter gene controlled by the hMTIIA promoter in vivo. These findings suggest that hMTIIA transcription initiation is controlled by a mechanism different from most mammalian and viral promoters and that the previously identified RPA may also be involved in transcription regulation.

Transcriptional regulation of c-Fes in myeloid leukemia cells

The c-Fes proto-oncogene encodes a myeloid-specific protein-tyrosine kinase that is expressed preferentially in differentiated myeloid cells, but not in early myeloblast progenitor cells. To examine the basis for the phenotypic expression of c-Fes, the transcription initiation sites of the human c-Fes gene were mapped in myeloid leukemia cells and regulatory elements in the genomic c-Fes sequence were characterized. Two major transcription initiation sites were found in the myeloid leukemia cell line THP-1 which delineated exon 1 to be 72-83 bp. When the activity of the CAT reporter gene under the control of the c-Fes promoter region, untranslated exon 1 and intron 1 was measured in TF-1, K562 and MCF-7 cells, only TF-1 cells exhibited chloramphenicol acetyltransferase activity. In contrast, all cell lines supported reporter gene activity when intron 1 was deleted. Deletion analyses revealed a negative regulatory region in intron 1, which was localized by Southwestern analysis and DNA footprinting to a 14 bp region. This negative regulatory region suppressed reporter CAT activity in K562 and TF-1 cells when inserted downstream to the SV40 early promoter. These results suggest that the tissue-specific expression of c-Fes may result, in part, from the negative regulation of transcription in myeloid and nonmyeloid cells.

Genomic organization and chromosomal mapping of the bovine Fas/APO-1 gene

The cell-surface protein Fas (APO-1) is a member of the tumor necrosis factor receptor (TNFR) superfamily and transduces apoptosis following binding of Fas ligand or exposure to certain anti-Fas antibodies. We have isolated the bovine Fas (bFas) gene and determined its genomic organization and chromosomal location. Our data indicate that bFas is a single-copy gene that contains 9 exons and spans approximately 31.5 kb. The 5'-flanking region lacks conventional TATA and CCAAT elements, but contains several putative regulatory elements, including multiple copies of Sp1, AP-2, E-box, and N-box consensus sites. Linkage analysis of two (CA) dinucleotide repeat microsatellites within intron 1 and physical assignment by fluorescence in situ hybridization (FISH) placed the bFas gene on bovine chromosome 26. Collectively, these data provide a basis for understanding the regulatory mechanisms that control bFas gene expression.

Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence

Detection of RNA polymerase II promoters and polyadenylation sites helps to locate gene boundaries and can enhance accurate gene recognition and modeling in genomic DNA sequence. We describe a system which can be used to detect polyadenylation sites and thus delineate the 3' boundary of a gene, and discuss improvements to a system first described in Matis et al. (1995) [Matis S., Shah M., Mural R. J. & Uberbacher E.C. (1995) Proc. First Wrld Conf. Computat. Med., Public Hlth, Biotechnol. (Wrld Sci.) (in press).], which predicts a large subset of RNA polymerase II promoters. The promoter system used statistical matrices and distance information as inputs for a neural network which was trained to provide initial promoter recognition. The output of the network was further refined by applying rules which use the gene context information predicted by GRAIL. We have reconstructed the rule-based system which uses gene context information and significantly improved the sensitivity and selectivity of promoter detection.

Identification of sequences which regulate the expression of Drosophila melanogaster Doc elements

Long interspersed nuclear elements (LINEs) are mobile DNA elements which propagate by reverse transcription of RNA intermediates. LINEs lack long terminal repeats, and their expression is controlled by promoters located inside to the transcribed region of unit-length DNA copies. Doc elements constitute one of the seven families of LINEs found in Drosophila melanogaster. Plasmids in which the chloramphenicol acetyltransferase (CAT) gene is preceded by DNA segments from different Doc family members were used as templates for transient expression assays in Drosophila S2 cells. Transcription is initiated at the 5' end of Doc elements within hexamers fitting the consensus (C/G)AYTCG and is regulated by a DNA region which is located approximately 20 base pairs (bp) downstream from the RNA start site(s). The region includes a sequence (RGACGTGY motif, or DE2) which stimulates transcription in other Drosophila LINEs, and two adjacent elements, DE1 and DE3. Moving the downstream region either 4 bp away from, or 5 bp closer to the RNA start site region inhibited transcription. Sequences located approximately 200 bp downstream from the Doc 5' end repressed CAT expression in an orientation- and position-dependent manner. The inhibition reflects impaired translation of the CAT gene possibly consequent to the interaction of specific Doc RNA sequences with a cellular component.

Analysis of a Mycoplasma hominis membrane protein, P120

The monoclonal antibody mAb 26.7D generated against a clinical isolate of Mycoplasma hominis 7488 was shown to react with a surface-exposed epitope on a 120-kDa protein (P120). The gene encoding the protein was cloned and sequenced, and the transcriptional start point was determined by primer extension analysis. The gene contained an open reading frame of 3237 bp encoding a peptide of 1079 amino acids with a deduced molecular mass of 123 kDa. A putative amino-terminal signal peptide and cleavage site for signal peptidase II were found. This suggests that the protein was synthesized as a precursor with subsequent processing to a mature lipoprotein. Surface exposure was confirmed by immunoelectron microscopy. mAb 26.7D reacted with 11 of 19 M. hominis strains. The gene was, however, present in all strains.

Direct binding of yeast transcription factor (TFIID) to the ribosomal protein L32 (rpL32) TATA-less promoter sequence

The ribosomal protein L32 (rpL32) gene transcribed by RNA polymerase II lacks a canonical TATA element, that binds the transcription factor TFIID tau or TBP (TATA binding protein). Instead this promoter contains an element, termed gamma, located at -30 relative to the transcription initiation site. We previously reported that, despite the lack of a canonical TATA element the rpL32 gene utilizes yeast TFIID tau for its transcriptional initiation. Whether TFIID tau participates in rpL32 gene transcription by binding directly to a promoter element or through another protein has not been resolved. These studies reveal that proteins ranging in size from 20-40 kDa binds to the gamma-element. The 40 kDa protein(s) displays strong affinity for the canonical TATA element and may be related or equivalent to TFIID tau. Furthermore, cloned and purified yeast TFIID (TBP) binds directly to the gamma-element implying that the gamma-element directs RNA polymerase II-dependent transcription of the rpL32 gene.

Characterization of the alpha-amylase-encoding gene from Thermomonospora curvata

The nucleotide sequence of a 3007-bp DNA fragment from Thermomonospora curvata CCM3352 containing the coding and regulatory region of the alpha-amylase-encoding gene (tam) was determined. Primer extension mapping was used to determine the 5' end of the transcript, and it was demonstrated that the gene is transcribed from a unique promoter which is also functional in Streptomyces lividans TK24. Transcription of tam in T. curvata was induced by maltose, even in the presence of glucose. In S. lividans, tam was expressed constitutively. The deduced amino acid sequence reveals a considerable similarity with alpha-amylases from streptomycetes.

Expression of the gene encoding glycerol-3-phosphate dehydrogenase (glpD) in Bacillus subtilis is controlled by antitermination

The Bacillus subtilis glpD gene encodes glycerol-3-phosphate (G3P) dehydrogenase. A sigma A type promoter and the transcriptional startpoint for glpD were identified. Between the transcriptional startpoint and glpD there is an inverted repeat followed by a run of T residues. The inverted repeat prevents expression of a reporter gene, xylE, when positioned between this gene and a constitutive promoter. Expression of xylE, like expression of glpD, is induced by G3P and repressed by glucose. Induction also requires the product of the glpP gene. Our results suggest that glpD expression is controlled by antitermination of transcription. The inverted repeat appears to be a target for induction by G3P and GlpP. We speculate that glucose repression is mediated via an inhibitory effect on synthesis or activity of GlpP.

Characterization of a second promoter for the mouse liver/bone/kidney-type alkaline phosphatase gene: cell and tissue specific expression

The second leader exon and the relative promoter of the mouse liver/bone/kidney-type alkaline phosphatase gene were identified and characterized. The transcription initiation site was determined by S1 mapping analysis. The differential expression of the two alternatively spliced transcripts was assessed in cell lines of different origin and in various tissues by polymerase chain reaction and RNase mapping analysis. The first promoter is active in embryo derived cells, whereas the second promoter is silent in basal conditions but it is activated by dibutyryl cAMP in fibroblastic cells. In the whole animal, the transcript driven by the first promoter is found in most tissues albeit at different levels, while the one driven by the second promoter is specifically expressed at high levels only in the heart.

Analysis of the HSV-1 strain 17 DNA polymerase gene reveals the expression of four different classes of pol transcripts

We have investigated the structure and the expression of transcripts of the HSV-1 strain 17 DNA polymerase gene (pol) by various mapping methods including cDNA cloning. The majority of mature pol transcripts is strictly colinear with the pol gene. But additionally, pol cDNAs show a defined heterogeneity in respect to their 5'-terminal regions and can be divided into four classes with characteristic differences; (i) class 1 represents the major transcript (pol-R1) with initiation at HSV-1 positions 62,605-62,610, (ii) class 2 initiates about 70 bp downstream, (iii) class 3 is generated by splicing the short open reading frame (SORF) to a 5'-truncated part of the long open reading frame (LORF) which results in a partially different coding potential, and (iv) class 4 starts 120 bp upstream of the major initiation site in the central part of the origin of replication (oriL). S1 and Exo VII nuclease and RNase protection assays as well as primer extension analyses confirm the classification regarding the genuine structure of pol mRNAs and the differential usage of transcriptional start sites. Furthermore, the transcript classes can be distinguished from each other by their kinetics of appearance/disappearance in the cytoplasm: The first transcription of the pol gene is indicated by the predominant presence of class 2 and class 4 mRNAs at 2 hr postinfection (h.p.i.), followed by an increase of class 1 transcripts up to 4 h.p.i. and a parallel decrease of class 2 mRNAs. These data suggest that expression of the pol gene is finely regulated already at the transcriptional and/or posttranscriptional level prior to the translation of pol mRNAs.

Trans-activation of viral tk promoters by proteins encoded by varicella zoster virus open reading frames 61 and 62

Plasmids containing the varicella zoster virus (VZV) open reading frames (ORFs) 61 and 62 were used in a transient co-transfection assay to test for trans-activation of the VZV and herpes simplex virus type 1 (HSV-1) thymidine kinase (tk) promoters. The trans-activating potential of the polypeptides encoded by these VZV ORFs, designated p51 and p140, was compared to that of their HSV-1 homologs ICP0 and ICP4, respectively. VZV p51 was functionally inactive in this system while p140 appeared to be a much stronger transcriptional activator than ICP4. Co-transfection of plasmids encoding VZV p140 and HSV-1 ICP0 resulted in a synergistic activation of the reporter gene as has been shown for the combination of ICP4 and ICP0.

The "initiator" as a transcription control element

Transcription of the lymphocyte-specific terminal deoxynucleotidyltransferase gene begins at a single nucleotide, but no TATA box is present. We have identified a 17 bp element that is sufficient for accurate basal transcription of this gene both in vitro and in vivo. This motif, the initiator (Inr), contains within itself the transcription start site. Homology to the Inr is found in many TATA-containing genes, and specific mutagenesis influences both the efficiency and accuracy of initiation. Moreover, in the presence of either a TATA box or the SV40 21 bp repeats, a greatly increased level of transcription initiates specifically at the Inr. Thus, the Inr constitutes the simplest functional promoter that has been identified and provides one explanation for how promoters that lack TATA elements direct transcription initiation.

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

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