Requirement of stereospecific alignments for initiation from the simian virus 40 early promoter

The functional activity of the rat c-Ha-ras promoter requires the coordinate involvement of multiple elements

Promoter activity in the rat c-Ha-ras promoter region was assessed in NIH 3T3 cells using the chloramphenicol acetyltransferase (CAT) reporter gene. Promoter activity was orientation dependent. Deletion of the GC box closet to the transcriptional start site, or the upstream GC box and the two CAAT boxes, greatly diminished promoter activity. The GC boxes in the SV40 early promoter could not functionally replace the downstream c-Ha-ras GC box, but specifically competed for expression of rat c-Ha-ras promoter activity. Serum-stimulated growth of 3T3 cells stably transfected with p035-ras-CAT was not associated with increased promoter activity. These data indicate that the GC and CAAT boxes in the rat c-Ha-ras gene are related to constitutive, and not regulatory, promoter activity, and that these elements are involved in a coordinate manner.

Duplicated CArG box domains have positive and mutually dependent regulatory roles in expression of the human alpha-cardiac actin gene

An upstream region from the transcription initiation site to -177 base pairs (bp) of the human alpha-cardiac actin gene directs the transient expression of a bacterial chloramphenicol acetyltransferase (CAT) gene only in muscle cells (A. Minty and L. Kedes, Mol. Cell. Biol. 6:2125-2136, 1986). We modified this promoter region by additional 5' deletions, linker-scanning mutations, and insertion-deletion mutations and demonstrated that the asymmetrical sequences in and adjacent to two CArG [for CC(A + T rich)6GG] motifs, located at -140 and -100 bp, play an important positive role in transcription. The significant impairment of transcriptional activity that accompanies the disruption of one CArG box region can be restored by either. This demonstrated that these two elements interact in a mutually dependent and similar manner. Furthermore, a DNA fragment that includes the CArG boxes had significant competitive activity for transcription directed by the alpha-cardiac actin promoter in an in vivo competition assay. We conclude that the two sequences around each CArG box may interact with the same class of trans-acting positive factor(s) and that these interactions may mediate muscle-specific expression. Each of the two CArG regions appears to be bound independently by such a positive factor(s), and the regions support high-level transcription in a synergistic manner. The transcriptional activity of this regulatory region is proportional to its distance from a TATA box (at -30 bp) and is strictly orientation dependent relative to the direction of transcription. Therefore this upstream region is not an enhancer but is a tissue-specific regulatory upstream element.

Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements

A DNA binding protein (RAP1, previously called SBF-E) has been shown to bind to putative regulatory sites at both yeast mating-type silencers, yet is not the product of genetically identified regulators of the silent loci. Here, we report the purification of RAP1 by DNA affinity chromatography, and the isolation of its gene from a lambda gt11 genomic library using antibodies raised against the protein. Disruption of the chromosomal copy of this gene is lethal. We show that RAP1 protein also binds in vitro to the upstream activation site (UAS) of MAT alpha and ribosomal protein genes. In addition, we show that two different UAS-associated RAP1 binding sites can substitute in vivo for a silencer binding site. Our results suggest that RAP1 may be a transcriptional regulator that can play a role in either repression or activation of transcription, depending upon the context of its binding site.

Interactions of cellular proteins involved in the transcriptional regulation of the human immunodeficiency virus

The human immunodeficiency virus (HIV) is a human retrovirus which is the etiologic agent of the acquired immunodeficiency syndrome. To study the cellular factors involved in the transcriptional regulation of this virus, we performed DNase I footprinting of the viral LTR using partially purified HeLa cell extracts. Five regions of the viral LTR appear critical for DNA binding of cellular proteins. These include the negative regulatory, enhancer, SP1, TATA and untranslated regions. Deletion mutagenesis of these binding domains has significant effects on the basal level of transcription and the ability to be induced by the viral tat protein. Mutations of either the negative regulatory or untranslated regions affect factor binding to the enhancer region. In addition, oligonucleotides complementary to several of the binding domains specifically compete for factor binding. These results suggest that interactions between several distinct cellular proteins are required for HIV transcriptional regulation.

A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer

Numerous eukaryotic upstream promoter and enhancer regions contain a functional octamer sequence ATGCAAAT. We have examined the interactions between an octamer binding protein isolated from HeLa cells and the SV40 and immunoglobulin heavy-chain (IgH) gene enhancers. A partially purified octamer binding activity forms a single complex with the IgH enhancer octamer in a gel retardation assay, but two complexes with a SV40 enhancer fragment containing a single 72-bp element. By using point mutants and both dimethyl sulfate and diethyl pyrocarbonate modification interference assays, we show that the SV40 complexes result from binding of a factor to the octamer-related sequence ATGCAAAG (Octa1) and to an adjacent previously unidentified octamer-related sequence ATGCATCT (Octa2). The base-specific interactions with Octa1 and Octa2 differ; chemical modifications over a 10-bp sequence TATGCAAAGC affect Octa1 binding whereas Octa2 binding is affected by modifications spanning a 13-bp sequence ATGCATCTCAATT in which the octamer-like sequence is not centered. The octamer binding activity has been purified extensively by a DNA affinity precipitation procedure and SDS-polyacrylamide gel electrophoresis. The purified protein, OBP100, has an apparent molecular weight of 100 kD and binds both SV40 Octa1 and Octa2, as well as the IgH enhancer. The distinct interactions of OBP100 with the differently sized Octa1 and Octa2 binding sites suggest remarkably flexible sequence recognition between OBP100 and its binding sites.

Upstream sequences of dosage-compensated and non-compensated alleles of the larval secretion protein gene Sgs-4 in Drosophila

The X chromosomal gene Sgs-4 coding for a larval secretion protein of Drosophila melanogaster is expressed stage and tissue specifically and is hyperexpressed in male larvae of most Drosophila stocks which show dosage compensation. We analysed three Sgs-4 alleles which differ in the size of their coding region, in the intensity of their expression and in the level of dosage compensation. The size and amount of Sgs-4 proteins directly reflect those of RNAs. Different RNA sizes result from different numbers of 21 bp repeats within the structural genes. We sequenced 2.8 kb of DNA upstream of the transcription initiation site of the three alleles. Sequences known to be essential for correct gene expression were located. The only difference within DNA sequences from -1 to -1200 between two alleles with different degrees of expression and differing in dosage compensation is a C to T transition at -344 within a supposed consensus sequence for ecdysone receptor complex binding (ECR). This mutation is partly located within a region of dyad symmetry. Alleles with identical expression show identical mutations within a GTT-rich region at -1.2 kb, but differ within a GT-rich region at -2.0 kb. A polyadenylated 0.5 kb RNA was found to be transcribed from the GTT-rich region of the strand opposite to that of Sgs-4. The corresponding gene is active only in larval salivary glands and, therefore, is named gland specific gene, gsg.

A rat histone H4 gene closely associated with the testis-specific H1t gene

A rat histone H4 gene closely associated with the testis-specific H1t gene was isolated by screening the Sargent-Bonner rat genomic library using cloned human histone genes as probes. Both the H4 gene and the H1t gene are located on a 7-kb EcoRI genomic DNA fragment. Although the deduced amino acid sequence of the rat H4 histone is identical to that of the sequence of human histone H4, the nucleotide sequence of the coding region differs significantly from the coding region of the human H4 gene. Moreover, the relative spacing between the 5'-consensus sequence elements is unique for an H4 gene. S1-nuclease protection analyses reveal that both the H4 and H1t mRNA species are present in a fraction of rat testis cells highly enriched in pachytene spermatocytes, while only the H4 mRNA species is present in a rat myeloma cell line (Y3-Ag1.2.3). During a 1-h hydroxyurea treatment of the Y3 cells, which produces a 99% inhibition of DNA synthesis, the level of this H4 mRNA drops by only 50%, indicating that the stability of this mRNA is only partially coupled with DNA synthesis.

cis- and trans-acting sequences required for expression of simian virus 40 genes in mouse oocytes

To determine the requirements for gene expression in mammalian germ cells, circular double-stranded simian virus 40 (SV40) DNA molecules containing deletions in sequences controlling transcription and replication were injected into the nucleus of mouse oocytes. Expression of large (T-Ag) and small (t-Ag) tumor antigens ("early gene products") required at least three GGGCGG boxes, but did not require either the origin of viral DNA replication (ori) or a TATA box. Expression of capsid antigen VP1 ("late gene products") required at least three GGGCGG boxes, sequences between nucleotides 197 and 273 in the 72-bp repeat region, and transactivation by T-Ag. These results are consistent with the requirements for expression of the same genes in differentiated mammalian cells. Surprisingly, however, the 72-bp repeats ("enhancer elements") that are required for expression of T-Ag and t-Ag genes in differentiated cells were not required in mouse oocytes. Similarly, expression of both the early and late genes was unaffected in mouse oocytes by the absence of either DNA replication or an intact ori sequence, components required for maximum expression of late genes in differentiated cells. Thus, mammalian oocytes effectively utilize promoters that are fully active in mammalian differentiated cells only when associated with either enhancer elements or DNA replication. Furthermore, requirements for expression of SV40 genes in mouse oocytes are distinctly different from those reported for Xenopus oocytes. This suggests that caution should be exercised when extrapolating conclusions drawn from experiments with amphibian germ cells to mammalian germ cells.

Functional analysis of the regulatory region adjacent to the cargB gene of Saccharomyces cerevisiae. Nucleotide sequence, gene fusion experiments and cis-dominant regulatory mutation analysis

In Saccharomyces cerevisiae the expression of the cargB gene (coding for ornithine aminotransferase) is submitted to dual regulation: an induction by allophanate and a specific induction process by arginine. We have determined the nucleotide sequence of the cargB gene along with its 5' region. The coding portion of the gene encodes a protein of 423 amino acid residues with a calculated Mr value of 46049. To characterize further the regulatory mechanisms modulating the expression of the gene we have analyzed fusions of several fragments of the 5' non-coding region to lacZ, compared the 5' sequences of the cargA (coding for arginase) and cargB coregulated genes and determined the nature of two constitutive cis-dominant mutations affecting the arginine control. These approaches allowed us to define three domains in the 5' non-coding region. The upstream one is implicated in the induction by allophanate. The two other domains are involved in the specific control by arginine; the target of the ARGR gene products, that mediate a positive regulation by arginine, lies upstream of another site where a repression by the CARGRI molecule occurs. The constitutive cargB+O- mutations are located in this repressor domain. The 5' non-coding region of cargA presents the same two-domain organization. These two domains contain three sequences homologous to the cargA and cargB 5' regions.

Activation of mutated simian virus 40 enhancers by amplification of wild-type enhancer elements

We show that duplication of any one of three separate simian virus 40 enhancer elements, A, B, or C, can compensate for loss of function in the remaining two. Simian virus 40 revertants containing point mutations within the A and C (dpm16) or B and C (dpm26) enhancer elements contain tandem duplications that include the remaining wild-type element. These simple tandem duplications can create enhancers 25-fold more active than that of the parental mutant. These revertants can arise by illegitimate recombination between heterologous viral genomes. This was demonstrated by the recombinants resulting from a mixed infection with the viruses dpm16 and dpm2, which contain mutations in the A and C elements and the B element, respectively.

Upstream regulatory regions required to stabilize binding to the TATA sequence in an adenovirus early promoter

Of the five early adenovirus promoters, the early region 3 (E3) promoter is one of the most strongly induced by the E1A protein. To identify cellular proteins involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, DNase I footprinting using partially purified Hela cell extracts was performed. Four regions of the E3 promoter serve as binding domains for cellular proteins. These regions are found between -156 to -179 (site IV), -83 to -103 (site III), -47 to -67 (site II), and -16 to -37 (site I), relative to the start of transcription. Examination of the DNA sequences in each binding domain suggests that site III likely serves as a binding site for activator protein 1 (AP-1), site II for the cyclic AMP regulatory element binding protein (CREB), and site I for a TATA binding factor. The factors binding to either site II or III were sufficient to stabilize binding to the TATA sequence (site I). Mutagenesis studies indicated that both sites II and III, in addition to site I, are needed for complete basal and E1A-induced transcription. These results suggest that multiple cellular factors are involved in both the basal and E1A-induced transcriptional regulation of the E3 promoter, and that either of two upstream regions are capable of stabilizing factor binding to the TATA sequence.

Spatial relationship of the Fis binding sites for Hin recombinational enhancer activity

Site-specific recombination reactions involve the joining or rearrangement of discrete DNA segments in a highly precise manner. A site-specific DNA inversion regulates the expression of flagellin genes in Salmonella by switching the orientation of a promoter. Analysis of the reaction has shown that, in addition to DNA sequences at the two boundaries of the 1-kilobase invertible segment where strand exchange occurs, another cis acting sequence is required for efficient inversion. This 60-base-pair enhancer-like sequence can function at many different locations and in either orientation in a plasmid substrate. It includes two binding sites for a host protein called Factor II or Fis (refs 4 and 5). Here we have investigated the importance of the spatial relationship between the two Fis binding sites for enhancer activity and have found that the correct helical positioning of the binding sites on the DNA is critical. However, this result could not be accounted for by effects on Fis binding. We propose a model for enhancer function in which the enhancer region acts to align the recombination sites into a specific conformation required for productive synapsis.

In vitro binding of several cell-specific and ubiquitous nuclear proteins to the GT-I motif of the SV40 enhancer

We have investigated the specific in vitro binding of nuclear proteins from several cell lines to the GT-I motif of the SV40 enhancer which overlaps with the canonical enhancer "core" homology. The binding of three proteins (GT-IA, GT-IB, and GT-IC), one of which (GT-IC) exhibits cell specificity, was detected. Competition and direct binding experiments demonstrated that the two ubiquitous proteins also bind to the GC-rich motif III from the 21-bp repeat upstream element of the SV40 early promoter and that protein GT-IA is most probably the transcription factor Sp1. The third, cell-specific protein GT-IC exhibited a high affinity for both the GT-I motif and an upstream element in the promoter of the mouse beta-major-globin gene, suggesting that this protein can act both as an enhancer and an upstream element trans-acting factor. The good correlation between the known cell-specific in vivo activity of the wild-type and mutated GT-I motif and the cell-specific binding of protein GT-IC in vitro strongly supports the conclusion that this protein is an enhancer factor. Interestingly, its cognate recognition sequence does not coincide with the core homology.

Metal-dependent binding of a factor in vivo to the metal-responsive elements of the metallothionein 1 gene promoter

Using the technique of genomic footprinting, we demonstrate cadmium-inducible protection from dimethyl sulfate (DMS) modification of guanine residues in vivo in five metal-responsive elements (MREs) in the promoter of the rat metallothionein 1 (MT-1) gene. We also identify a site of extreme DMS hyperreactivity which, like the MRE protection, occurs only after metal ion induction. With this hyperreactive site as an indicator, we can measure the kinetics of induction and deinduction. Changes in the intracellular metal ion concentrations are reflected in alterations in the reactivity with DMS of guanine residues in the MT-1 gene promoter. Lastly, for both control and metal-induced cells, we observe DMS protection and enhancement of a binding site (located 5' of the distal MRE) which is a consensus sequence for the Sp1 transcription factor. Transfection experiments with deletion mutations of a fusion gene construct indicate both that a sequence region which includes this GC box regulates the basal level of expression of the MT-1 gene and that increasing the number of MREs in the promoter increases the induced level of transcription. Our genomic footprinting and transfection data together suggest that (i) a transcription factor, possibly Sp1, plays an important role in regulating the basal level of expression of the MT-1 gene and (ii) metal induction involves the metal-dependent binding to a sequence-specific binding factor which responds to changes in intracellular metal ion levels.

Effects of position and orientation of the 72-base-pair-repeat transcriptional enhancer on replication from the simian virus 40 core origin

A number of recent studies have reported that in papovaviruses such as simian virus 40 (SV40) and polyomavirus, the replication of the viral DNA in vivo is activated by the viral transcriptional enhancer or promoter sequences. Both viral and cellular transcriptional enhancers are well known for their ability to activate transcription in a position- and orientation-independent manner. In the present study, we investigated the effect of the position and orientation of the SV40 72-base-pair (bp) repeat enhancer on its replication activation function. We constructed plasmids containing one copy each of the SV40 core origin and enhancer placed in either order and orientation and at different distances from each other. We assayed the replication efficiencies of these plasmids in the presence of an internal control plasmid in COS-1 monkey kidney cells producing the SV40 T antigen required for replication. We found that the 72-bp repeat was capable of activating replication equally well in either orientation when placed 8 or 9 bp from the core origin. The activation of replication was totally abolished, and replication efficiencies in most instances were found to be lower than that obtained with the core origin alone, when the 72-bp repeat was separated from the core origin by distances of 99 bp or more. This was in direct contrast to the situation with polyomavirus, in which activation of replication by the homologous enhancer or by the SV40 72-bp repeat enhancer is known to be position independent. We also found that when the SV40 core origin and the 72-bp repeat enhancer were adjacent to each other, efficient activation of replication was obtained only if the end of the core origin containing the 17-bp A + T block was linked with the enhancer. In the other orientation of the core origin, activation of replication was either diminished or abolished. Hypotheses such as alteration of chromatin structure by the enhancer and interaction between trans-acting factors binding to the enhancer and the core origin mediating the activation effect are discussed.

Distinguishing between mechanisms of eukaryotic transcriptional activation with bacteriophage T7 RNA polymerase

To distinguish between mechanisms of eukaryotic transcriptional activation, we tested whether yeast upstream promoter elements can stimulate transcription by a heterologous transcription machinery, bacteriophage T7 RNA polymerase. The gal enhancer-like element recognized by GAL4 protein or the ded1 poly(dA-dT) element was placed upstream of the T7 promoter and his3 structural gene, and T7 RNA polymerase was produced in yeast cells. Under conditions where the gal element would normally be either activating or nonactivating, his3 transcription by T7 RNA polymerase was not stimulated above the level observed in the absence of any upstream element. In contrast, the ded1 poly(dA-dT) element stimulated transcription 7-fold, similar to the enhancement observed on the native ded1 promoter. Activation by the ded1 element thus may involve effects on the chromatin template that facilitate entry of the transcription machinery, whereas activation by the gal element may involve specific contacts between GAL4 and the transcriptional machinery.

Negative regulation contributes to tissue specificity of the immunoglobulin heavy-chain enhancer

We have identified in and around the immunoglobulin heavy-chain enhancer two apparently distinct negative regulatory elements which repress immunoglobulin H enhancer, simian virus 40 enhancer, and heterologous promoter activity in fibroblasts but not in myeloma cells. We propose that in nonlymphoid cells, negative regulatory elements prevent activation of the immunoglobulin H enhancer by ubiquitous stimulatory trans-acting factors.

Regulation and function of the Drosophila segmentation gene fushi tarazu

The Drosophila segmentation gene fushi tarazu (ftz) is expressed in a pattern of seven stripes at the blastoderm stage. Two cis-acting control elements are required for this expression: the zebra element, which confers the striped pattern by mediating the effects of a subset of segmentation genes; and the upstream element, an enhancer element requiring ftz+ activity for its action. Fusion of the upstream element to a basal promoter results in activation of the heterologous promoter in a ftz-dependent striped pattern, supporting the idea that ftz regulates itself by acting through its enhancer. The upstream element can also confer expression patterns similar to that of the homeotic gene Antennapedia, suggesting that a similar element may play a role in the activation of Antennapedia.

An octamer oligonucleotide upstream of a TATA motif is sufficient for lymphoid-specific promoter activity

The octamer sequence ATGCAAAT or its inverse complement ATTTGCAT is well-conserved in all immunoglobulin gene promoters and has been implicated in promoter function by deletion analysis. Although immunoglobulin promoters are tissue-specific, the octamer is also a functional element in non-tissue-specific upstream regions--like those controlling U1 and U2 small nuclear RNA and histone H2B genes--where it is associated with additional canonical elements. Specific interactions occur between the octamer motif and both lymphoid-specific and ubiquitous proteins. By using a synthetic octamer oligonucleotide inserted upstream of the beta-globin TATA box we show here that the octamer element by itself is sufficient for directing lymphocyte-specific RNA synthesis when within 70 base pairs of the start site of transcription. We also demonstrate that mutations in any position of the conserved motif interfere with this function.

Transcriptional regulation in the yeast life cycle

The transition from haploid to diploid in homothallic yeast involves a defined sequence of events which are regulated at the level of transcription. Transcription factors encoded by SWI genes activate the HO endonuclease gene at a precise stage in the cell cycle of mother cells. The HO endonuclease initiates a transposition event which activates genes of the opposite mating type by causing them to move away from a silencer element. The activated mating type genes then regulate genes involved in cell signaling such as the mating type-specific pheromones and their receptors. Since HO is only activated in one of the sister cells after division (the mother), adjacent cells of opposite mating type are generated which respond to each others' secreted pheromones by inducing genes involved in conjugation. This leads to the formation of a diploid in which many of the genes involved in mating and mating-type switching become repressed due to the heterozygosity of the mating-type locus. This article summarizes what is known about these transcriptional controls and discusses possible parallels in higher eukaryotes.

Cis- and trans-acting elements responsible for the cell-specific expression of the human alpha 1-antitrypsin gene

The 5' flanking region of the human alpha 1-antitrypsin (alpha 1-AT) gene contains cis-acting signals for liver-specific expression and, when fused to a reporter gene, is able to drive the expression of this gene specifically in liver cells. Here we report the results of a functional dissection of the alpha 1-AT regulatory region. The expression of the bacterial chloramphenicol-transacetylase (CAT) gene, fused to a set of alpha 1-AT 5' flanking regions shortened by progressive deletions or mutated by base pair substitutions, has been compared by transfection in HepG2 (hepatocyte) and HeLa (non-hepatocyte) human cell lines. A minimal tissue-specific element has been identified between the nucleotides -137 and -37 (from the transcriptional start site). This DNA segment activates the heterologous SV40 promoter in hepatoma cell lines but not in HeLa cells. This element contains at least two regions referred to as the A (-125/-100) and B (-84/-70) domains, both essential for transcription. There are at least two other regulatory domains located upstream of the 'minimal element'; the most active of these is located between positions -261 and -210 from the cap site. These upstream elements activate the heterologous SV40 early promoter both in hepatoma cell lines and in HeLa cells. Upon fractionation of rat liver nuclear extracts two proteins have been identified, alpha 1TF-A and alpha 1TF-B, which bind specifically to the A and B domains respectively. Transcriptionally inactive A and B domain mutants are not able to bind these proteins.

Conserved major histocompatibility complex class II boxes--X and Y--are transcriptional control elements and specifically bind nuclear proteins

A conserved sequence motif exists at the 5' end of all major histocompatibility complex class II genes. This motif consists of the 14-base X and Y boxes separated by a short stretch of variable sequence. In this report, we provide evidence that the X and Y boxes play an important role in controlling transcription of the murine class II gene E kappa alpha. We have developed transgenic mouse lines that carry E alpha genes cleanly deleted for either the X or Y box and have compared the expression of these mutant transgenes with that of a nondeleted control. Both the X and Y segments appear critical for accurate and efficient transcription of E kappa alpha. The most drastic effect is seen with gamma-interferon-treated macrophages, where deletion of the Y box completely abrogates transcription initiated by the normal promoter. In addition, we identify proteins from nuclear extracts that bind specifically to the X or Y box.

Characterization of the trans-activation-responsive element of the parvovirus H-1 P38 promoter

The parvovirus early protein NS1 positively regulates the expression of the P38 promoter for the viral capsid protein gene. We have examined the trans-activation of P38 by NS1 by using fusions of P38 to the reporter gene, chloramphenicol acetyltransferase (cat). Maximal trans-activation requires a small 5' cis element (tar) between -137 and -116. The tar element has activity in both orientations when 5' to the P38 promoter, but no activity has been detected 3' to the promoter. The wild-type P38 has a biphasic response to NS1 depending on the dosage of the NS1-expressing plasmid. Promoters lacking the tar also have a biphasic response that is reduced about 10-fold, and they can be inhibited by larger doses of the NS1 plasmid. Heterologous promoters from other viruses and the Harvey-ras oncogene promoter are inhibited by NS1. Truncated and internally deleted versions of NS1 lose the trans-activation, but some of them retain the inhibitory properties. Thus transactivation can be uncoupled from inhibition. The tar element has shown no activity with the heterologous simian virus 40 early promoter. In contrast, the P38 promoter responds to a heterologous enhancer, but the enhanced promoter loses activity to trans-activation by NS1. In summary, the P38 tar element has some of the properties of an enhancer with a high preference for a 5' position and a stringent requirement for the P38 promoter.

Interactions between a DNA-binding transcription factor (COUP) and a non-DNA binding factor (S300-II)

We have identified previously two transcription factors, COUP (chicken ovalbumin upstream promoter) and S300-II, from HeLa cell nuclear extracts. In this paper, the purine base and the phosphate backbone contact sites for the COUP transcription factor were defined. These studies indicate that the COUP box transcription factor interacts with specific base residues in the major groove of the DNA helix. In addition, we have purified the S300-II factor over 100,000-fold. The polypeptide possessing functional transcriptional activity has been identified by SDS-PAGE followed by gel-slice elution and a renaturation assay. It is absolutely required for in vitro function of the ovalbumin promoter. In addition, S300-II stimulates transcription from the MMTV and lysozyme promoters. Kinetic studies probing the interaction of S300-II with COUP factor suggest that it may stabilize COUP-promoter complexes by slowing their rate of dissociation.

Eukaryotic RNA polymerase I promoter binding is directed by protein contacts with transcription initiation factor and is DNA sequence-independent

RNA polymerase I binding to the eukaryotic ribosomal RNA gene promoter-transcription initiation factor (TIF) complex was examined by in vitro transcription and footprinting of a series of spacer mutants. Polymerase binds efficiently to the TIF-promoter complex independently of the DNA sequence in the polymerase interaction region and initiates transcription a fixed distance downstream of the TIF binding site on AT-rich templates. Methidiumpropyl-EDTA.FE(II) footprinting confirms minimal contacts between polymerase and DNA. We infer that polymerase is directed to the promoter by a DNA sequence-independent mechanism, solely by protein-protein contacts with TIF. An initiation step subsequent to binding requires special sequence characteristics in the transcription start site region.

Only two of the four sites of interaction with nuclear factors within the Xenopus U2 gene promoter are necessary for efficient transcription

An analysis, performed by DNase I footprinting, of the interactions between factors present in Molt-4 nuclear extracts and a Xenopus U2 snRNA gene promoter is presented. Four distinct regions of sequence-specific DNA-factor interaction are found. Two of these correspond to the previously identified proximal and distal sequence elements (PSE and DSE) of the promoter. Both of these elements are important in U2 transcription, indicating a functional role for the observed interactions. The other two sites of interaction correspond to a sequence element conserved in many, but not all, vertebrate U snRNA gene promoters (the MSE) and to a region adjacent to the site of transcription initiation (the "cap site"). Site-directed mutants of these latter two elements are constructed which no longer bind nuclear factors. Transcriptional analysis in Xenopus oocytes reveals that these mutants are transcribed as efficiently as wild-type U2. Other possible roles for the two factors are discussed.

Duplicated CArG box domains have positive and mutually dependent regulatory roles in expression of the human alpha-cardiac actin gene

An upstream region from the transcription initiation site to -177 base pairs (bp) of the human alpha-cardiac actin gene directs the transient expression of a bacterial chloramphenicol acetyltransferase (CAT) gene only in muscle cells (A. Minty and L. Kedes, Mol. Cell. Biol. 6:2125-2136, 1986). We modified this promoter region by additional 5' deletions, linker-scanning mutations, and insertion-deletion mutations and demonstrated that the asymmetrical sequences in and adjacent to two CArG [for CC(A + T rich)6GG] motifs, located at -140 and -100 bp, play an important positive role in transcription. The significant impairment of transcriptional activity that accompanies the disruption of one CArG box region can be restored by either. This demonstrated that these two elements interact in a mutually dependent and similar manner. Furthermore, a DNA fragment that includes the CArG boxes had significant competitive activity for transcription directed by the alpha-cardiac actin promoter in an in vivo competition assay. We conclude that the two sequences around each CArG box may interact with the same class of trans-acting positive factor(s) and that these interactions may mediate muscle-specific expression. Each of the two CArG regions appears to be bound independently by such a positive factor(s), and the regions support high-level transcription in a synergistic manner. The transcriptional activity of this regulatory region is proportional to its distance from a TATA box (at -30 bp) and is strictly orientation dependent relative to the direction of transcription. Therefore this upstream region is not an enhancer but is a tissue-specific regulatory upstream element.

Herpes simplex virus virion stimulatory protein mRNA leader contains sequence elements which increase both virus-induced transcription and mRNA stability

To investigate the role of 5' noncoding leader sequence of herpes simplex virus type 1 (HSV-1) mRNA in infected cells, the promoter for the 65,000-dalton virion stimulatory protein (VSP), a beta-gamma polypeptide, was introduced into plasmids bearing the chloramphenicol acetyltransferase (cat) gene together with various lengths of adjacent viral leader sequences. Plasmids containing longer lengths of leader sequence gave rise to significantly higher levels of CAT enzyme in transfected cells superinfected with HSV-1. RNase T2 protection assays of CAT mRNA showed that transcription was initiated from an authentic viral cap site in all VSP-CAT constructs and that CAT mRNA levels corresponded to CAT enzyme levels. Use of cis-linked simian virus 40 enhancer sequences demonstrated that the effect was virus specific. Constructs containing 12 and 48 base pairs of the VSP mRNA leader gave HSV infection-induced CAT activities intermediate between those of the leaderless construct and the VSP-(+77)-CAT construct. Actinomycin D chase experiments demonstrated that the longest leader sequences increased hybrid CAT mRNA stability at least twofold in infected cells. Cotransfection experiments with a cosmid bearing four virus-specified transcription factors (ICP4, ICP0, ICP27, and VSP-65K) showed that sequences from -3 to +77, with respect to the viral mRNA cap site, also contained signals responsive to transcriptional activation.

Identification of proteins interacting with the enhancer of human U2 small nuclear RNA genes

Protein/DNA interactions in the human U2 RNA gene enhancer have been characterized by DNase I footprint and DMS methylation protection analyses. Nuclear factors present in both HeLa and B cell extracts have been shown to protect an approximately 70 bp region from DNase I digestion. DMS and DNase I footprint competition studies demonstrated that the entire footprint can be accounted for by interactions with two previously identified transcription factors. One of these recognizes the so called octanucleotide-motif ATGCAAAT (transcription factor IgNF-A) which has been shown to be essential for transcription. The other is the transcription factor Sp1 which binds to three target sequences located adjacent to the octameric motif. The Sp1 interactions appear to be required for full transcriptional activity. No differences in the DNase I footprint patterns or in the DMS methylation protections were observed when nuclear extracts from HeLa cells, two different B cell lines, or from the adenovirus-transformed 293 cell line were compared.

Negative regulation contributes to tissue specificity of the immunoglobulin heavy-chain enhancer

We have identified in and around the immunoglobulin heavy-chain enhancer two apparently distinct negative regulatory elements which repress immunoglobulin H enhancer, simian virus 40 enhancer, and heterologous promoter activity in fibroblasts but not in myeloma cells. We propose that in nonlymphoid cells, negative regulatory elements prevent activation of the immunoglobulin H enhancer by ubiquitous stimulatory trans-acting factors.

Regulation of inducible and tissue-specific gene expression

Molecular genetics approaches have been used to identify and characterize cis-acting DNA sequences required for eukaryotic gene regulation. These sequences are modular in nature, consisting of arrays of short (10- to 12-base pair) recognition elements that interact with specific transcription factors. Some transcription factors have been extensively purified and the corresponding genes have been cloned, but the mechanisms by which they promote transcription are not yet understood. Positive and negative regulatory elements that function only in specific cell types or in response to extracellular inducers have been identified. A number of cases of inducible and tissue-specific gene expression involve the activation of preexisting transcription factors, rather than the synthesis of new proteins. This activation may involve covalent modification of the protein or an allosteric change in its structure. The modification of regulatory proteins may play a central role in the mechanisms of eukaryotic gene regulation.

The conserved decanucleotide from the immunoglobulin heavy chain promoter induces a very high transcriptional activity in B-cells when introduced into an heterologous promoter

A conserved decanucleotide (ATGCAAATNA) is present 45-60 nucleotides upstream from the transcription startpoint in all immunoglobulin heavy chain promoters (VH promoters). We have introduced this decanucleotide (cd sequence) at a similar position into the upstream flanking sequence of the mouse Renin-1 gene. This gene is only transcribed in highly specialized tissues, and the fragment used here (-449 to +30 with respect to the main transcription startpoint) has little promoter activity in fibroblastic or myeloma cell lines, even if coupled to a functional enhancer. In contrast, after insertion of the decanucleotide, this fragment, while still inactive in non-lymphoid cells, becomes a potent promoter in B-cells when associated with SV40 or immunoglobulin heavy chain enhancer. In all respects, the engineered fragment behaves like an authentic VH promoter isolated in this laboratory, except that it is even more active in B-cells. Deletion experiments show that all renin sequences are dispensable for the activity of the chimaeric promoter, except probably for the renin TATA box which defines the precise transcription startpoint. We conclude that the decanucleotide is sufficient to activate a promoter in B-cells but not in non-B-cells, and therefore that no other element is needed to account for the B-cell specificity of the VH promoter. In addition, our results suggest that the lack of activity of the renin promoter in non cognate cells is not due to the binding of a repressor.

A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements

Maximal expression of the Drosophila heat shock gene hsp70 can be activated by a pair of heat shock consensus elements (HSE's) positioned close to the transcription start site. In contrast, required HSE's of other heat shock genes (i.e., hsp26, 27, 23) are located several hundred base pairs (bp) farther upstream of their start sites. Using germline transformation, we analyzed the requirements for HSE organization in the hsp70 and hsp26 regulatory regions. A 51 bp fragment containing the two proximal hsp70 HSE's was sufficient to rescue the heat shock response of an hsp26-lacZ gene devoid of its HSE's. Heat inducibility was restored with either orientation of the fragment relative to the hsp26 transcription start. In hsp70 gene constructions, relocation of hsp70 HSE's to more remote positions by inserting 127 or 331 bp into the regulatory region failed to substantially reduce expression. Thus, in contrast to their native configurations, the hsp26 promoter can be activated by HSE's solely in a proximal position and the hsp70 promoter can be activated by remote HSE's. In addition, a simple and sensitive assay for quantitative measurement of beta-galactosidase activity in crude fly extracts is described.

Evidence for altered DNA conformations in the simian virus 40 genome: site-specific DNA cleavage by the chiral complex lambda-tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III)

lambda-Tris(4,7-diphenyl-1,10-phenanthroline)cobalt(III), a photoactivated DNA-cleaving agent, is a small molecular probe of DNA structure. Because of its chirality, the complex cannot bind to regular right-handed B-form DNA but exhibits site-specific cleavage along the polymer strand at conformationally distinct sites such as those in a left-handed conformation. Both coarse and higher resolution mapping experiments using the chiral cobalt complex indicate intriguing conformational variations along the simian virus 40 genome. Highly specific cleavage is evident in the enhancer and promoter blocks and in the region downstream of 3' termini. A specific cleavage pattern borders an alternating purine/pyrimidine stretch within the enhancer, which was found earlier to bind anti-Z-DNA antibodies. Throughout the simian virus 40 genome, variations in structure delineated with the cobalt complex appear to correlate with regions important for control of gene expression.

An interactive dot matrix system for locating potentially significant features in nucleic acid molecules

An interactive computer system using a dot matrix approach has been developed and used to determine potentially significant features due to distortions in the B-DNA helix as a result of variations of purine and pyrimidine patterns. Sequences were compared using matrices which were generated using the Calladine-Dickerson rules (C.R. Calladine, J. Mol. Biol. 161, 343-352, 1982 and R.E. Dickerson, J. Mol. Biol. 166, 419-441, 1983). Having control over various parameters to enhance different aspects of the visual appearance of these matrices was helpful in discovering patterns that were not known a priori. Specifically, it was found that a pattern of alternating doublets of purines and pyrimidines appear to exist in regulatory regions. This event is shown to be beyond probabilistic expectation.

Properties of a U1 RNA enhancer-like sequence

The properties of a X.laevis U1B snRNA gene enhancer have been studied by microinjection in Xenopus oocytes. The enhancer-like sequence, defined as a short DNA stretch that is able to activate transcription in an orientation independent manner, is interchangeable between different U snRNA genes. The enhancer sequence alone does not, however, efficiently activate transcription from an SV40 pol II promoter but regains its activity when combined with the U-gene specific proximal sequence element. DNase I protection experiments show that the X.laevis U1B enhancer can interact specifically with a nuclear factor present in mammalian cells.

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

The simian virus 40 (SV40) enhancer element is constituted of two domains which contain sequences important for late transcription (M. Ernoult-Lange, F. Omilli, D. O'Reilly and E. May, J. Virol. 61, 167-176, 1987). By analysing a series of clustered point mutations generated throughout the enhancer region we mapped domain I from nt 232 to 272 and domain II from nt 184 to 216. These two domains which are required for late promoter activity both in the presence and in the absence of T antigen correspond closely to the domains B and A respectively, identified for enhancer function (M. Zenke, T. Grundström, H. Matthes, M. Wintzerith, C. Schatz, A. Wildeman and P. Chambon, EMBO J., 5, 387-397, 1986). Similarly to the enhancer function the late promoter elements defined by these two domains contain multiple sequence motifs. Moreover there is a striking overlap between the sequence motifs within domain A, active for early enhancer function and those within domain II involved in efficient late transcription.

Theoretical molecular biology: prospectives and perspectives

I briefly discuss some aspects of theoretical molecular biology. Specifically, I include the issues of searches for homologies via string matchings, for patterns of specific nucleotide groupings and of sequence-structure relationship. The various approaches developed in order to achieve this end are described, attempting to convey some of the excitement in this quickly growing field.

The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity

The SV40 enhancer is known to be active in a wide variety of tissues and species. It contains a number of sequence motifs that can be bound by protein factors and whose integrity is essential for full enhancer activity. We have individually analyzed three synthetic oligonucleotides derived from sequences present within the SV40 enhancer: two oligonucleotides contain variants of the enhancer "core" sequence (designated corePVUII and coreC) and the third represents a region containing a decanucleotide homology to the immunoglobulin promoters/enhancers (designated SPHI). The oligonucleotides were multimerized and linked to a beta-globin test gene. Transcripts of the test gene were analyzed following transient expression in 10 cell lines representing a broad spectrum of tissues. We show that each of the three short segments can individually act as an enhancer when present in multiple copies. None of these enhancers is ubiquitously active; however, each shows activity in a distinctive subpopulation of cell lines. This cell type specificity is most remarkable in the case of the two oligonucleotide segments containing the core sequences. One of these is primarily active in CV-1 cells, whereas the other exhibits a cell type specificity identical to that of the entire enhancer, possibly identifying it as the most important sequence element within the native SV40 enhancer. Our data suggest that a particular cell type specificity is typical for individual enhancer segments, and that enhancers of differing specificity can be assembled from the individual sequence motifs by combining them in different patterns.

Long-range cooperativity between gene regulatory sequences in a prokaryote

Regulation of transcription initiation by proteins binding at DNA sequences some distance from the promoter region itself seems to be a general phenomenon in both eukaryotes and prokaryotes. Proteins bound to an enhancer site in eukaryotes can turn on a distant gene, whereas efficient repression of some prokaryotic genes such as the gal, ara and deo operons of Escherichia coli, requires the presence of two operator sites, separated by 110, 200 and 600 base pairs (bp) respectively. In the deo operon, which encodes nucleoside catabolizing enzymes, we have shown that efficient and cooperative repression can be obtained when the distance between the two sites ranges from 224 to 997 bp. Here, we report that transcription initiation can be regulated from an operator site placed 1 to 5 kilobases (kb) downstream of the deoP2 promoter (and downstream of the transcribed gene), and present the first experimental data for prokaryotic regulation at distances greater than 1 kb. Our results support the model of DNA loop formation as a common regulatory mechanism explaining both some prokaryotic regulation and the action of eukaryotic enhancers.

Minimal transcriptional enhancer of simian virus 40 is a 74-base-pair sequence that has interacting domains

We have assayed the ability of segments of the simian virus 40 (SV40) 72-base-pair (bp) repeat enhancer region to activate gene expression under the control of the SV40 early promoter and to compete for trans-acting enhancer-binding factors of limited availability in vivo in monkey CV-1 or human HeLa cells. The bacterial chloramphenicol acetyltransferase and the herpes simplex virus type 1 thymidine kinase genes were used as reporters in these assays. A 94-bp sequence located between SV40 nucleotides 179 and 272, including one copy of the 72-bp repeat, has been termed the minimal enhancer in previous studies. In the present study, we found that the 20-bp origin-proximal region located between nucleotides 179 and 198 was dispensable, since its removal caused only a slight reduction in enhancer activity. However, the deletion of another 4 bp up to nucleotide 202 abolished the enhancer activity. We propose that the minimal enhancer is a 74-bp sequence located between nucleotides 199 and 272, including 52 bp of one copy of the 72-bp repeat and a 22-bp adjacent sequence up to the PvuII site at 272. The nonamer 5'-AAGT/CATGCA-3', which we term the K core, occurred as a tandem duplication around the SphI site at nucleotide 200, and we found that this duplication was essential for enhancement and factor-binding activities. A heterologous core element (which we term the C core), 5'-GTGGA/TA/TA/TG-3', identified earlier (G. Khoury and P. Gruss, Cell 33:313-314, 1983; Weiher et al., Science 219:626-631, 1983) also occurred in duplicate, with one of the copies located within the 22-bp sequence near nucleotide 272 present outside the 72-bp repeat. We provide direct evidence that this 22-bp sequence augments enhancer activity considerably. We also found that in addition to the heterologous interaction occurring normally between the K and C cores within the minimal enhancer, certain homologous interactions were also permitted provided there was proper spacing between the elements.

Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants

To examine the internal organization of the promoter of the Xenopus laevis rRNA gene, we constructed a series of linker-scanning mutants that traverse the rDNA initiation region. The mutant genes, which have 3 to 11 clustered base substitutions set within an otherwise unaltered rDNA promoter sequence, were injected into Xenopus oocyte nuclei, and their transcriptional capacity was assessed by S1 nuclease analysis of the resultant RNA. The data demonstrate that there are two essential promoter domains, the distal boundaries of which coincide with the promoter boundaries established previously by analysis of 5' and 3' deletion mutants. The upstream promoter domain is relatively small and extends from residues ca. -140 to -128. The downstream domain is considerably larger, encompassing residues ca. -36 to +10, and exactly corresponds in both size and position to the mammalian minimal promoter region. The Xenopus rDNA sequence between these two essential domains has a much smaller effect on the level of transcriptional initiation. In light of the fact that a large portion of this intervening region consists of a segment (residues -114 to -72) that is duplicated many times in the upstream spacer to form an rDNA enhancer sequence, it is noteworthy that a "-115/-77 linker scanner," in which virtually this entire segment is replaced by a polylinker sequence, has full promoter activity in the injected Xenopus borealis oocytes. Analysis of a parallel series of spacing change linker-scanning mutants revealed the unexpected result that the relative positions of the upstream and downstream promoter domains are very critical: all spacing alterations of more than 2 base pairs within this 100-base-pair region virtually abolish promoter activity. We conclude that the factors that bind to these two distant promoter domains must interact in a very precise stereospecific manner.

The c-Ha-ras oncogene and a tumor promoter activate the polyoma virus enhancer

A c-Ha-ras oncogene, to a lesser extent the c-Ha-ras proto-oncogene, and the tumor promoter 12-O-tetradecanoylphorbol-13-acetate activate the inactive polyoma virus (Py) enhancer in a myeloma cell line and the partially active Py enhancer in NIH 3T3 fibroblasts, but have no effect on the active Py enhancer in LMTK- fibroblasts. In addition, c-Ha-ras can stimulate the inactive Py enhancer in embryonal carcinoma F9 cells. c-Ha-ras activation in embryonal carcinoma cells does not appear to involve reversal of "E1A-like" inhibition of the enhancer. We suggest that modulation of cellular enhancer activity could play a key role in tumorigenesis by oncogenes.

Functional analysis of the role of the A + T-rich region and upstream flanking sequences in simian virus 40 DNA replication

One boundary of the minimal origin of replication of simian virus 40 DNA lies within the A + T-rich region. Deletion of only a few bases into the adenine-thymine (AT) stretch results in a DNA template which is defective for replication both in vivo and in vitro (B. Stillman, R. D. Gerard, R. A. Guggenheimer, and Y. Gluzman, EMBO J. 4:2933-2939, 1985). In the present study, such deletion mutations have been reconstructed into a simian virus 40 genome containing an intact early promoter-enhancer region. The resulting mutants synthesized wild-type levels of T antigen, but were defective for replication and would not form plaques on CV-1 monkey cells. Replication-competent phenotypic revertants were selected after transfection of large quantities of the replication-defective viral DNAs into CV-1 cells. DNA sequence analysis showed that most of these revertants contained insertions or point mutations which partially regenerate the length of the AT stretch. These genotypic alterations were shown to be responsible for the revertant phenotype by replication analysis in vivo of subcloned revertant origin fragments. In general, our results emphasize the importance of the AT region to simian virus 40 origin function. However, one revertant retained the altered AT region but deleted six nucleotides upstream. Experiments using this mutant indicate that the 21-base-pair repeats identified as part of the early transcriptional promoter may compensate for defects in simian virus 40 DNA replication in vivo caused by mutations in the A + T-rich region when positioned at an appropriate distance from the core origin.

A new method for constructing linker scanning mutants

A new procedure for the construction of linker scanning mutants is described. A plasmid containing the target DNA is randomly linearized and slightly shortened by a novel combination of established methods. After partial apurination with formic acid a specific nick or small gap is introduced at the apurinic site by exonuclease III, followed by nuclease S1 cleavage of the strand opposite the nick/gap. Synthetic linkers are ligated to the ends and plasmids having the linker inserted in the target DNA are enriched. Putative linker scanning mutants are identified by their topoisomer patterns after relaxation with topoisomerase I. This technique allows the distinction of plasmids differing in length by a single basepair. We have used this rapid and efficient strategy to generate a set of 32 linker scanning mutants covering the chicken lysozyme promoter from -208 to +15.

The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing

Systematic oligonucleotide-directed mutagenesis within the internal control region of the Xenopus laevis somatic 5S RNA gene identifies three distinct sequence elements that regulate transcription activity: box A, containing the common, conserved class III promoter domain, and two 5S-gene-specific segments, termed intermediate element and box C. Analysis of the individual steps in the formation of the stable initiation complex reveals that the two 5S-gene-specific elements are the main determinants for the stable binding of TFIIIA. In contrast, TFIIIC binding appears to be dependent on interactions with TFIIIA and on direct DNA interactions in box A as well as probably in box C. Alterations of the spacing between the two major promoter domains of from -3 to +10 nucleotides are tolerated, although they reduce transcription activity and were found to prevent the formation of a stable initiation complex.

Genetic analysis of the human thymidine kinase gene promoter

The promoter of the human thymidine kinase gene was defined by DNA sequence and genetic analyses. Mutant plasmids with deletions extending into the promoter region from both the 5' and 3' directions were constructed. The mutants were tested in a gene transfer system for the ability to transform TK- cells to the TK+ phenotype. This analysis delimited the functional promoter to within an 83-base-pair region upstream of the mRNA cap site. This region contains sequences common to other eucaryotic promoters including G X C-rich hexanucleotides, a CAAT box, and an A X T-rich region. The CAAT box is in an inverted orientation and is part of a 9-base-pair sequence repeated twice in the promoter region. Comparison of the genomic sequence with the cDNA sequence defined the first exon of the thymidine kinase gene.