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

DNA bending induced by specific interaction of decamer binding proteins with immunoglobulin gene control sequences

In order to investigate the properties of specific DNA-binding proteins involved in tissue-specific regulation of immunoglobulin genes, we have analyzed the interaction of nuclear proteins from mouse B-cell hybridomas with promoter and enhancer sequences of a mouse immunoglobulin heavy chain gene. Visualization of specific complexes has shown that protein binding induces a sharp bend at the position of the conserved decamer sequence. After fractionation of nuclear extracts, several sequence-specific DNA binding proteins could be distinguished by UV crosslinking to radioactive synthetic oligonucleotides. Decamer binding factor I (DBF-I) a protein of 100-105 kDa and DBF-II, a family of proteins of 25-35 kDa were purified on specific DNA-affinity columns. Both proteins bend the DNA at the dc sequence as shown by electron microscopy and by gel retardation. These data suggest that one possible function of sequence-specific regulatory proteins may be to locally change the DNA topology, thereby facilitating the interaction of additional transcription factors with the primary complex.

The role of operator position in SV40 T-antigen-mediated repression

We have manipulated positional relationships between the SV40 early operator and promoter to study the repression of transcription by T antigen. Single or multiple insertions of T-antigen-binding region I resulted in only weak repression even when the operator was placed immediately adjacent to known promoter elements. The low levels of repression appear to reflect the intrinsic strength of the T-antigen-operator interaction.

Cooperativity and hierarchical levels of functional organization in the SV40 enhancer

We have investigated the cell-specific activity of the GT-IIC, GT-I, Sph-II, Sph-I, and octamer motifs of the SV40 enhancer in four cell lines (HeLa cells, MPC11 plasmocytoma B cells, and non-differentiated and retinoic acid-differentiated F9 embryonal carcinoma cells). Our present results reveal the existence of three classes of motifs that interact with cell-specific enhancer factors but that have no enhancer activity of their own: those (class A) that generate enhancer activity following oligomerization of tandem repeats of the motif; those (class B) that cannot enhance transcription when oligomerized as a tandem repeat but whose association with a second motif results in transcription activation after oligomerization; and those (class C) that exhibit enhancer activity when a single copy of the motif is oligomerized. Three levels of functional organization of enhancers can also be defined. The possible implications for enhancer functions are discussed.

The HeLa cell protein TEF-1 binds specifically and cooperatively to two SV40 enhancer motifs of unrelated sequence

We have purified a protein (TEF-1) that specifically binds to two sequence unrelated motifs (GT-IIC and Sph) of the simian virus 40 (SV40) enhancer. TEF-1 binds cooperatively to templates containing tandem but not inverted or spaced repeats of its cognate motifs. This cooperative binding correlates with the ability of the tandem repeats to generate enhancer activity in vivo. In contrast, TEF-1 and a second SV40 enhancer binding protein, TEF-2, bind independently to templates containing the cognate motifs of both proteins (GT-I and either GT-IIC or Sph motifs) even though these motifs cooperate in enhancer activity in vivo. These results allow us to distinguish different classes of enhancer factors.

The 5' flanking region of the gene for the Epstein-Barr virus-encoded nuclear antigen 2 contains a cell type specific cis-acting regulatory element that activates transcription in transfected B-cells

We have recently identified the promoter that positions the initiation (cap) site for RNA encoding the Epstein-Barr virus (EBV) determined nuclear antigen 2 (EBNA2) in transfected COS-1 cells. The cells were transfected with recombinant vectors that contained the BamHI WYH region of the EBV genome. In order to delineate regulatory DNA sequences required for the expression of EBNA2 the 5' flanking region of the gene was linked to reporter genes in expression vectors and transfected into EBV genome-negative lymphoid DG75 cells. We demonstrate that several cis-acting elements contribute to a transcriptional enhancer activity found in the region between nucleotides-553 and -86 relative to the cap site. The enhancer was active in lymphoid DG75 cells but not in HeLa cells and stimulated transcription also from the heterologous thymidine kinase (TK) and beta-globin promoters. Nuclear extracts of lymphoid cells contained protein factors that bound to the enhancer. The in vitro introduction of a mutation in the enhancer sequence that substantially reduced the transcription stimulatory activity concurrently blocked the binding of one of the factors.

Helical-repeat dependence of integrative recombination of bacteriophage lambda: role of the P1 and H1 protein binding sites

The efficiency of site-specific recombination of bacteriophage lambda was found to depend on the spacing between distant protein binding sites. Insertions and deletions of up to 30 base pairs were made in the nonessential regions between the H1 and H2 protein binding sites. Recombination was found to occur in substrates with changes of integral multiples of a DNA helical repeat, whereas recombination was defective in substrates with nonintegral changes. The lambda recombinogenic complex is especially interesting because two different proteins are involved: integration host factor (IHF), which has been shown to bend DNA, and the phage-encoded integrase protein (Int), which has been shown to have two distinct DNA-binding domains. The importance of angular displacement of protein binding sites was confirmed by addition of ethidium bromide to defective substrates. Significant stimulation of recombination was observed when sufficient drug intercalated and unwound the DNA to allow improved orientation of sites. The orientation effects are dependent on supercoiling, as spacing is less important in conditions where supercoiling and the P1-H1 sites are not required for recombination.

The CGTCA sequence motif is essential for biological activity of the vasoactive intestinal peptide gene cAMP-regulated enhancer

cAMP-regulated transcription of the human vasoactive intestinal peptide gene is dependent upon a 17-base-pair DNA element located 70 base pairs upstream from the transcriptional initiation site. This element is similar to sequences in other genes known to be regulated by cAMP and to sequences in several viral enhancers. We have demonstrated that the vasoactive intestinal peptide regulatory element is an enhancer that depends upon the integrity of two CGTCA sequence motifs for biological activity. Mutations in either of the CGTCA motifs diminish the ability of the element to respond to cAMP. Enhancers containing the CGTCA motif from the somatostatin and adenovirus genes compete for binding of nuclear proteins from C6 glioma and PC12 cells to the vasoactive intestinal peptide enhancer, suggesting that CGTCA-containing enhancers interact with similar transacting factors.

Linker scan analysis of the early regulatory region of human papovavirus BK

BK virus (BKV) is a human papovavirus which latently infects a majority of the world population. Reactivation of this virus is associated with acute hemorrhagic cystitis, and BKV DNA has been found in human tumor tissue. BKV is one of many highly homologous papovaviruses, including simian virus 40 and JC virus, which display distinct host and cell-type specificities, transformation potentials, and pathologies. These differences are thought to be determined, in part, by the noncoding regulatory region of each virus, which contains the origin of replication and regulatory elements for both early and late gene expression. We have used linker scan mutants to map functional elements of a truncated BKV early promoter and enhancer and have studied the stereospecific requirements of these elements. We have also identified protein-binding regions through DNase protection studies. Our results show that a minimum of four elements are necessary for efficient early transcription, at least three of which correspond to DNase-protected domains. These protein-binding elements map to the TATA box and two nuclear factor 1 consensus sequences, one located within the enhancer repeat unit and the other located to the late side of the enhancer. The sequence of the fourth element is similar to the transcription factor Sp1 consensus sequence. Additional DNase-protected sites are centered over AP-1 and Sp1 consensus sequences. Finally, we find that the functional elements of the BKV early promoter and enhancer lack strict stereospecific requirements for efficient transcription.

GAL4 derivatives function alone and synergistically with mammalian activators in vitro

We show that derivatives of the yeast transcriptional activator GAL4, synthesized in and purified from E. coli, stimulate transcription of a mammalian gene (the adenovirus E4 gene) in a HeLa cell nuclear extract. Stimulation depended upon GAL4 binding sites inserted in the template. When the GAL4 sites were placed immediately upstream of the E4 TATA box, GAL4 stimulated efficiently. When the GAL4 sites were further upstream from TATA, however, efficient stimulation by GAL4 required, in addition, a site for a mammalian transcriptional activator immediately upstream of TATA. Under these conditions, the GAL4 derivatives functioned synergistically with the proximally bound activator. Previous experiments have defined two "activating regions" in GAL4, and our current experiments define a third, whose function is observed in vitro but not in vivo.

Stereospecific positioning of the cis-acting sequence with respect to the canonical promoter is required for activation of the ompC gene by a positive regulator, OmpR, in Escherichia coli

Expression of the ompC gene coding for a major outer-membrane protein of Escherichia coli is regulated by a transcriptional activation mechanism that requires the ompR gene product, OmpR. It was demonstrated that multiple OmpR molecules bind to a cis-acting sequence located upstream from the canonical -35 and -10 regions of the ompC promoter. Using an ompC-lacZ fusion gene, the distance between the cis-acting upstream sequence (OmpR-binding site) and the -35 and -10 regions (RNA polymerase-binding site) has been changed. We demonstrated that the ompC transcription was activated in an OmpR-dependent manner even when the cis-acting upstream sequence was separated from the -35 and -10 regions by several turns of the DNA helix, providing that the distance between them was a near-integral multiple of one turn of the DNA helix. Evidence is presented that stereospecific positioning of the cis-acting upstream sequence with respect to the canonical promoter is required for activation of the ompC gene by the positive regulator, OmpR.

Replication from a proximal simian virus 40 origin is severely inhibited by multiple reiterations of the 72-base-pair repeat enhancer sequence

In a previous study in our laboratory, the effect of the reiteration frequency of the simian virus 40 (SV40) 72-base-pair (bp) repeat enhancer on transcription from the proximal SV40 early promoter was investigated (R. Kumar, T. A. Firak, C. T. Schroll, and K. N. Subramanian, Proc. Natl. Acad. Sci. USA 83:3199-3203, 1986). Increasing the enhancer copy number to four increased transcription proportionately; further increments in enhancer copy number reversed this effect, resulting in a decrease in the transcriptional activation. In the present study, the effect of enhancer reiteration on the replication efficiency of plasmids containing the SV40 origin of replication was investigated in transient replication assays in vivo in COS-1 monkey kidney cells producing the SV40 large tumor antigen required for replication. A plasmid containing the SV40 core origin and three copies of the replication-activating, G+C-rich 21-bp repeat promoter element replicated efficiently. Plasmids containing multiple copies of the 72-bp repeat enhancer cloned in head-to-tail linkage adjacent to the 21-bp repeat and the core origin replicated less efficiently; the decrease in replication efficiency could be correlated with the number of copies of the 72-bp repeat; replication was severely curtailed when 10 or more copies of the 72-bp repeat were present. Replication was not significantly inhibited by an increase in the number of copies of the 21-bp repeat to 15 or by the presence of three copies of a 360-bp pBR322 sequence in the immediate vicinity. Multiple copies of the 72-bp enhancer in cis were unable to inhibit replication from a second SV40 origin of replication situated 2 kilobase pairs away from the enhancer reiteration. Replication of four different test plasmids was not inhibited in trans by cotransfection of an excess of a potential competitor plasmid containing a 24-copy reiteration of the 72-bp enhancer. These results indicate that multiple tandem reiterations of the 72-bp enhancer inhibit replication only when they are present in cis adjacent to the origin of replication. Possible explanations for this inhibitory effect, such as an unfavorable local chromatin structure induced by the multimeric enhancer region or reduced or improper communications between factors bound to the multimeric region and the adjacent replication origin, are discussed.

Differential protein binding in lymphocytes to a sequence in the enhancer of the mouse retrovirus SL3-3

An electrophoretic mobility shift assay was used to characterize interactions of nuclear proteins with a DNA segment in the enhancer element of the leukemogenic murine retrovirus SL3-3. Mutation of a DNA sequence of the 5'-TGTGG-3' type decreased transcription in vivo specifically in T-lymphocyte cell lines. Extracts of nuclei from different T-lymphocyte cell lines or cells from lymphoid organs resulted in much higher amounts of complexes in vitro with this DNA sequence than did extracts from other cell lines or organs tested. Differences were also found in the sets of complexes obtained with extracts from the different types of cells. The DNA sequence specificities of the different SL3-3 enhancer factor 1 (SEF1) protein complexes were found to be distinct from those of several other previously identified DNA motifs of the TGTGG type because of differences in several nucleotides critical for binding and because these other DNA motifs could not compete with the identified DNA sequence for binding of SEF1. Limited treatment with several different proteases cleaved the SEF1 proteins such that their DNA-binding domain(s) remained and created complexes with decreased and nondistinguishable electrophoretic mobility shifts and with new properties. These results indicate that the SEF1 proteins have a structure with a flexible and relatively vulnerable hinge region linking a DNA-binding domain(s) to a more variable domain(s) with other functions. We suggest that the binding of SEF1 is an essential factor for the T-cell tropism of SL3-3 and the ability of this virus to cause T-cell lymphomas.

Characterization of antigen receptor response elements within the interleukin-2 enhancer

T-cell activation and induction of interleukin-2 (IL-2) expression in human T lymphocytes require both interaction of foreign antigen with the T-cell antigen receptor and protein kinase C (PKC) stimulation. Agents such as phorbol 12-myristate 13-acetate (PMA) that stimulate PKC augment the effects of antigen but are not sufficient for IL-2 activation. By analysis of deletion mutants, we identified three DNA sequences extending from -73 to -89, -217 to -255, and -263 to -279, designated IL-2 sites A, D, and E, respectively, that are required for maximal induction of IL-2 expression. One of these regions, site E, interacted with a protein (NF-IL-2E) present only in the nuclei of cells which have been stimulated. The other two sequences interacted with a protein (NF-IL-2A) that is constitutively expressed in T cells. When multiple tandem copies of either the E site or the A site were placed upstream of the gamma-fibrinogen promoter, they activated expression via this promoter in response to signals initiated at the antigen receptor but not following PMA stimulation. For this reason, we denoted them antigen receptor response elements. The uncoupling of antigen receptor and PKC requirements in these studies indicates that these signal pathways are, at least in part, distinct and integrated at the level of the gene.

Identification of a protein factor binding to the 5'-flanking region of a tRNA gene and being involved in modulation of tRNA gene transcription in vivo in Saccharomyces cerevisiae

Control mechanisms of tRNA gene transcription were studied in vivo in Saccharomyces cerevisiae. In order to be able to monitor in vivo transcription products of an individual tRNA gene, a 'tester gene' was used which is readily transcribed in vivo in yeast but does not cross-hybridize with any cellular yeast tRNA. A series of insertion mutants were constructed, modifying thereby the immediate and further distant 5'-flanking region of the 'tester tRNA gene'. Small linker molecules of different length and different sequence were inserted at positions -3 and -56 on the non-coding strand. Resulting tRNA gene variants were transformed into yeast cells and in vivo synthesized products were monitored by primer extension analysis. From the experimental data we suggest that a few essential nucleotides within the flanking region are able to determine the in vivo transcription activity of the 'tester tRNA gene'. Our results are rationalized on a biochemical level by protein binding assays: At least one protein binds to the 5'-flanking region of the 'tester tRNA gene' and different protein complexes are sequestered on active or less active tRNA gene variants.

Mutational analysis of the contribution of sequence motifs within the IgH enhancer to tissue specific transcriptional activation

We have investigated the role of sequence motifs in the immunoglobulin heavy chain (IgH) enhancer on its activity in myeloma and fibroblast cell-lines. In transient transfection assays the transcription stimulatory activity of the enhancer is decreased in myeloma cells by mutating the E motifs 1, 2 and 3, the core motifs C1, C2, C3 and the octamer motif (OC) and in fibroblasts by mutating E2, E3, and C2. Our results suggest that transcription factors binding to E1, C1, C3 and OC contribute in a positive manner to the tissue specificity of the IgH enhancer.

Tissue specific sequence motifs in the enhancer of the leukaemogenic mouse retrovirus SL3-3

The long terminal repeat (LTR) of the retrovirus SL3-3 determines its tropism for T-lymphocytes and its ability to induce T-cell lymphomas in mice. We have studied the ability of different DNA sequences located upstream of the "TATA" box in the LTR of SL3-3 to enhance transcription in T-lymphocyte cell lines and other cell lines, employing a transient assay and quantitative S1 nuclease mapping. The enhancer was found to be composed of many DNA domains which determines different activities in different cell lines. We find enhancer sequence motifs with a high T-lymphocyte specificity in the DNA repetitions of the LTR, and other enhancer motifs active in a broader range of cells in the surrounding DNA segments. The localization of sequences preferentially active in T-cells within the repeated sequences containing differences between SL3-3 and the very closely related Akv virus, which is without the T cell tropism and leukaemogenicity of SL3-3, supports the notion that the enhancer sequence motifs with T-cell preferences are primary determinants of these properties.

A yeast activity can substitute for the HeLa cell TATA box factor

Most class B (II) promoter regions from higher eukaryotes contain the TATA box and upstream and enhancer elements. Both the upstream and enhancer elements and their cognate factors have regulatory functions, whereas the TATA sequence interacts with the TATA box factor BTF1 to position RNA polymerase B and its ancillary initiation factors (STF, BTF2 and BTF3) to direct the initiation of transcription approximately 30 base pairs downstream. In many respects, class B promoter regions from the unicellular eukaryote Saccharomyces cerevisiae are similarly organized, containing upstream activating sequences that bear many similarities to enhancers. Although they are essential for initiation, the yeast TATA sequences are located at variable distances and further from the start sites (40-120 base pairs), whose locations are primarily determined by an initiator element. The basic molecular mechanisms that control initiation of transcription are known to be conserved from yeast to man: the yeast transcriptional transactivator GAL4 can activate a minimal TATA box-containing promoter in human HeLa cells, and a human inducible enhancer factor, the oestrogen receptor, can activate a similar minimal promoter in yeast. This striking evolutionary conservation prompted us to look for the presence in yeast of an activity that could possibly substitute for the human TATA box factor. We report here the existence of such an activity in yeast extracts.

The enhancer in an MHC class II gene, in vitro and in mouso

The E alpha class II gene of the major histocompatibility complex is expressed in a variety of immunocompetent cells. Part of the control of tissue-specific expression is mediated by a block of sequences found far upstream of the transcriptional startsite; this stretch is necessary for expression in the B lymphocytes of transgenic mice, but largely dispensable elsewhere. We review the evidence for the role of this region in E alpha transcription in transgenic animals, as well as data from transfections into tissue-culture cells, which indicate that this region has non-specific enhancer activity. We discuss possible models to explain how a non-specific enhancer can participate in cell-specific control.

Characterization of response elements for androgens, glucocorticoids and progestins in mouse mammary tumour virus

We have characterized steroid response elements in mouse mammary tumour virus (MMTV) by transient transfection. Four partial inverted repeats of the sequence TGTTCT function as response elements for androgen, as well as for glucocorticoid and progestins, although the relative hormone inductions mediated by each oligonucleotide were different. Mutational analysis of the left half of the palindrome showed that a perfect dyad symmetry is not required for optimum activity as a steroid response element. To investigate potential interactions between steroid receptors and transcription factors we have analysed the minimum sequence requirements for a hormone response. Interestingly, a single 15 bp steroid response element and a TATA box are sufficient for steroid inductions. When the distance between the two elements was increased by up to two turns of the helix the hormone induction initially increased and then gradually declined with no obvious periodicity.

Synergism of closely adjacent estrogen-responsive elements increases their regulatory potential

Recent gene transfer experiments have shown that an estrogen-responsive DNA element (ERE) GGTCANNNTGACC mediates the estrogen inducibility of the Xenopus laevis vitellogenin A1 and A2 genes as well as the chicken vitellogenin II gene. We report here on experiments that explain the estrogen regulation of the Xenopus vitellogenin B1 and B2 genes. In these genes, two ERE homologues, which have only low, if any, regulatory capacity on their own, act synergistically to achieve high estrogen inducibility. Furthermore we show that synergism of EREs is most efficient, when the two elements are closely adjacent and that it is lost when the synergistic elements are separated by 125 basepairs. In-vitro estrogen receptor binding experiments indicate that co-operative binding of estrogen receptors to closely adjacent EREs is not essential for synergism of ERE homologues that have no intrinsic regulatory capacity. Functional synergism of EREs is observed in the human estrogen-responsive MCF-7 cell line as well as in mouse fibroblasts (Ltk-) cotransfected with estrogen receptor expression vectors. Even expression of a truncated receptor protein lacking 178 amino acid residues of the amino-terminal end allows synergism, suggesting that the amino-terminal end preceding the DNA-binding domain of the estrogen receptor is not required.

Zeste encodes a sequence-specific transcription factor that activates the Ultrabithorax promoter in vitro

Zeste is a Drosophila regulatory gene that is required for transvection at the bithorax complex. Here we find that purified zeste protein binds to multiple sites just 5' of the initiation site of Ubx RNA. Zeste protein purified from Drosophila cells or from E. coli expressing the zeste gene activates Ubx transcription in vitro. This activation is dependent on the presence of zeste protein binding sites, as it is not observed with a Ubx promoter lacking these sites or with an Adh promoter. These results suggest that transvection involves regulatory elements that act at the level of transcriptional initiation and may be mechanistically similar to activation of transcription by enhancer elements, except that transvection occurs across paired chromosomes. These findings are consistent with the hypothesis that zeste may play a more important role in the normal regulation of Ubx and its other target genes than current genetic evidence implies.

No strict alignment is required between a transcriptional activator binding site and the "TATA box" of a yeast gene

GAL4 is a transcriptional activator of the galactose metabolism genes in the yeast Saccharomyces cerevisiae. We show that GAL4 expressed in yeast activated transcription equally well when a single GAL4 binding site was placed at any of nine positions upstream of the GAL1 (galactokinase gene) "TATA box." We chose a sufficient number of positions for the binding site to ensure that, in several of these positions, GAL4 was on the opposite side of the DNA helix with respect to the TATA box. Smaller GAL4 derivatives were similar to wild-type GAL4 in that they also activated transcription in a manner independent of the side of the DNA helix they bound with respect to the TATA box. Unlike wild-type GAL4, however, these smaller GAL4 derivatives activated transcription better when we placed a binding site progressively closer to the TATA box over a distance of 34 base pairs.

Z DNA and loop structures by immunoelectronmicroscopy of supercoiled pRW751, a plasmid containing left-handed helices

Single and multiple loops were seen when the plasmid pRW751 was allowed to react with anti-Z-DNA or with a Z-specific cross-linking agent. Loop formation was dependent upon negative supercoiling and the presence of Z-specific antibody or cross-linking agent. Restriction enzyme mapping located 18 sites at the bottoms of loops, in addition to the two (dG-dC)n inserts of pRW751. No more than 5 loops were seen in any of the measured molecules; thus, not all potential Z-sites assume the Z conformation at any particular time. Stretches of alternating purine-pyrimidine sequences occur at all 20 sites. Almost all of the Z sites could be mapped to regions located at the beginnings or ends of reading frames or at various regulatory sites. Our findings support the concept that supercoiling brings distant sequences to within 5A of one another, allowing joint participation in regulatory processes controlled by DNA-binding proteins.

Compartmentalization of MHC class II gene expression in transgenic mice

A set of transgenic mouse lines carrying Ek alpha genes with promoter region deletions was created in an attempt to compartmentalize MHC class II gene expression. Fine immunohistological analyses established that one transgenic line is essentially devoid of E complex in the thymic cortex, another displays almost no E in the thymic medulla or on peripheral macrophages, and two lines display no E on greater than 98% of B cells. We have assayed these mice for immune function: E-dependent tolerance, antigen presentation, T cell priming, and antibody response. Certain of the findings are difficult to reconcile with currently popular hypotheses, e.g., tolerance induction to E molecules in the virtual absence of E complex in the thymic medulla and efficient antibody responses to E-restricted antigens when almost all B cells are E-.

Localization of a repressive sequence contributing to B-cell specificity in the immunoglobulin heavy-chain enhancer

The immunoglobulin heavy-chain enhancer is a cis-acting element which activates transcription of nearby genes only in cells of the lymphoid lineage. To identify the minimal sequences necessary to impart cell type transcriptional specificity, we tested the activity of several deletions and internal mutations in the mu enhancer. Experiments involving measurement of both chloramphenicol acetyltransferase activity and RNA levels indicated the presence of a dominant repressor element within the mu enhancer. This repressive activity was detected in fibroblasts but not in myeloma cells. Removal or disruption of this repressor element revealed the presence of elements within the mu enhancer that activate transcription in fibroblasts. Thus, enhancer tissue specificity is in part due to the composite of both constitutive activation and cell-type-specific repressive activity. The possible biological roles of this phenomenon are discussed.

Periodic interactions of heat shock transcriptional elements

The activity of some genes is known to be a periodic function of the amount of DNA between the binding sites of its regulatory proteins. The period observed is close to 10.5 base pairs (bp), that is, one turn of the B form of the DNA helix. Such periodicity is also seen in the cooperative binding of phage lambda and lac repressors. These periodic phenomena have been attributed to a requirement for a unique rotational alignment in forming essential contacts between the bound proteins. Here we report a strong periodic dependence of the transcription of a cloned Drosophila melanogaster heat shock gene on the amount of DNA inserted between its two heat shock consensus elements. In addition, we find a similar periodicity for insertions just 3' to the proximal heat shock element. Consistent with the torsional flexibility of DNA, these periodic effects are seen for short insertions, up to approximately 80 bp, but not for much longer ones. We conclude that maximal transcription requires rotationally unique contacts between proteins bound to the two heat shock elements and also requires correct alignment of additional sites of DNA-protein binding downstream of the proximal element.

Action at a distance along a DNA

A number of ways are known by which an event at one location on a DNA molecule can affect an event at a distant location on the same molecule. Three classes of mechanisms are described for such distal actions: tracking or translocation of a protein along a DNA, the association of two proteins bound at separate sites to form a DNA loop in between, and distal interactions that are affected by the topology of the DNA. The basic characteristics of each type of mechanism are discussed in terms of the known physicochemical properties of DNA. The various modes of action at a distance are often interrelated. Examples include the formation of positively and negatively supercoiled DNA loops by tracking and the strong effects of DNA topology on looping.

Enhancer binding factors AP-4 and AP-1 act in concert to activate SV40 late transcription in vitro

The simian virus 40 (SV40) transcriptional enhancer is composed of multiple cis-acting DNA sequence motifs, each individually having a two- to fourfold effect on the efficiency of transcription. When various distinct cis-elements act in combination, however, a dramatic enhancement of transcription initiation often results. SV40-enhancer A-domain sequences were previously shown to be important for early and late transcription in vivo. Here we report the isolation of the enhancer binding factor AP-4, which recognizes a motif in this domain. Purified AP-4 activates SV40 late transcription in vitro, and this stimulation is augmented by the addition of transcription factor AP-1 which binds to adjacent sequences in the A-domain, suggesting coordinate action of the two factors for transcriptional enhancement. AP-1 also represses late transcription from a major in vitro start site which is poorly used in vivo, indicating that AP-1 can act as both a positive and negative regulator of SV40 late transcription. Thus by manipulating the levels of different trans-acting factors in vitro, we can recreate the pattern of SV40 late initiation observed during the viral lytic cycle in vivo.

Functional anatomy of the simian virus 40 late promoter

We have examined the control sequences for the late promoter function of simian virus 40 (SV40) in COS-1 cells which produce SV40 T antigen constitutively. Plasmids were constructed by cloning mutant late promoter segments upstream from sequences coding for the bacterial chloramphenicol acetyltransferase (CAT) gene, and were converted to "double-origin" type by inserting functional replication origin segments downstream from the CAT gene for replicative competence when necessary. The late promoter activity was determined by transient expression assay of the CAT mRNA and enzyme activity levels following DNA-mediated gene transfer into COS-1 cells. We find that the minimal replication origin and the 21-bp repeat containing T antigen and transcription factor Sp1 binding sites, respectively, are dispensable for late promoter function provided that one copy of the 72-bp repeat enhancer is present. We have mapped within the 72-bp repeat the major late promoter component in a 68-bp fragment (located between nucleotides 205 and 272), and found an overlapping 55-bp fragment (located between nucleotides 179 and 234) to have about one-fifth of the late promoter activity. Both the 68- and 55-bp fragments lack some of the core sequence elements required of the 72-bp repeat for transcriptional enhancer activity, and lack the ability to enhance the activity of the SV40 early promoter. The results suggest that the organization of functional units of the 72-bp repeat required for transcriptional enhancement of the early promoter is different from that required for late promoter function. The 21-bp repeat was found to have some late promoter activity located within the origin-distal copy in the absence of the 72-bp repeat. In association with the 21-bp repeat, the otherwise dispensable origin-proximal 22-bp of the 72-bp repeat containing activator protein AP-1 binding site augmented late promoter activity by three- to fourfold.

Characterization of antigen receptor response elements within the interleukin-2 enhancer

T-cell activation and induction of interleukin-2 (IL-2) expression in human T lymphocytes require both interaction of foreign antigen with the T-cell antigen receptor and protein kinase C (PKC) stimulation. Agents such as phorbol 12-myristate 13-acetate (PMA) that stimulate PKC augment the effects of antigen but are not sufficient for IL-2 activation. By analysis of deletion mutants, we identified three DNA sequences extending from -73 to -89, -217 to -255, and -263 to -279, designated IL-2 sites A, D, and E, respectively, that are required for maximal induction of IL-2 expression. One of these regions, site E, interacted with a protein (NF-IL-2E) present only in the nuclei of cells which have been stimulated. The other two sequences interacted with a protein (NF-IL-2A) that is constitutively expressed in T cells. When multiple tandem copies of either the E site or the A site were placed upstream of the gamma-fibrinogen promoter, they activated expression via this promoter in response to signals initiated at the antigen receptor but not following PMA stimulation. For this reason, we denoted them antigen receptor response elements. The uncoupling of antigen receptor and PKC requirements in these studies indicates that these signal pathways are, at least in part, distinct and integrated at the level of the gene.

Replication from a proximal simian virus 40 origin is severely inhibited by multiple reiterations of the 72-base-pair repeat enhancer sequence

In a previous study in our laboratory, the effect of the reiteration frequency of the simian virus 40 (SV40) 72-base-pair (bp) repeat enhancer on transcription from the proximal SV40 early promoter was investigated (R. Kumar, T. A. Firak, C. T. Schroll, and K. N. Subramanian, Proc. Natl. Acad. Sci. USA 83:3199-3203, 1986). Increasing the enhancer copy number to four increased transcription proportionately; further increments in enhancer copy number reversed this effect, resulting in a decrease in the transcriptional activation. In the present study, the effect of enhancer reiteration on the replication efficiency of plasmids containing the SV40 origin of replication was investigated in transient replication assays in vivo in COS-1 monkey kidney cells producing the SV40 large tumor antigen required for replication. A plasmid containing the SV40 core origin and three copies of the replication-activating, G+C-rich 21-bp repeat promoter element replicated efficiently. Plasmids containing multiple copies of the 72-bp repeat enhancer cloned in head-to-tail linkage adjacent to the 21-bp repeat and the core origin replicated less efficiently; the decrease in replication efficiency could be correlated with the number of copies of the 72-bp repeat; replication was severely curtailed when 10 or more copies of the 72-bp repeat were present. Replication was not significantly inhibited by an increase in the number of copies of the 21-bp repeat to 15 or by the presence of three copies of a 360-bp pBR322 sequence in the immediate vicinity. Multiple copies of the 72-bp enhancer in cis were unable to inhibit replication from a second SV40 origin of replication situated 2 kilobase pairs away from the enhancer reiteration. Replication of four different test plasmids was not inhibited in trans by cotransfection of an excess of a potential competitor plasmid containing a 24-copy reiteration of the 72-bp enhancer. These results indicate that multiple tandem reiterations of the 72-bp enhancer inhibit replication only when they are present in cis adjacent to the origin of replication. Possible explanations for this inhibitory effect, such as an unfavorable local chromatin structure induced by the multimeric enhancer region or reduced or improper communications between factors bound to the multimeric region and the adjacent replication origin, are discussed.

Constraints on spacing between transcription factor binding sites in a simple adenovirus promoter

The adenovirus 2 E1B transcription unit has an extremely simple promoter consisting of a TATA box and a closely situated GC box. The interaction between the TATA box and the GC box was analyzed using insertion mutations which expand the distance between the two elements. We observed that the E1B promoter has an unusually rigid architecture. When the GC box, which is a binding site for transcription factor Sp1, was separated further from the TATA box than in the wild-type promoter, in vivo transcription quickly diminished to a level comparable to the elimination of the Sp1 site. Yet all the insertion mutants bound Sp1 factor in vitro with an affinity approximately equal to that of the wild-type promoter. From these results, we argue that Sp1 binding alone is not sufficient to stimulate transcription. The increased distance might disrupt direct contacts between Sp1 and transcription factors bound at the TATA box, contacts required for transcription stimulation by Sp1. The insertion mutations do not interfere with the transcription activation process mediated by the adenovirus large E1A protein or the pseudorabies virus immediate early protein.

Differential protein binding in lymphocytes to a sequence in the enhancer of the mouse retrovirus SL3-3

An electrophoretic mobility shift assay was used to characterize interactions of nuclear proteins with a DNA segment in the enhancer element of the leukemogenic murine retrovirus SL3-3. Mutation of a DNA sequence of the 5'-TGTGG-3' type decreased transcription in vivo specifically in T-lymphocyte cell lines. Extracts of nuclei from different T-lymphocyte cell lines or cells from lymphoid organs resulted in much higher amounts of complexes in vitro with this DNA sequence than did extracts from other cell lines or organs tested. Differences were also found in the sets of complexes obtained with extracts from the different types of cells. The DNA sequence specificities of the different SL3-3 enhancer factor 1 (SEF1) protein complexes were found to be distinct from those of several other previously identified DNA motifs of the TGTGG type because of differences in several nucleotides critical for binding and because these other DNA motifs could not compete with the identified DNA sequence for binding of SEF1. Limited treatment with several different proteases cleaved the SEF1 proteins such that their DNA-binding domain(s) remained and created complexes with decreased and nondistinguishable electrophoretic mobility shifts and with new properties. These results indicate that the SEF1 proteins have a structure with a flexible and relatively vulnerable hinge region linking a DNA-binding domain(s) to a more variable domain(s) with other functions. We suggest that the binding of SEF1 is an essential factor for the T-cell tropism of SL3-3 and the ability of this virus to cause T-cell lymphomas.

Point mutation in the polyomavirus enhancer alters local DNA conformation

A point mutation in the enhancer of polyomavirus host range mutant, PyEC F441, permits productive infection of the murine embryonal carcinoma cell line, F9. This mutation at nucleotide position 5258 introduces a local conformational change in naked viral DNA. The effect of all four possible nucleotide sequences at position 5258 on local DNA conformation was analyzed by gel electrophoresis of fragments produced by ligation of synthetic oligonucleotides having these sequences. The results indicated that both the wild-type and the F441 sequences introduced local structural polymorphism that can lead to DNA bending. The wild-type sequence had a greater effect on DNA curvature than the F441 sequence. The two other sequences at nucleotide 5258 did not appear to introduce detectable amounts of DNA curvature.

The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer

Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. We have examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer. This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.

Localization of a repressive sequence contributing to B-cell specificity in the immunoglobulin heavy-chain enhancer

The immunoglobulin heavy-chain enhancer is a cis-acting element which activates transcription of nearby genes only in cells of the lymphoid lineage. To identify the minimal sequences necessary to impart cell type transcriptional specificity, we tested the activity of several deletions and internal mutations in the mu enhancer. Experiments involving measurement of both chloramphenicol acetyltransferase activity and RNA levels indicated the presence of a dominant repressor element within the mu enhancer. This repressive activity was detected in fibroblasts but not in myeloma cells. Removal or disruption of this repressor element revealed the presence of elements within the mu enhancer that activate transcription in fibroblasts. Thus, enhancer tissue specificity is in part due to the composite of both constitutive activation and cell-type-specific repressive activity. The possible biological roles of this phenomenon are discussed.

The yeast UASG is a transcriptional enhancer in human HeLa cells in the presence of the GAL4 trans-activator

The yeast trans-activator protein GAL4, when expressed in HeLa cells, stimulates transcription from several class B (II) eukaryotic promoters containing GAL4 binding sites either as the full UASG or as synthetic 17-mers. The characteristics of this activation are indistinguishable from those of the SV40 enhancer. Transcription was similarly stimulated from either complex promoter regions containing multiple upstream elements or from a simple promoter region composed of only a TATA box. Addition of a 17-mer GAL4 binding site to the SV40 enhancer resulted in a synergistic enhancement of transcription in the presence of GAL4. Furthermore, chimeras of the human estrogen receptor DNA binding domain and either GAL4 or GCN4 activating "acidic" regions can activate a promoter region controlled by an estrogen-responsive enhancer. Together, these data indicate that the molecular mechanisms responsible for transcriptional enhancement have been conserved from yeast to man.

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.

A promoter of the rat insulin-like growth factor II gene consists of minimal control elements

We have characterized the cis-control signals in one of the two promoters of the developmentally regulated rat insulin-like growth factor II gene (rIGF-II) by a combination of in-vivo transient expression, in-vitro transcription, footprinting, gel band-shifting and methylation-interference experiments, using a series of deletion mutant templates. Our results indicate that this simple (minimal) promoter (P2) consists of no more than 128 base-pairs, which include an ATA box and four proximal upstream GC boxes binding the general transcription factor Sp1. Three of the latter sites deviate from the known Sp1 consensus recognition sequence. The two types of cis-acting regulatory signals (GC/ATA motif) of the P2 promoter are inter-dependent and sufficient for transcription. A model for the operation of this type of minimal promoter is discussed. S1 nuclease-hypersensitive sites, localized by in-vitro mapping to the region of the P2 Sp1-binding sites, are also present in vivo and correlate with the transcriptional state of chromatin in the rIGF-II locus. We show that recognition sites for Sp1 binding are a subset of sequences that exhibit hypersensitivity to S1.

Cooperative DNA binding of the yeast transcriptional activator GAL4

The yeast transcriptional regulatory protein GAL4 binds to four sites in the GAL upstream activating sequence and stimulates transcription of the adjacent GAL1 and GAL10 genes. We show here that binding to at least two of these sites is cooperative in vivo. We also measure stimulation of transcription by pairs of GAL4 binding sites and find that the activities of low-affinity binding sites combine synergistically, whereas the activities of high-affinity binding sites combine only additively. We suggest that the synergistic transcriptional stimulatory activity of the naturally occurring GAL4 binding sites is solely a manifestation of cooperative binding of GAL4 protein to DNA and that the activity of a GAL upstream activating sequence is roughly proportional to the number of GAL4 molecules bound.

Transcription elements and factors of RNA polymerase B promoters of higher eukaryotes

The promoter for eukaryotic genes transcribed by RNA polymerase B can be divided into the TATA box (located at -30) and startsite (+1), the upstream element (situated between -40 and about -110), and the enhancer (no fixed position relative to the startsite). Trans-acting factors, which bind to these elements, have been identified and at least partially purified. The role of the TATA box is to bind factors which focus the transcription machinery to initiate at the startsite. The upstream element and the enhancer somehow modulate this interaction, possibly through direct protein-protein interactions. Another class of transcription factors, typified by viral proteins such as the adenovirus EIA products, do not appear to require binding to a particular DNA sequence to regulate transcription. The latest findings in these various subjects are discussed.

The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer

Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. We have examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer. This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.

Putative elements in the vicinity of viral transcription initiation sites

1. Animal virus sequences present in GenBank have been aligned according to their mRNA transcription initiation sites and common elements have been searched. 2. Such elements can conceivably serve as recognition sequences to the RNA polymerase and/or other DNA binding proteins involved in the regulation of viral transcription. 3. The distributions of the 64 triplets and 256 quartets with respect to these initiation sites have been examined. 4. In addition to subsets of the TATAAAT sequence, some G-C containing oligomers are frequently present. 5. Sequences of the latter type have been shown to bind the Sp1 protein. 6. The biological data is reviewed and the DNA structural implications are discussed.

Prediction of 'hot spots' in SV40 enhancer and relation with experimental data

A theoretical method for prediction of the points in the sequence which are relevant for its biological function, the so-called 'hot spots', is presented. This method is based on significant correlation between the spectrum of numerical presentation of any genetic sequence and its biological function. One number corresponds to the particular nucleotide, thus forming a numerical sequence. The 'hot spot' prediction has been tested on the SV40 enhancer as a model system. The SV40 enhancer was chosen because of existing detailed data about activities of systematically obtained mutants. These results have been compared with results obtained theoretically.