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Results for “TATA Box”

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At least 19 recordsLinked to original sources

PubMed1989

Cloning and structure of a yeast gene encoding a general transcription initiation factor TFIID that binds to the TATA box.

The TATA sequence-binding factor TFIID plays a central role both in promoter activation by RNA polymerase II and other common initiation factors, and in promoter regulation by gene-specific factors. The sequence of yeast TFIID, which seems to be encoded by a single gene, contains interesting structural motifs that are possibly involved in these functions, and is similar to sequences of bacterial sigma factors.

Amino Acid Sequence↗

PubMed1992

Functional binding of the "TATA" box binding component of transcription factor TFIID to the -30 region of TATA-less promoters.

Many viral and cellular promoters transcribed in higher eukaryotes by RNA polymerase II lack obvious A+T-rich sequences, called "TATA" boxes, that bind the transcription factor TFIID. One such TATA-less promoter, the simian virus 40 major late promoter, contains a genetically important sequence element 30 base pairs upstream of its transcription initiation site that has no obvious sequence similarity to a TATA box. We show here that the cloned human TATA box-binding protein, hTFIID tau, functionally binds to this upstream sequence element, although with an affinity one-sixth of that to which it binds the TATA box of the adenovirus type 2 major late promoter. Analysis of point mutations in the -30 element of the simian virus 40 major late promoter shows that the affinity of binding correlates with the efficiency of transcription from this promoter. Furthermore, this element has genetic properties similar to those of a TATA box. (i) It directs RNA polymerase II to initiate transcription approximately 30 base pairs downstream of its location, and (ii) inactivation of this element results in increased heterogeneity in the sites of transcription initiation. All of five other TATA-less promoters tested were found to contain a sequence approximately 30 base pairs upstream of their major transcription initiation sites to which hTFIID tau binds. We conclude that many, if not all, TATA-less promoters differ from TATA box-containing promoters simply in the affinity of their -30 regions for binding of TFIID, with functional binding of TFIID supported in part by other nearby sequence elements of the promoter.

Base Sequence↗

PubMed1990

The progesterone receptor can regulate transcription in the absence of a functional TATA box element.

We have investigated the importance of the TATA box element in the induction of transcription by the progesterone receptor. Transcription was analyzed from promoters containing a steroid response element upstream of a wild-type or mutated TATA box. Mutation of the TATA box resulted in a loss of correctly initiated transcripts and abolished binding of TATA factor to the TATA box in vitro but did not inhibit transcriptional activation by the progesterone receptor. Thus we conclude that the receptor is able to stimulate the rate of transcription in the absence of a functional TATA box.

Animals↗

PubMed1989

Sp1 activates transcription without enhancing DNA-binding activity of the TATA box factor.

We have studied the interactions of the Sp1 and IID transcription factors with a simple RNA polymerase II promoter. The adenovirus E1B core promoter consists essentially of a GC box and a TATA box, binding sites for the Sp1 and IID transcription factors, respectively. The E1B promoter is accurately transcribed in vitro using a mammalian transcription system. Sp1 activates E1B transcription in vitro in reactions using IID factor isolated from either human or yeast cells. In DNase I footprinting studies, Sp1 bound rapidly to its recognition sequence even at 0 degrees C (t1/2 less than 1 min). In contrast, yeast IID bound more slowly (t1/2 approximately 6 min at 25 degrees C) and required thermal energy for stable binding to the TATA box sequence. Dissociation rates were measured by the addition of specific oligonucleotide competitors to preformed DNA-protein complexes. Sp1 dissociates rapidly (t1/2 less than 1 min) at 25 degrees C, while yeast IID dissociates with an estimated t1/2 of 1 h at 25 degrees C. Sp1 and yeast IID bound to the E1B promoter simultaneously but independently. The rates of binding and dissociation of these factors were not significantly affected by the presence of the other factor. Bound Sp1 factor did not alter or enhance the yeast IID footprint. Oligonucleotide challenge of in vitro transcription reactions indicated that Sp1 also did not enhance the binding of the human IID factor to the E1B promoter. Thus the Sp1 factor activates transcription of the E1B gene by a mechanism that does not enhance the DNA-binding activity of the IID factor. Sp1 factor activates E1B transcription by 5- to 10-fold in vitro. Under these in vitro transcription conditions, transcripts due to reinitiation from an individual promoter complex contribute only a small portion of the total yield of E1B transcripts. Thus Sp1 cannot activate transcription by increasing the rate of initiation events per complex. Instead it appears that Sp1 acts by increasing the number of productive transcription complexes formed in vitro.

Adenoviridae↗

PubMed1992

Identification of three mammalian proteins that bind to the yeast TATA box protein TFIID.

The TATA box binding transcription factor TFIID of S. cerevisiae was used as a ligand for affinity chromatography. Polypeptides that bind specifically to yeast TFIID (TFIID-associated proteins, DAPs) were purified from human HeLa (heDAPs) and calf thymus (ctDAPs) whole cell extracts. Both heDAP and ctDAP fractions altered the binding of TFIID to the TATA element, and substituted for the TFIIA transcription activity in a reconstituted in vitro system. The heDAP fraction also behaved like TFIIA in its ability to form a promoter-TFIID-TFIIA complex and to recruit TFIIB to such a complex. The interaction of DAPs with TFIID can confer heat-resistance (47 degrees C) on recombinant yeast or human TFIID. SDS-PAGE analysis revealed that three polypeptides from HeLa extracts specifically bound to yTFIID columns (heDAP35, heDAP21, and heDAP12). These data suggest that a multi-subunit transcription factor with the properties of TFIIA can bind to TFIID in the absence of DNA.

Base Sequence↗

PubMed1992

Substitution of a TATA box from a herpes simplex virus late gene in the viral thymidine kinase promoter alters ICP4 inducibility but not temporal expression.

The role of cis-acting promoter elements associated with herpes simplex virus type 1 (HSV-1) early and late genes was evaluated during productive infection with regard to activation of gene expression by the HSV-1 transactivator ICP4 and control of temporal regulation. A set of recombinant viruses was constructed such that expression of an HSV-1 early gene, thymidine kinase (tk), was placed under the control of either the tk TATA box or the TATA box from the late gene, glycoprotein C (gC), in the presence or absence of the upstream Sp1 and CCAAT sites normally found in the tk promoter. The presence of Sp1 sites in the promoter or replacement of the tk TATA box with the gC TATA box resulted in a decreased activation of tk mRNA expression by ICP4. Substitution of the A + T-rich region from the gC TATA box in the context of the remainder of the surrounding tk sequences resulted in a promoter that bound recombinant TATA-binding protein (TBP) better at lower concentrations than the wild-type tk promoter did. These results indicate that tk promoters that are better able to utilize TBP are less responsive to ICP4 activation and suggest that activation by ICP4 involves the general transcription factors that interact with TBP or TBP itself. Additionally, all of the viruses expressed tk at early times postinfection, indicating that cis-acting promoter elements that control the level of expression of HSV-1 early and late genes do not determine temporal regulation.

Animals↗

PubMed1992

Regulation of delayed-early gene transcription by dual TATA boxes.

The 39K Autographa californica nuclear polyhedrosis virus (AcMNPV) gene is highly expressed throughout the virus life cycle and is controlled by tandem promoters that exhibit features of early and late baculovirus promoters. Late transcripts initiate at a conserved TAAG motif, while early transcripts are heterogeneous and initiate near a conserved CAGT motif. To define the nucleotide sequences that regulate early transcription of the 39K gene, a series of mutations was generated by substitution of 10-bp stretches in the 39K promoter with a BglII linker. The effects of these mutations on transcription from the early promoter were determined by transient expression and primer extension assays in the presence of the viral trans-activator IE1 gene. Mutations in the region from -15 to -44 revealed that early 39K transcription was controlled by dual TATA boxes. These TATA boxes are separated by 10 bp, which partially accounts for the heterogeneity in early 39K transcripts. Transcripts initiating at the CAGT motif (proximal transcripts) were abolished by deletion of the proximal TATA box located at -29 relative to CAGT. Proximal transcripts were not affected by alterations in the distal TATA motif located at -39 relative to the CAGT. Similarly, transcripts initiating upstream of CAGT (distal transcripts) were eliminated by mutations in the distal TATA but were unaffected by substitutions in the proximal TATA box. Proximal transcripts were not detected with a plasmid containing mutations in the CAGT motif, although the distal transcripts were unaffected by CAGT mutations. When the sequences surrounding the initiation site for the distal transcripts were altered, the start site was shifted one nucleotide, but transcription was not quantitatively affected. These results suggest that early 39K transcription is controlled by two distinct TATA elements, one that is dependent on an initiator and one in which the site of initiation is determined by the TATA element alone. Mutations in an upstream region from -45 to -68 relative to the CAGT motif had a quantitative effect but did not alter the heterogeneous pattern of early transcripts, suggesting these sequences function as an upstream regulatory region. Analysis of late transcription indicated that the TAAG element was essential, while transcription was unaffected by other mutations.

Animals↗

PubMed1989

Yeast TATA-box transcription factor gene.

The first step in the transcription of most protein-encoding genes in eukaryotes is the binding of a transcription factor to the TATA-box promoter element. This TATA-box transcription factor was purified from extracts of the yeast Saccharomyces cerevisiae by using reconstitution of in vitro transcription reactions as an assay. The activity copurified with a protein whose sodium dodecyl sulfate/polyacrylamide gel mobility is 25 kDa. The sequence of the amino-terminal 21 residues of this protein was determined by sequential Edman degradation. A yeast genomic library was screened with mixed oligonucleotides encoding six residues of the protein sequence. The yeast TATA-box factor gene was cloned, and DNA sequencing revealed a 720-base-pair open reading frame encoding a 27,016-Da protein. The identity of the clone was confirmed by expressing the gene in Escherichia coli and detecting TATA-box factor DNA binding and transcriptional activities in extracts of the recombinant E. coli. The TATA-box factor gene was mapped to chromosome five of S. cerevisiae. RNA blot hybridization and nuclease S1 analysis indicated that the major TATA-box factor mRNA is 1.3 kilobases, including an unusually long 5' untranslated region of 188 +/- 5 nucleotides. Homology searches showed a region of distant similarity to the calcium-binding structures of calpains, a structure that has a conformation similar to the helix-turn-helix motif of DNA binding proteins.

Amino Acid Sequence↗

PubMed1987

Effects of mutations in the TATA box region of the Agrobacterium T-cyt gene on its transcription in plant tissues.

We have generated mutations in the promoter region of the octopine type cytokinin gene of Agrobacterium tumefaciens, and studied their effects on mRNA formation in different plant species. The promoter region of this gene contains several putative TATA boxes. Phenotypic expression and Northern blot hybridization showed that TATA boxes are essential for expression, but that one TATA box leads to wild-type transcript levels. Analysis of the 5' ends of T-cyt transcripts by primer extension using RNA from T-cyt gene transformed tobacco shoots revealed two major cap site clusters and one minor cap site. TATA box consensus sequences can be found approximately 30 bp upstream from each cap site cluster. Deletion of a TATA box results in loss of the corresponding cap sites. An insertion of 7 bp between the right TATA box and corresponding cap sites results in a shift of the position of the cap sites, so that the original distance of TATA box to cap sites is conserved as much as possible.

Arginine↗

PubMed1989

Nuclear factor ETF specifically stimulates transcription from promoters without a TATA box.

Transcription factor ETF stimulates the expression of the epidermal growth factor receptor (EGFR) gene which does not have a TATA box in the promoter region. Here, we show that ETF recognizes various GC-rich sequences including stretches of deoxycytidine or deoxyguanosine residues and GC boxes with similar affinities. ETF also binds to TATA boxes but with a lower affinity. ETF stimulated in vitro transcription from several promoters without TATA boxes but had little or no effect on TATA box-containing promoters even though they had strong ETF-binding sites. These inactive ETF-binding sites became functional when placed upstream of the EGFR promoter whose own ETF-binding sites were removed. Furthermore, when a TATA box was introduced into the EGFR promoter, the responsiveness to ETF was abolished. These results indicate that ETF is a specific transcription factor for promoters which do not contain TATA elements.

Base Sequence↗

PubMed1992

Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway.

The eukaryotic transcription factor TFIID recognizes and binds a promoter sequence element called the TATA box. We have analyzed the interaction of yeast TFIID with the consensus TATA box sequence of the adenovirus major late promoter. To facilitate this detailed characterization, we developed a method for obtaining quantitative information from a gel retardation (bandshift) assay, allowing measurement of the rate and extent of TFIID-TATA box complex formation. Using this assay and DNase I protection assays, we determined that the association rate constant for TFIID binding to the major late promoter was too low to be consistent with a simple diffusion-limited association, suggesting that the binding proceeds by a multi-step pathway. Furthermore, we found that the slow rate of TFIID binding reported by other research groups was not the consequence of a rate-limiting conformational change, as has been previously suggested. Instead, we observed that the formation of a stable TFIID-TATA box complex was relatively rapid (complete in less than 1 min) at saturating concentrations of TFIID. We have proposed a two-step pathway consistent with the observed kinetics and have considered the possible contributions of each step to the overall rate of TFIID binding. This study lays the groundwork for a systematic characterization of the interaction of TFIID with additional TATA box sequences, including an experimental test of the possibility that different steps in the binding reaction are rate-limiting for different promoters.

DNA Fingerprinting↗

PubMed1990

Functional dissection of a mouse ribosomal protein promoter: significance of the polypyrimidine initiator and an element in the TATA-box region.

All of the mammalian ribosomal protein (rp) genes examined to date initiate transcription with high precision despite the fact that they do not contain a well-defined TATA box. The initiation sites are situated within polypyrimidine tracts that are flanked by both upstream and intragenic promoter elements. In the TATA-box region of each rp promoter, there is a functionally critical element with nuclear factor binding specificity that is distinct from that of a conventional TATA box. To understand how the various elements contribute to rp promoter function, we have used site-specific mutagenesis-transfection protocols and factor binding analyses to evaluate the significance of the polypyrimidine initiator and the TATA-box counterpart for efficient and accurate transcription of the rpS16 gene. Our results indicate (i) that the polypyrimidine initiator sequence critically defines the position of the transcriptional start site, whereas a much less specific sequence is sufficient to satisfy the efficiency requirement; (ii) that an uninterrupted stretch of pyrimidines in the initiator region is not necessary for efficient transcription of rpS16 gene; and (iii) that the TATA-box counterpart or even a substituted conventional TATA box primarily influences promoter efficiency. The great diversity of promoter design, which is becoming evident as more RNA polymerase II promoters are being carefully dissected, suggests that the requirements for building a functional initiation complex may be much more flexible than was previously appreciated.

Animals↗

PubMed1991

Regulation of herpes simplex virus true late gene expression: sequences downstream from the US11 TATA box inhibit expression from an unreplicated template.

The true late genes of herpes simplex virus type 1 (HSV-1) are expressed only after the onset of viral DNA replication. Previous studies demonstrated that late promoters lack elements upstream of the TATA box and suggested that only a subset of TATA elements can function in the context of true late promoters. We determined which structural features of true late promoters are responsible for the stringent requirement for viral DNA replication by inserting a series of simple model constructs into the HSV-1 genome in place of one of the two promoters of the UL24 gene. An oligonucleotide consisting of 19 nucleotides spanning the TATA box of the HSV-1 true late US11 gene drove barely detectable levels of expression; by contrast, the corresponding regions of the Adenovirus type 2 major late promoter and the HSV-1 true late glycoprotein C promoter were much more active. Transcripts driven from all of these minimal TATA box promoters accumulated without viral DNA replication. The activity of the US11 TATA box was stimulated by adding upstream Sp1-binding sites or placing the US11 or rabbit beta-globin cap/leader region (-11 to +39) downstream. The Sp1-TATA and TATA-beta-globin cap/leader constructs remained replication independent, while the TATA-US11 cap/leader promoter displayed true late regulation. These results demonstrate that sequences located within the US11 cap/leader region impose a strict requirement for viral DNA replication on a minimal TATA box promoter.

Adenoviruses, Human↗

PubMed1985

Conformation, dynamics, and structural transitions of the TATA box region of self-complementary d[(C-G)n-T-A-T-A-(C-G)n] duplexes in solution.

Structural and kinetic features of the TATA box located in the center of the alternating self-complementary d(C-G-C-G-T-A-T-A-C-G-C-G) duplex (TATA 12-mer) and d(C-G-C-G-C-G-T-A-T-A-C-G-C-G-C-G) duplex (TATA 16-mer) have been probed by high-resolution proton and phosphorus NMR spectroscopy in aqueous solution. The imino exchangeable Watson-Crick protons and the nonexchangeable base protons in the TATA box of the TATA 12-mer and TATA 16-mer duplexes have been assigned from intra and inter base pair nuclear Overhauser effect (NOE) measurements. Imino proton line-width and hydrogen exchange saturation recovery measurements demonstrate that the dA X dT base pairs in the TATA box located in the center of the TATA 12-mer and TATA 16-mer duplexes are kinetically more labile than flanking dG X dC base pairs. The proton and phosphorus NMR parameters of the TATA 12-mer monitor a cooperative premelting transition in the TATA box prior to the onset of the melting transition to unstacked strands. Phosphorus NMR studies have been unable to detect any indication of a right-handed B DNA to a left-handed Z DNA transition for the TATA 12-mer duplex in saturated NaCl solution. By contrast, we do detect the onset of the B to Z transition for the TATA 16-mer in saturated NaCl solution. Proton and phosphorus NMR studies demonstrate formation of a loop conformation with chain reversal at the TATA segment for the TATA 12-mer and TATA 16-mer duplexes on lowering the DNA and counterion concentration. The imino protons (10-11 ppm) and phosphorus resonances (3.5-4.0 ppm; 4.5-5.0 ppm) of the loop segment fall in spectral windows well resolved from the corresponding markers in fully paired segments so tha it should be possible to identify loops in longer DNA helixes. The equilibrium between the loop and fully paired duplex conformations of the TATA 12-mer and TATA 16-mer is shifted toward the latter on addition of moderate salt.

Base Sequence↗

PubMed1988

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.

Base Sequence↗

PubMed1992

Parvovirus H-1 P38 promoter requires the trans-activation region (tar), an SP1 site, and a TATA box for full activity.

In the parvovirus H-1 P38 promoter, there are sequences identified as a TATA box, an SP1 site, and a trans-activation responsive element (tar). It was previously shown that the parvovirus H-1 nonstructural protein NS1 positively regulates the expression of the P38 promoter for the viral capsid protein gene via the tar. To characterize the tar element further, a series of single-point mutations of the tar was constructed and the mutants were compared to wild-type for the trans-activation of the P38 promoter using a cat reporter gene. Most of the tar mutations had a negative effect on the P38 promoter and some of them reduced activity as much as 70%. However, when several mutants with multiple-point mutations in the tar were tested, no significant additive effect was observed. We examined the function of the SP1 site in the trans-activation of the P38 promoter by replacing the wild-type SP1 sequence with synthetic DNA fragments, OSP1 or 2SP1, containing no SP1 or two SP1 sites respectively, in a P38 construct with a cat reporter gene. The results indicate that P38 expression varies in proportion to the number of SP1 sites, suggesting a role for the SP1 site during trans-activation by NS1. The role of the TATA box on the P38 promoter was also examined by mutagenizing TATA to CACG. The activity of this promoter was reduced to 43%. When a construct mutated at both the SP1 and TATA box sites was tested for its activity, about 22% of the wild-type activity remained, implying that this remaining activity was contributed largely by the tar element. A model is proposed for how the tar element activates the wild-type and SP1-TATA minus promoters in the presence of NS1.

Base Sequence↗

PubMed1985

Functional analysis of a beta-globin gene containing a TATA box mutation from a Kurdish Jew with beta thalassemia.

We recently reported a TATA box mutation (ATAAAA to ATACAA) in a cloned beta-globin gene from a Kurdish Jew with homozygous beta thalassemia (Poncz, M., Ballantine, M., Solowiejczyk, D., Barak, I., Schwartz, E., and Surrey, S. (1982) J. Biol. Chem. 257, 5994-5996). We have now introduced this gene into HeLa cells after CaPO4 precipitation of the DNA and studied expression by analyzing globin-gene transcripts with a novel S1 nuclease mapping assay. Quantitative and qualitative comparison with the normal beta-globin gene revealed a promoter-down phenotype in the TATA box mutant, with normal RNA processing, and a normal start site for initiation of the primary transcript. Decreased transcriptional efficiency was confirmed directly by analysis of run-off transcripts using assays in vitro. The patient's phenotype of beta thalassemia major is probably the result of two different mutations since haplotype analysis of the beta-like globin gene clusters in genomic DNA from this patient shows heterozygosity for the Mediterranean-type haplotypes I and VII, with the TATA box mutation on a haplotype I chromosomal background.

Base Sequence↗

PubMed1988

A specific 15-bp TATA box promoter element is required for expression of a herpes simplex virus type 1 late gene.

The herpes simplex virus type 1 (HSV-1) glycoprotein C (gC) gene is a true late or gamma 2 gene in that its expression shows a strict requirement for viral DNA replication. Elements required for regulated expression of this gene were previously shown to consist of the gC TATA box, transcription start site and a large portion of the leader sequence of the gC gene. In this paper we show that transcription of the gC gene requires a 15-bp sequence, GGGTATAAATTCCGG, which contains the gC TATA box. This sequence contains specific promoter elements because replacement of this sequence with either the TATA box of the HSV-1 early thymidine kinase (tk) gene or two random TATA-like elements results in a transcriptionally inactive gC gene. In addition, we show that temporal expression of HSV beta and gamma genes at early and late times during infection are controlled by separate and distinct regulatory elements; regulatory signals distal to the TATA box are needed for early expression, whereas a gC-like TATA box is needed for late expression. These signals were identified by construction of a chimeric HSV gene that contained the distal control signals of the beta tk gene fused upstream of the TATA sequence of the gamma 2 gC gene. When RNA was isolated at various times postinfection from cells infected with a virus whose genome contained this chimeric tk-gC gene, synthesis of gC mRNA showed both early and late kinetics.

Base Sequence↗