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At least 181 records · Page 10Linked to original sources
PubMed1985

Characterization of a surrogate TATA box promoter that regulates in vitro transcription of the simian virus 40 major late gene.

The presence of a surrogate TATA box sequence located ca. 30 nucleotides upstream of the major late RNA start site at nucleotide position (np) 325 (Brady et al., Cell 31:625-633, 1982) has been confirmed, and its structural specificity has been determined by the generation of additional base substitution mutations at the KpnI restriction site (np 294) in cloned simian virus 40 DNA. Two mutants generated new RNA initiation sites upstream of the np 325 start site and continued to utilize the authentic start site, but with decreased efficiency. The replacement of either one or both cytosines by thymines at np 298 and np 299 specifically enhanced in vitro transcription from the np 325 start site by 430 and 800%, respectively. This enhancement was due to conversion of the simian virus 40 late promoter present in the wild-type virus to a sequence that is similar to the TATA box present in the simian virus 40 early promoter.

Base Sequence↗
PubMed1989

NF-kappa B-mediated activation of the human immunodeficiency virus enhancer: site of transcriptional initiation is independent of the TATA box.

The activation of the human immunodeficiency virus (HIV) enhancer in T cells can occur through multiple independent pathways. This enhancer is stimulated by NF-kappa B or through alternative mechanisms, including E1A transactivation, which is dependent on the TATA box. In this report, the role of the TATA box in activation by NF-kappa B is examined. E1A stimulation of the HIV enhancer requires the presence of the TATA sequence in the sense orientation. Analysis of mutant HIV enhancer plasmids shows that basal mRNA levels are reduced when the TATA sequence is altered but that inducibility of NF-kappa B and the site of transcriptional initiation are unchanged. These data suggest that transcriptional initiation in this class II promoter is determined by an initiator factor which does not require binding to the TATA sequence. Because kappa B is found in a variety of viruses, this mechanism may be relevant to the activation of other viral enhancers.

Adenovirus Early Proteins↗
PubMed1991

TFIID binds in the minor groove of the TATA box.

We have analyzed the interaction of the general RNA polymerase II transcription factor TFIID with its DNA-binding site, the TATA box (consensus sequence TATAAAA). We have demonstrated that TFIID, unlike most sequence-specific DNA-binding proteins, interacts primarily within the minor groove of the DNA helix. This was established by a novel approach involving complete replacement of the thymines and adenines in the TATA box with cytosines and inosines, respectively. This substitution exchanged the major groove of TATAAAA for that of the sequence CGCGGGG, without altering the surface of the minor groove. The unusual DNA-binding properties of TFIID revealed by this study have important implications for TFIID specificity and function and, more generally, for sequence-specific recognition by DNA-binding proteins.

Base Sequence↗
PubMed1999

Transcription reinitiation rate: a potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex.

Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional complex formation could be mimicked by pre-assembling activator and certain general transcription factors on the promoter and then adding nuclear extract. The minimal activated complex with this characteristic contained general factors TFIID and TFIIA. The ability of the TFIID:TFIIA complex to complete assembly rapidly was reduced by the same TATA box mutation that reduced reinitiation rate. Band shift experiments also showed that this same mutation lowered the stability of the TBP:TFIIA complex on the DNA. The results suggest that TATA-dependent variations in retention of the TFIID:TFIIA complex after release of the polymerase could be a primary determinant of reinitiation rate, allowing diversity in promoter strength to be related to diversity in TATA element sequences.

DNA↗
PubMed1993

Point mutations 5' to the tRNA selenocysteine TATA box alter RNA polymerase III transcription by affecting the binding of TBP.

The selenocysteine tRNA(Sec) gene possesses two external promoter elements, one of which is constituted by a strong TATA box. Point mutant analysis performed in this study led to the conclusion that the functional TATA promoter actually encompasses the sequence -34 GGGTATAAAAGG-23. Individual changes at T-31 do not affect transcription much. Position T-29 is less permissive to mutation since transversion to a G, for example, is less well tolerated than at T-31. Interestingly, a double point mutation, converting GG(-33/-32) to TT, causes abrogation of transcription in vivo and severe reduction of transcription in vitro with human TBP. Therefore, data obtained underscore the fact that, in the Xenopus tRNA(Sec), these two Gs are an integral part of the TATA promoter. Gel retardation experiments indicate that the GG to TT substitution, which led human TBP to lose its ability to support efficient transcription in vitro, correlates with the appearance of an altered pattern of retarded complexes. Altogether, the data presented in this report support a model in which TBP interacts directly with the TATA element of the tRNA(Sec) gene, in contrast to the type of interaction proposed for classical TATA-less tRNA genes.

Animals↗
PubMed1981

A T to A base substitution and small deletions in the conalbumin TATA box drastically decrease specific in vitro transcription.

We have previously shown that a T to G transversion at the second T of the conalbumin "TATA" box drastically decreases specific initiation of transcription by RNA polymerase B (1). We now report that a T to A transcription at the same nucleotide also drastically decreases transcription, suggesting that these mutations influence transcription mainly by altering nucleotide recognition rather than helix stability. Small deletions of 2, 3 and 4 nucleotides in the "TATA" box also drastically decrease specific initiation of transcription.

Animals↗
PubMed1992

Eukaryotic coactivators associated with the TATA box binding protein.

Recent studies of regulated RNA polymerase II transcription have uncovered a new class of molecules called coactivators. These are tightly associated with the TATA box binding protein and are required in addition to promoter-specific activators and the basal transcription factors in order to achieve stimulated levels of transcription.

Animals↗
PubMed1990

Maize high mobility group proteins bind to CCAAT and TATA boxes of a zein gene promoter.

A 216-base pair promoter fragment of the 19-kDa zein storage protein gene pMS1, containing the CCAAT and TATA boxes, was analyzed for its in vitro interactions with purified high mobility group (HMG) proteins from maize endosperm tissue. It was found that the HMG proteins display a preferential binding of A/T-rich DNA regions like their animal counterparts, although the A/T content seems not to be the only determinant for binding specificity. Surprisingly, a specific binding of the HMG proteins occurs at the CCAAT and the TATA boxes as indicated by footprinting experiments.

Base Sequence↗
PubMed1993

TATA box mutations in the Schizosaccharomyces pombe nmt1 promoter affect transcription efficiency but not the transcription start point or thiamine repressibility.

The nmt1 gene of Schizosaccharomyces pombe is highly expressed and subject to transcriptional repression by thiamine. The nmt1 promoter, in common with other strong promoters in this organism, contains a canonical sequence element, 5'-ATATATAAA, located 25 bp upstream from the transcription start point (tsp). We have made stepwise deletions of the TATA box and quantitated the effects of the mutations by assaying the expression of the chloramphenicol acetyltransferase (CAT)-encoding gene (cat) cloned downstream. Our results demonstrate that progressive truncation of the TATA box results in a concomitant decrease in promoter strength as judged both by the loss of CAT activity in cell extracts and by a reduction in the steady-state level of cat mRNA. Both the induced level and the residual, repressed level of expression observed in the presence of thiamine are similarly down-regulated. On the other hand, even in the most extreme mutant, the tsp is unaffected, suggesting that other elements in the nmt1 promoter are important in determination of the tsp. The properties of the modified promoters have made them useful for extending the range of the pREP inducible expression vectors.

Base Sequence↗
PubMed1998

Inherent DNA curvature and flexibility correlate with TATA box functionality.

Four 1.5 ns molecular dynamics (MD) simulations were performed on the d(GCTATAAAAGGG).d(CCCTTTTATAGC) double helix dodecamer bearing the Adenovirus major late promoter TATA element and three iso-composition mutants for which physical and biochemical data are available from the same laboratory. Three of these DNA sequences experimentally induce tight binding with the TATA box binding protein (TBP) and induce high transcription rates; the other DNA sequence induces much lower TBP binding and transcription. The x-ray crystal structures have previously shown that the duplex DNA in DNA-TBP complexes are highly bent. We performed and analyzed MD simulations for these four DNAs, whose experimental structures are not available, in order to address the issue of whether inherent DNA structure and flexibility play a role in establishing these observed preferences. A comparison of the experimental and simulated results demonstrated that DNA duplex sequence-dependent curvature and flexibility play a significant role in TBP recognition, binding, and transcriptional activation.

Adenoviridae↗
PubMed1999

TIT for TAT: the properties of inosine and adenosine in TATA box DNA.

The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation with the TATA box-binding protein (TBP) with different sequences but identical chemical surfaces. The reference promoter Adenovirus 2 Major Late Promoter (mlp) is formed by the apposition of two sequences with very different dynamic properties: an alternating TATA sequence and an A-tract. For a comparative study, we carried out molecular dynamics simulations of two DNA oligomers, one containing the mlp sequence (2 ns), and the other an analog where AT basepairs were substituted by IC basepairs (1 ns). The simulations, carried out with explicit solvent and counterinons, yield straight purine tracts, the A-tract being stiffer than the I-tract, an alternating structure for the YRYR tracts, and hydration patterns that differ between the purine tracts and the alternating sequence tracts. A detailed analysis of the proposed interactions responsible for the stiffness of the purine tracts indicates that the stacking between the bases bears the strongest correlation to stiffness. The hydration properties of the minor groove in the two oligomers are distinctly different. Such differences are likely to be responsible for the stronger binding of TBP to mlp over the inosine-substituted variant. The calculations were made possible by the development, described here, of a new set of forcefield parameters for inosine that complement the published CHARMM all-hydrogen nucleic acid parametrization.

Adenosine↗
PubMed1991

The pituitary-specific regulatory gene GHF1 contains a minimal cell type-specific promoter centered around its TATA box.

GHF-1 is a pituitary-specific transcription factor responsible for activation of the growth hormone (GH) gene. The GHF1 gene is expressed exclusively in cells of the somatotrophic lineage, and its transcription is extinguished in somatic cell hybrids. The minimal sequences required for differential transcription of GHF1 in GH-expressing and -nonexpressing cell lines and somatic cell hybrids were localized to a 15-bp region surrounding and including its TATA box. This 15-bp fragment acts as a cell type-specific promoter element and is recognized by a transcription factor present in GH-expressing cell lines. Hence, in addition to enhancers and upstream promoter elements, the TATA element (TATA box plus surrounding sequences) can be, in certain cases, an important determinant of cell-type-specific transcription.

Animals↗
PubMed1986

A novel mutation in the TATA box in a Japanese patient with beta +-thalassemia.

A single base substitution (A-G) at position -31 within the highly conserved proximal promoter element, the TATA box, was identified in the beta-globin gene cloned from a Japanese woman with beta +-thalassemia. It appears that she is homozygous for this specific allele, as determined by haplotype analysis using seven different polymorphic sites in the beta-globin gene cluster. Transient expression of the mutant gene in COS cells revealed a 45% reduction in beta-globin RNA production, relative to normal. These results establish the functional significance of the second base of the TATA box for in vivo transcription of the human beta-globin gene.

Base Sequence↗
PubMed2001

Isolation and characterization of the rat prolactin-releasing peptide gene: multiple TATA boxes in the promoter region.

The prolactin-releasing peptide (PrRP) gene is a novel bioactive peptide expressed in very restricted regions in the brain. To explore the molecular mechanism of PrRP gene expression, we cloned and characterized the gene and its promoter region. The gene spans approximately 2.4 kb and contains three exons and two introns. 3'RACE analysis showed that a polyadenylation signal 103 bp downstream from the stop codon was functional. Primer extension analysis indicated three transcriptional start sites (TSSs) 92, 199, and 325 bp upstream from the translational start site. Interestingly, in addition to the putative binding sites for SP1-1, AP-2, and Oct-2A, three characteristic TATA boxes were identified close to these TSSs. Transient transfection study using a series of deletion mutants revealed that the middle TATA box is important for the promoter activity. Furthermore, the cloned 1.6 kb promoter region was active only in neuron- and pituitary-derived cell lines, and the promoter region -1600 approximately -800 bp worked as a negative regulatory element. We demonstrated for the first time, the genomic organization and promoter function of the PrRP gene, and this knowledge will facilitate elucidation of transcriptional control of the PrRP gene.

3' Untranslated Regions↗
PubMed1994

Independent control of transcription initiations from two sites by an initiator-like element and TATA box in the human c-erbB-2 promoter.

Transcription of the human c-erbB-2-proto-oncogene starts mainly at two sites, nucleotide positions +1 and -69. The present studies have identified an initiator-like element that specifies the position of transcription initiation at position -69. This initiator-like element contains six GGA repeats and is located just downstream from the transcription start site between positions -68 and -45. In addition, both in vitro and in vivo studies indicated that transcription initiation at position +1 is specified by a TATA box 25 bp upstream from the transcription startpoint. Thus, initiation at two sites in the c-erbB-2 promoter is controlled independently by the initiator-like element and the TATA box.

Base Sequence↗
PubMed2006

Exposure of mouse cumulus cell nuclei to porcine ooplasmic extract eliminates TATA box protein binding to chromatin, but has no effect on DNA methylation.

PURPOSE: The low cloning efficiency with SCNT is due to incomplete or partial reprogramming of the donor somatic cell nuclei after microinjection into the enucleated oocyte. A possible solution may be to initiate nuclear reprogramming prior to SCNT. METHODS: Pre-exposure of donor somatic cell nuclei to a novel porcine ooplasmic extract prior to microinjection could possibly extend the duration of exposure to ooplamic nuclear reprogramming factors. The effects of the porcine ooplamic extract on two major markers of nuclear preprogramming: (1) TATA box protein binding to chromation and (2) DNA methylation was investigated. RESULTS: The results showed that pre-exposure of mouse cumulus cell nuclei to porcine ooplamic extract drastically reduced TATA box protein binding to chromatin, but had no effect on DNA methylation. CONCLUSIONS: Pre-exposure to the porcine ooplasmic extract had some limited effects on nuclear reprogramming. Whether this can lead to enhanced cloning efficiency needs to be further investigated.

Animals↗
PubMed2005

Role of cis-acting sites NorL, a TATA box, and AflR1 in nor-1 transcriptional activation in Aspergillus parasiticus.

The transcription factor AflR is required for up-regulation of specific pathway genes involved in aflatoxin biosynthesis in the filamentous fungus Aspergillus. nor-1 encodes an early aflatoxin pathway enzyme; its promoter contains a consensus AflR binding site (AflR1). Proteins in Aspergillus parasiticus cell extracts and AflR expressed in Escherichia coli do not bind to A. parasiticus AflR1 in vitro, so it was not clear if this site was required for nor-1 expression or if other transcription factors contributed to gene regulation. In this study we defined the role of AflR1 in nor-1 expression in A. parasiticus and identified additional cis-acting sites required for maximum nor-1 transcriptional activation. Deletion and substitution of AflR1 in the nor-1 promoter in A. parasiticus nor-1::GUS reporter strains showed that this site is required for nor-1 transcriptional activation in vivo. Substitution of a putative TATA box in the nor-1 promoter resulted in nondetectable beta-glucuronidase (GUS) activity, demonstrating that this TATA box is functional in vivo. We also identified a novel cis-acting site, designated NorL, between residues -210 and -238 that was required for maximum nor-1 transcriptional activation in A. parasiticus grown in liquid medium and on solid medium. Using an electrophoretic mobility shift assay, we identified a specific NorL-dependent DNA-protein complex that relies on a functional AflR, either directly or indirectly, for maximum binding capacity. Because the NorL site appears only once in the aflatoxin gene cluster, its association with the nor-1 promoter may have important implications for the overall regulatory scheme for the aflatoxin pathway.

Aflatoxins↗
PubMed2001

The TATA box and a Myb binding site are essential for anaerobic expression of a maize GapC4 minimal promoter in tobacco.

The maize GapC4 promoter harbours a complex arrangement of cis-sequences involved in activation of anaerobic gene expression in tobacco. As shown by transient expression assays, four copies of a 50 bp anaerobic response element (ARE) increase anaerobic gene expression compared to the ARE alone. Expression strength is similar to a 190 bp fragment that contains most sequences required for anaerobic expression, including the 50 bp ARE. This supports the notion that redundancy of cis-acting sequences contribute to the anaerobic expression strength of the promoter. Mutation analysis of the 50 bp ARE revealed that cis-regulatory sequences are located within 30 bp at the 5' end of the ARE. Of these 30 bp a putative binding site for a Myb transcription factor is essential for anaerobic induction. The TATA box of the GapC4 promoter is also required for anaerobic gene expression and is bound specifically by a recombinant TATA box binding protein (TBP) from tobacco. A model for anaerobic induction of the GapC4 minimal promoter in tobacco that summarizes the presented data is discussed.

Anaerobiosis↗