TATA elements direct bi-directional transcription by RNA polymerases II and III

The Determinants of Directionality in Transcriptional Initiation

A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA have been abandoned. A richer picture has taken shape, integrating transcription of coding genes, enhancer RNAs (eRNAs), and various other noncoding transcriptional events. In this review we give an overview of recent studies detailing the mechanisms of RNA polymerase II (RNA Pol II)-based transcriptional initiation and discuss the ways in which transcriptional direction is established as well as its functional implications.

Analysis of the 5S rRNA gene promoter from Acanthamoeba castellanii

The promoter region of the Acanthamoeba 5S rRNA gene was analysed by in vitro transcription of several 5' and 3' deletion and substitution mutants, as well as a series of linker scanning mutants. The promoter consists of three sequence regions contained entirely within the gene; two of these correspond to the A and C boxes that bind TFIIIA, found in the genes from other genera. In addition, a region immediately 3' to the transcription start site has a strong effect on initiation efficiency. No strict requirement was found for specific sequences 5' to the transcription start site. Substitution of a consensus TATA box at -29 had only a modest effect on transcription, and deletion or substitution of sequences between -15 and -10 as well as -34 and -21 was only modestly more active than the wild-type template. Analysis of 3' deletions sets the 3' end-point of the promoter between +79 and +97, and demonstrates the importance of a T-rich region in transcription termination. Taken together, these results suggest that promoter elements within the Acanthamoeba 5S RNA gene are somewhat redundant, with the exception of a sequence between +50 and +60, which functions in binding TFIIIA. Remarkably, polymerase chain reaction product templates containing only non-specific 5' ends between -6 and +1 relative to the transcription start site are fully functional, demonstrating that no external DNA scaffold is needed for TFIIIB and RNA polymerase III binding, and that productive initiation can be mediated solely by protein-DNA interactions within the coding region of the 5S gene.

Mechanism of cyst specific protein 21 mRNA induction during Acanthamoeba differentiation

The Acanthamoeba cyst specific protein 21 (CSP21) gene is tightly repressed in growing cells and highly induced early during differentiation into a dormant cyst. This increase is mediated by the rate of transcription of the CSP21 gene as determined by nuclear run-on assays. The promoter region of the CSP21 gene was analyzed by transcript start site mapping and in vitro transcription of wild-type or mutant templates, using extracts from growing cells. A sequence located 3' to a modified TATA box completely inhibits transcription and removal of this region permits robust transcription utilizing a start site approximately 35 base pairs downstream of the TATA box. Sequences 5' to the TATA box had no effect on transcription, suggesting that anti-repression is the only mechanism required for CSP21 induction. Fractionation of nuclear extracts yielded a fraction capable of transcription from the CSP21 promoter, and a fraction containing a promoter-specific repressing activity. Anti-repression may thus be a major mechanism regulating differentiation or maintenance of the proliferative cycle in Acanthamoeba.

TFIIIC-independent in vitro transcription of yeast tRNA genes

The most peculiar transcriptional property of eukaryotic tRNA genes, as well as of other genes served by RNA polymerase III, is their complete dependence on the intragenic interaction platform provided by transcription factor IIIC (TFIIIC) for the productive assembly of the TBP-containing initiation factor TFIIIB. The sole exception, in yeast, is the U6 RNA gene, which is able to exploit a TATAAATA element, 30 bp upstream of the transcription start site, for the TFIIIC-independent assembly of TFIIIB. To find out whether this extragenic core promoter organization and autonomous TFIIIB assembly capacity are unique features of the U6 gene or also apply to other genes transcribed by RNA polymerase III, we scanned the 5'-flanking regions (up to position -100) of the entire tRNA gene set of Saccharomyces cerevisiae searching for U6-like TATA motifs. Four tRNA genes harboring such a sequence motif around position -30 were identified and found to be transcribed in vitro by a minimal system only composed of TFIIIB and RNA polymerase III. In this system, start site selection is not at all affected by the absence of TFIIIC, which, when added, significantly stimulates transcription by determining an increase in the number, rather than in the efficiency of utilization, of productive initiation complexes. A specific TBP-TATA element interaction is absolutely required for TFIIIC-independent transcription, but the nearby sequence context also contributes to the efficiency of autonomous TFIIIB assembly. The existence of a TFIIIB assembly pathway leading to the faithful transcription of natural eukaryotic tRNA genes in the absence of TFIIIC provides novel insights into the functional flexibility of the eukaryotic tRNA gene transcription machinery and on its evolution from an ancestral RNA polymerase III system relying on upstream, TATA- centered control elements.

Linker scanning analysis of TBP promoter binding factor DNA binding, activation, and repression domains

The transcription activator TATA box-binding protein promoter-binding factor (TPBF) is both an activator and repressor of TBP gene expression in Acanthamoeba. TPBF bears little similarity to previously characterized families of factors. In order to identify domains that are involved in DNA binding, activation, and repression, we constructed several alanine linker scanning mutants and tested them for their ability to function in a variety of assays. The DNA binding domain comprises a large 100-amino acid domain within the central third of the protein, suggesting that DNA recognition is accomplished by interactions derived from several structural units within this domain. Surprisingly, transcription activation and repression are impaired by mutations within either of two discrete amino acid sequences located on either side of the DNA binding domain. These data suggest that TPBF activation and repression are accomplished by interactions with the same target. Since TATA elements can function bidirectionally, and in solution TBP can bind to TATA elements in either orientation, we propose that TPBF functions in part by orienting TBP or TFIID correctly on the TATA box.

Components of vectors for gene transfer and expression in mammalian cells

Progress in diverse scientific fields has been realized partly by the continued refinement of mammalian gene expression vectors. A growing understanding of biological processes now allows the design of vector components to meet specific objectives. Thus, gene expression in a tissue-selective or ubiquitous manner may be accomplished by selecting appropriate promoter/enhancer elements; stabilization of labile mRNAs may be effected through removal of 3' untranslated regions or fusion to heterologous stabilizing sequences; protein targeting to selected tissues or different organelles is carried out using specific signal sequences; fusion moieties effect the detection, enhanced yield, surface expression, prolongation of half-life, and facile purification of recombinant proteins; and careful tailoring of the codon content of heterologous genes enhances protein production from poorly translated transcripts. The use of viral as well as nonviral genetic elements in vectors allows the stable replication of episomal elements without the need for chromosomal integration. The development of baculovirus vectors for both transient and stable gene expression in mammalian cells has expanded the utility of such vectors for a broad range of cell types. Internal ribosome entry sites are now widely used in many applications that require coexpression of different genes. Progress in gene targeting techniques is likely to transform gene expression and amplification in mammalian cells into a considerably less labor-intensive operation. Future progress in the elucidation of eukaryotic protein degradation pathways holds promise for developing methods to minimize proteolysis of specific recombinant proteins in mammalian cells and tissues.

Distamycin A selectively inhibits Acanthamoeba RNA synthesis and differentiation

The effects of distamycin A on Acanthamoeba transcription, growth and differentiation were determined. Distamycin A inhibits transcription both in vitro and in vivo and can displace from DNA the transcription activator TATA binding protein promoter binding factor (TPBF). Inhibition in vivo is surprisingly selective for large rRNA precursors, 5S rRNA, profilin, S-adenosylmethionine synthetase, and extendin. Transcription from the TATA binding protein (TBP), TPBF, protein disulfide isomerase, tubulin and RNA polymerase II large subunit genes is only slightly inhibited. Moreover the rate of 5S rRNA transcription eventually recovers and exceeds that of untreated cells, while profilin transcription remains inhibited. Distamycin A inhibition is accompanied by a complex pattern of alterations to steady state levels of mRNAs. Actin, profilin and S-adenosylmethionine synthetase mRNAs are degraded, whereas mRNA encoding TBP is increased slightly in abundance. Transcription inhibition is accompanied by cessation of growth and severe morphological changes to Acanthamoeba, which are consistent with loss of production of mRNA encoding cytoskeletal proteins. Distamycin A also prevents starvation-induced differentiation of Acanthamoeba, in part due to complete prevention of cellulose production and cell wall formation.

The TATA element and its context affect the cooperative interaction of TATA-binding protein with the TFIIB-related factor, TFIIIB70

We have conducted a quantitative thermodynamic study of the effects of the TATA element and TATA-flanking sequences on the assembly of complexes containing TATA-binding protein (TBP) and the TFIIB-related factor, TFIIIB70. TBP binds to the sequence TATAAAAG in the context of the yeast U6 gene (yU6 hybrid TATA) or the adenovirus major late promoter (AdMLP) with different affinities demonstrating that the sequence context of a TATA element contributes to TBP binding. We also determined the cooperative free energies of formation of TBP.TFIIIB70.DNA complexes on the yU6 TATA element, the yU6 hybrid TATA element and a nonconsensus TATA element. The yU6 hybrid TATA displayed a moderate, less than 5-fold, increase in TBP affinity similar to the 3-fold increase observed for the AdMLP. In contrast, the nonconsensus and yU6 TATAs increased the affinity of TBP for DNA 12- and 17-fold, respectively. Since the TBP-TFIIIB70 cooperativity is greater on lower affinity TATA boxes and most polymerase III genes contain low affinity "TATA boxes," we conclude that the cooperative binding of TFIIIB70 and TBP to DNA represents an important driving force in the assembly of polymerase III-specific transcription complexes. An effect of the sequences surrounding the TATA box was also observed on TBP-TFIIIB70 cooperativity. The mechanistic implications of the thermodynamic linkage between DNA sequence and binding cooperativity are discussed.

Bidirectional binding of the TATA box binding protein to the TATA box

By selective attachment of a DNA cleavage agent to specific residues in the yeast TATA box binding protein (yTBP), we demonstrate that, in solution, yTBP binds to the TATA boxes of both the adenovirus major late promoter and the yeast CYC1 promoter with only a modest preference in orientation and binds well to several overlapping binding sites. The general factors TFIIA and TFIIB each increase the rotational and translational selectivity of yTBP but are not sufficient, at least individually, to confer a unique polarity to the preinitiation complex. We conclude that TBP alone cannot define the productive orientation of general factor assembly on a promoter.

Transcription of the Acanthamoeba TATA-binding protein gene. A single transcription factor acts both as an activator and a repressor

Transcription of the Acanthamoeba TATA-binding protein (TBP) gene is regulated by TBP promoter-binding factor (TPBF), a previously described transactivator that binds as a tetramer to the TBP Promoter Element (TPE) and stimulates transcription up to 10-fold in vitro. Here we report that TPBF also functions as a transcription repressor by binding to a negative cis-element, located between the TATA box and the transcription initiation site. The negative element, referred to as the nTPE, is structurally similar to the TPE, and its disruption increases the transcription potency of the TBP promoter. TPBF binds to the nTPE, as demonstrated by mobility shift assays. However, the binding affinity of TPBF for the nTPE is about 10-fold lower than for the TPE. When placed upstream of the TATA box, the nTPE has very little effect on transcription. However, it inhibits transcription when placed at several positions downstream of the TATA box. Mechanistic studies with the TBP promoter suggest that binding of TPBF to the nTPE not only prevents TBP from binding to the TATA box but also displaces bound TBP, thereby inhibiting further assembly of the preinitiation complex. These results suggest a mechanism in which the cellular TPBF concentration controls the level of TBP gene transcription and show that a single factor can be stimulatory, inhibitory, or neutral depending on the sequence and the context of its binding site.

Expression and purification of the RNA polymerase III transcription specificity factor IIIB70 from Saccharomyces cerevisiae and its cooperative binding with TATA-binding protein

Transcription by RNA polymerase III (pol III) in yeast requires the assembly of an initiation complex comprising the TATA-binding protein (TBP), a 90-kDa polypeptide (TFIIIB90), and a 70-kDa polypeptide (TFIIIB70). TFIIIB70 interacts with TBP, a unique pol III subunit, C34, and the 131-kDa subunit of the pol III-specific complex, TFIIIC. TFIIIB70 was expressed in Escherichia coli and purified to homogeneity. The specific transcription activity of rTFIIIB70 is 22-58% that of the native yeast and in vitro synthesized factor. However, only a small fraction (0.07-0.32%) of the TFIIIB70 from these sources results in the synthesis of full-length RNA. The data suggest that TFIIIB70 function may be limited by an unfavorable recruitment equilibrium into the preinitiation complex. Quantitative DNase I "footprint" titrations of yeast TBP to the adenovirus major late promoter were conducted at a series of constant TFIIIB70 concentrations. A value of -0.7 +/- 0.2 kcal/mol was determined for the cooperative free energy of formation of the TBP.TFIIIB70.DNA complex at concentrations of TFIIIB70 sufficient to partition all of the binding cooperativity to the TBP binding isotherm. A Kd of 44 +/- 23 nM characterizes the TFIIIB70 concentration dependence of the TBP.TFIIIB70 cooperativity. The relationship deltalog K/deltalog (TFIIIB70) is consistent with the linkage of a single molecule of TFIIIB70 with the TBP-promoter binding reaction.

Role of TATA box sequence and orientation in determining RNA polymerase II/III transcription specificity

Work from a number of laboratories has indicated that the TATA box sequence can act as a basal promoter element not only for RNA polymerase II (RNAP II) transcription, but also for transcription by RNA polymerase III (RNAP III). We previously reported that, in the absence of other cis-acting elements, the canonical TATA sequence TATAAAAA specifically supported transcription by RNAP II in an unfractionated Drosophila nuclear extract, whereas the sequence TTTTTATA (the same sequence in reverse orientation) directed RNAP III transcription. We have now examined a variety of other TATA box sequences with regard to RNA polymerase selectivity and their ability to support RNAP III transcription. The results have allowed us to rank these TATA box sequences with respect to their relative strengths as RNAP III promoter elements in unfractionated Drosophila extracts. Further, the data indicate that T residues at positions 2 and 4 of the TATA box appear to be important determinants of RNAP III selectivity in this system, whereas A residues at these positions favor RNAP II transcription. Finally, the data suggest that transcription factors TFIID and TFIIIB, although both capable of binding a variety of TATA elements, have distinct sequence preferences for recognizing the TATA box and possibly the surrounding DNA.