Yeast NC2 associates with the RNA polymerase II preinitiation complex and selectively affects transcription in vivo

The Ccr4-not complex and yTAF1 (yTaf(II)130p/yTaf(II)145p) show physical and functional interactions

The Saccharomyces cerevisiae Ccr4-Not complex is a global regulator of transcription that is thought to regulate TATA binding protein (TBP) function at certain promoters specifically. In this paper, we show interactions between the essential domain of Not1p, which interacts with Not4p and Not5p, and the N-terminal domain of yTAF1. We isolated a temperature-sensitive nonsense allele of TAF1, taf1-4, which is synthetically lethal at the permissive temperature when combined with not4 and not5 mutants and which produces high levels of a C-terminally truncated yTAF1 derivative. Overexpression of C-terminally truncated yTAF1 is toxic in not4 or not5 mutants, whereas overexpression of full-length yTAF1 suppresses not4. Furthermore, mutations in the autoinhibitory N-terminal TAND domain of yTAF1 suppress not5, and the overexpression of similar mutants does not suppress not4. We find that, like Not5p, yTAF1 acts as a repressor of stress response element-dependent transcription. Finally, we have evidence for stress-regulated occupancy of promoter DNA by Not5p and for Not5p-dependent regulation of yTAF1 association with promoter DNA. Taken together with our finding that Not1p copurifies with glutathione S-transferase-yTaf1 in large complexes, these results provide the first molecular evidence that the Ccr4-Not complex might interact with yTAF1 to regulate its association at promoters, a function that might in turn regulate the autoinhibitory N-terminal domain of yTAF1.

SALSA, a variant of yeast SAGA, contains truncated Spt7, which correlates with activated transcription

Spt-Ada-Gcn5 acetyltransferase (SAGA) is a previously described histone acetyltransferase/transcriptional coactivator complex in yeast. At promoters of certain genes (HIS3 and TRP3), SAGA has an inhibitory function involving a nonproductive TATA-binding protein interaction mediated by the Spt3 and Spt8 subunits. Related to this, Spt8-less SAGA is a major form of the complex under activating conditions for these genes. In the present study, we purify this activation-specific complex, called SALSA (SAGA altered, Spt8 absent). Besides lacking Spt8, SALSA contains Spt7 subunit that is truncated. Examining the role of this subunit, we find that C-terminally truncated SPT7 resulted in derepressed HIS3 transcription. Furthermore, when grown in rich media (repressing conditions), wild-type cells yielded predominantly SAGA, but Spt7 C-terminal truncations resulted primarily in a form of complex similar to SALSA. Thus, SALSA-like structure and activating function can be partially recapitulated in yeast by truncating the C terminus of Spt7. Overall, these results lead to a model that for a subset of promoters SAGA is inhibitory through Spt3, Spt8, and an Spt8-interacting subdomain of Spt7, whereas SALSA is a form of complex for positive transcriptional regulation. These data clarify a mechanism by which a transcriptional regulatory complex can switch between positive and negative modulation.

Mot1 activates and represses transcription by direct, ATPase-dependent mechanisms

Mot1 is an essential yeast Snf2/Swi2-related ATPase that exerts both positive and negative effects on gene expression. In vitro, Mot1 can disrupt TATA-binding protein-DNA complexes in an ATP-dependent reaction. This activity can explain Mot1-mediated transcriptional repression, but how Mot1 activates transcription is unknown. We demonstrate that, remarkably, Mot1 is localized in vivo to promoters for both Mot1-repressed and Mot1-activated genes. Moreover, Mot1 ATPase activity is required for both activation and repression of gene activity. These findings suggest a novel function for the Mot1 ATPase at activated genes, perhaps involving ATP-driven reorganization of the preinitiation complex. Mot1 regulates the expression of approximately 3% of yeast genes in cells grown in rich medium. Most of these genes are repressed by Mot1, consistent with Mot1's ATP-dependent TATA-binding protein-DNA dissociating activity. Additionally, approximately 77% of the Mot1-repressed genes are involved in the diauxic shift, stress response, mating, or sporulation. The gene sets controlled by NC2 and Srb10 are strongly correlated with the Mot1-controlled set, suggesting that these factors cooperate in transcriptional control on a global scale.

Association of human TFIID-promoter complexes with silenced mitotic chromatin in vivo

When eukaryotic cells enter mitosis, transcription is abruptly silenced. Earlier studies indicated that most transcription factors and RNA polymerase II (RNAP II) are displaced when chromatin is condensed into mitotic chromosomes. A more recent study suggested that hitherto unidentified factors might 'bookmark' previously active genes for rapid reactivation after cell division. Here we used chromatin immunoprecipitation (ChIP) assays to examine the association of TFIID, TFIIB, NC2 and RNAP II with various gene promoters in asynchronous and mitotic human cell populations. We show that TFIID and TFIIB can remain associated with active gene promoters during mitosis whereas RNA polymerase II is displaced, and also that NC2, originally identified as ubiquitous repressor of transcription, is associated with active gene promoters in asynchronous cell populations and is displaced from some, but not all, genes in mitotic cells. Consistent with the remarkable stability of TFIID-promoter complexes observed in vitro, our data suggest that these complexes can withstand condensation of chromatin into transcriptionally silent chromosomes. Stable TFIID-promoter complexes are therefore implicated in the propagation of cell-type-specific gene expression patterns through cell division.

Functional dissection of a Rice Dr1/DrAp1 transcriptional repression complex

We characterized rice cDNA sequences for OsDr1 and OsDrAp1, which encode structural homologs of the eukaryotic general repressors Dr1 and DrAp1, respectively. OsDr1 and OsDrAp1 are nuclear proteins that interact with each other and with the TATA binding protein/DNA complex. In vitro and in vivo functional analyses showed that OsDrAp1 functions as a repressor, unlike its role in other eukaryotic systems, in which DrAp1 is a corepressor. OsDr1 and OsDrAp1 functioned together as a much stronger repressor than either one alone. Functional dissections revealed that the N-terminal histone-fold domains of OsDr1 and OsDrAp1 were necessary and sufficient for their repression and protein-protein interaction with each other. The unique glutamine- and proline-rich domain of OsDr1 had no repression activity. The basic amino acid-rich region and an arginine and glycine repeat domain of OsDrAp1 enhanced its repression activity. Thus, although OsDr1 and OsDrAp1 function as repressors, the functions of the two components are reversed compared with those of their nonplant counterparts.

Fluorescence-based analyses of the effects of full-length recombinant TAF130p on the interaction of TATA box-binding protein with TATA box DNA

We have used a combination of fluorescence anisotropy spectroscopy and fluorescence-based native gel electrophoresis methods to examine the effects of the transcription factor IID-specific subunit TAF130p (TAF145p) upon the TATA box DNA binding properties of TATA box-binding protein (TBP). Purified full-length recombinant TAF130p decreases TBP-TATA DNA complex formation at equilibrium by competing directly with DNA for binding to TBP. Interestingly, we have found that full-length TAF130p is capable of binding multiple molecules of TBP with nanomolar binding affinity. The biological implications of these findings are discussed.

Gene-selective developmental roles of general transcription factors

Innumerable transcription factors integrate cellular and intercellular signals to generate a profile of expressed genes that is characteristic of the biochemical and cellular properties of the cell. This profile of expressed genes changes dynamically along with the developmental stage and differentiation state of the cell. The biochemical machinery upon which transcription factors integrate their signals is referred to as the general transcription machinery. However, this machinery is not of universal composition, and variants of the general transcription factors play specific roles in embryonic development, reflecting the constraints and requirements of developmental gene regulation.

Crystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex

The X-ray structure of a ternary complex of Negative Cofactor 2 (NC2), the TATA box binding protein (TBP), and DNA has been determined at 2.6 A resolution. The N termini of NC2 alpha and beta resemble histones H2A and H2B, respectively, and form a heterodimer that binds to the bent DNA double helix on the underside of the preformed TBP-DNA complex via electrostatic interactions. NC2beta contributes to inhibition of TATA-dependent transcription through interactions of its C-terminal alpha helix with a conserved hydrophobic feature on the upper surface of TBP, which in turn positions the penultimate alpha helix of NC2beta to block recognition of the TBP-DNA complex by transcription factor IIB. Further regulatory implications of the NC2 heterodimer structure are discussed.

TFIIS enhances transcriptional elongation through an artificial arrest site in vivo

Transcriptional elongation by RNA polymerase II has been well studied in vitro, but understanding of this process in vivo has been limited by the lack of a direct and specific assay. Here, we designed a specific assay for transcriptional elongation in vivo that involves an artificial arrest (ARTAR) site designed from a thermodynamic theory of DNA-dependent transcriptional arrest in vitro. Transcriptional analysis and chromatin immunoprecipitation experiments indicate that the ARTAR site can arrest Pol II in vivo at a position far from the promoter. TFIIS can counteract this arrest, thereby demonstrating that it possesses transcriptional antiarrest activity in vivo. Unexpectedly, the ARTAR site does not function under conditions of high transcriptional activation unless cells are exposed to conditions (6-azauracil or reduced temperature) that are presumed to affect elongation in vivo. Conversely, TFIIS affects gene expression under conditions of high, but not low, transcriptional activation. Our results provide physical evidence for the discontinuity of transcription elongation in vivo, and they suggest that the functional importance of transcriptional arrest sites and TFIIS is strongly influenced by the level of transcriptional activation.

Transcriptomes, transcription activators and microarrays

Gene-specific transcription activators are among the main factors which specifically shape the transcriptome profiles. It is tempting to take advantage of their properties to decipher the genome expression circuitry. The advent of microarray technology has offered fantastic opportunities to quickly analyze the expression profiles dictated by specific transcription factors. This review will first focus on the strategies which have been devised to control the activity of transcription factors and in the second part on the microarray experiments which addressed the role of these transcription factors in the genome-wide expression profile. This last part will mainly consider the case of the yeast Saccharomyces cerevisiae genome. All the collected data are available through the on-line database yTAFNET (http://transcriptome.ens.fr/ytafnet/). yTAFNET is designed to help the characterization of connections between the different yeast regulatory networks.