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Gene expression requires the recruitment of chromatin remodeling activities and general transcription factors (GTFs) to promoters. Whereas the role of activators in recruiting chromatin remodeling activities has been clearly demonstrated, the contributions of the transcription machinery have not been firmly established. Here we demonstrate that the remodeling of theRNR3promoter requires a number of GTFs, mediator and RNA polymerase II. We also show that remodeling is dependent upon the SWI/SNF complex, and that TFIID and RNA polymerase II are required for its recruitment to the promoter. In contrast, Gcn5p-dependent histone acetylation occurs independently of TFIID and RNA polymerase II function, and we provide evidence that acetylation increases the extent of nucleosome remodeling, but is not required for SWI/SNF recruitment. Thus, the general transcription machinery can contribute to nucleosome remodeling by mediating the association of SWI/SNF with promoters, thereby revealing a novel pathway for the recruitment of chromatin remodeling activities.

Publisher Summary This chapter reviews the general transcription factor transcription Factor II D (TFIID), playing a key role in the regulation of gene expression by RNA polymerase II. In yeast, the TFIID complex is composed of the TATA box-binding protein (TBP) plus 14 TBP-associated factors (TAFs). Roles of the TAF proteins in transcription have been examined by inactivating TAF function and monitoring the effects on gene expression. Conditional mutants must be isolated and employed in their analysis, as all but one of the subunit of the TFIID complex is essential for the viability in yeast. The chapter explores the conditional depletion/expression strategies used in the systems that place the TAF gene under the control of a tightly regulated promoter. The advantage of this strategy is that the protein is depleted from the cell, alleviating concerns that the gene function is partially inactivated.

Yeast TAF90p is a component of at least two transcription regulatory complexes, the general transcription factor TFIID and the Spt-Ada-Gcn5 histone acetyltransferase complex (SAGA). Broad transcription defects have been observed in mutants of other TAF(II)s shared by TFIID and SAGA but not in the only two TAF90 mutants isolated to date. Given that the numbers of mutants analyzed thus far are small, we isolated and characterized 11 temperature-sensitive mutants of TAF90 and analyzed their effects on transcription and integrity of the TFIID and SAGA complexes. We found that the mutants displayed a variety of allele-specific defects in their ability to support transcription and maintain the structure of the TFIID and SAGA complexes. Sequencing of the alleles revealed that all have mutations corresponding to the C terminus of the protein, with most clustering within the conserved WD40 repeats; thus, the C terminus of TAF90p is required for its incorporation into TFIID and function in SAGA. Significantly, inactivation of one allele, taf90-20, caused the dramatic reduction in the levels of total mRNA and most specific transcripts analyzed. Analysis of the structure and/or activity of both TAF90p-containing complexes revealed that this allele is the most disruptive of all. Our analysis defines the requirement for the WD40 repeats in preserving TFIID and SAGA function, demonstrates that the defects associated with distinct mutations in TAF90 vary considerably, and indicates that TAF90 can be classified as a gene required for the transcription of a large number of genes.

In yeast, inactivation of certain TBP-associated factors (TAFIIs) results in arrest at specific stages of the cell cycle. In some cases, cell cycle arrest is not observed because overlapping defects in other cellular processes precludes the manifestation of an arrest phenotype. In the latter situation, genetic analysis has the potential to reveal the involvement of TAFIIs in cell cycle regulation. In this report, a temperature-sensitive mutant of TAF68/61 was used to screen for high-copy dosage suppressors of its growth defect. Ten genes were isolated: TAF suppressor genes, TSGs 1–10. Remarkably, most TSGs have either a genetic or a direct link to control of the G2/M transition. Moreover, eight of the 10 TSGs can suppress a CDC28 mutant specifically defective for mitosis (cdc28-1N) but not an allele defective for passage through start. The identification of these genes as suppressors of cdc28-1N has identified four unreported suppressors of this allele. Moreover, synthetic lethality is observed between taf68-9 and cdc28-1N. The isolation of multiple genes involved in the control of a specific phase of the cell cycle argue that the arrest phenotypes of certain TAFII mutants reflect their role in specifically regulating cell cycle functions. Copyright © 2001 John Wiley & Sons, Ltd.

The budding yeast Saccharomyces cerevisiae was used as a model system to study the function of the adenovirus E1A oncoprotein. Previously we demonstrated that expression of the N-terminal 82 amino acids of E1A in yeast causes pronounced growth inhibition and specifically interferes with SWI/SNF-dependent transcriptional activation. Further genetic analysis identified the yeast transcription factor Adr1 as a high copy suppressor of E1A function. Transcriptional activation by Adr1 requires interaction with co-activator proteins Ada2 and Gcn5, components of histone acetyltransferase complexes including ADA and SAGA. Analysis of mutant alleles revealed that several components of the SAGA complex, including proteins from the Ada, Spt, and Taf classes were required for E1A-induced growth inhibition. Growth inhibition also depended on the Gcn5 histone acetyltransferase, and point mutations within the Gcn5 HAT domain rendered cells E1A-resistant. Also required was SAGA component Tra1, a homologue of the mammalian TRRAP protein which is required for c-myc and E1A induced cellular transformation. Additionally, Gcn5 protein could associate with E1A in vitro in a manner that depended on the N-terminal domain of E1A, and Tra1 protein was co-immunoprecipitated with E1A in vivo. These results indicate a strong requirement for intact SAGA complex for E1A to function in yeast, and suggest a role for SAGA-like complexes in mammalian cell transformation.

The DNA damage inducible gene ribonucleotide reductase (RNR3) is regulated by a transcriptional repression mechanism by the recruitment of the Ssn6-Tup1 corepressor complex to its promoter by the sequence-specific DNA-binding protein Crt1. Ssn6-Tup1 is reported to represses transcription by interfering with transcription factors, recruiting histone deacetylases, and positioning nucleosomes at the promoter of its target genes. Two of the three mechanisms involve effects on chromatin structure, and therefore, we have delineated the nucleosomal structure of RNR3 in the repressed and derepressed state using multiple nuclease mapping strategies. A regular array of positioned nucleosomes is detected over the repressed RNR3 promoter that extends into the coding sequence. Treating cells with DNA damaging agents or deleting CRT1, SSN6, or TUP1 derepresses RNR3 transcription, and causes a dramatic disruption of nucleosome positioning over its promoter. Furthermore, derepression of RNR3 correlated with changes in nuclease sensitivity within the upstream repression sequence (URS) region. Specifically, the loss of a MNase-hypersensitive site, and the appearance of strong DNase I hypersensitivity, was observed over the URS. Interestingly, we find that the binding of Crt1 to the promoter in the absence of Ssn6 or Tup1 is insufficient for nucleosome positioning or regulating chromatin structure at the URS; thus, these two functions are strictly dependent upon Ssn6-Tup1. We propose that RNR3 is regulated by changes in nucleosome positioning and chromatin structure that are mediated by Ssn6, Tup1, and Crt1.

The proteasome is well known for its regulation of the cell cycle and degradation of mis-folded proteins, yet many of its functions are still unknown. We show that RPN11, a gene encoding a subunit of the regulatory cap of the proteasome, is required for UV-stimulated activation of Gcn4p target genes, but is dispensable for their activation by the general control pathway. We provide evidence thatRPN11 functions downstream of RAS2, and show that mutation of two additional proteasome subunits results in identical phenotypes. Our analysis defines a novel function of the proteasome: regulation of the RAS- and AP-1 transcription factor-dependent UV resistance pathway.

The RNA polymerase II general transcription factor TFIID is a complex containing the TATA-binding protein (TBP) and associated factors (TAFs). We have used a mutant allele of the gene encoding yeast TAF(II)68/61p to analyze its function in vivo. We provide biochemical and genetic evidence that the C-terminal alpha-helix of TAF(II)68/61p is required for its direct interaction with TBP, the stable incorporation of TBP into the TFIID complex, the integrity of the TFIID complex, and the transcription of most genes in vivo. This is the first evidence that a yeast TAF(II) other than TAF(II)145/130 interacts with TBP, and the implications of this on the interpretation of data obtained studying TAF(II) mutants in vivo are discussed. We have identified a high copy suppressor of the TAF68/61 mutation, TSG2, that has sequence similarity to a region of the SAGA subunit Ada1. We demonstrate that it directly interacts with TAF(II)68/61p in vitro, is a component of TFIID, is required for the stability of the complex in vivo, and is necessary for the transcription of many yeast genes. On the basis of these functions, we propose that Tsg2/TAF(II)48p is the histone 2A-like dimerization partner for the histone 2B-like TAF(II)68/61p in the yeast TFIID complex.

Activation of eukaryotic class II gene expression involves the formation of a transcription initiation complex that includes RNA polymerase II, general transcription factors, and SRB components of the holoenzyme. Negative regulators of transcription have been described, but it is not clear whether any are general repressors of class II genes in vivo . We reasoned that defects in truly global negative regulators should compensate for deficiencies in SRB4 because SRB4 plays a positive role in holoenzyme function. Genetic experiments reveal that this is indeed the case: a defect in the yeast homologue of the human negative regulator NC2 (Dr1·DRAP1) suppresses a mutation in SRB4. Global defects in mRNA synthesis caused by the defective yeast holoenzyme are alleviated by the NC2 suppressing mutation in vivo , indicating that yeast NC2 is a global negative regulator of class II transcription. These results imply that relief from repression at class II promoters is a general feature of gene activation in vivo .

IN higher eukaryotes the RNA polymerase II transcription factor TFIID is composed of a TATA-box-binding protein (TBP) and a set of tightly bound polypeptides, designated TBP-associated factors (TAFIIS). One or more TAFIIS are coactivators that are required for activated but not basal transcription1–3. The eukary-otic transcription machinery is highly conserved and it is therefore puzzling that TAFIIS have not been identified in yeast. Here we use TBP as a protein-affinity ligand to isolate from yeast a multisubunit complex that is required specifically for activated transcription by RNA polymerase II. Microsequence analysis and cloning of two subunits of this complex reveal that they are the homologues of known mammalian and Drosophila TAFIIS. The genes encoding these two yeast TAFIIS are essential, suggesting that activated transcription is required for viability of Saccharo-myces cerevisiae.

We have undertaken studies to examine the ligand requirements for the DNA binding and functional activity of human estrogen receptor (ER) within intact cells. By employing an assay using competitive binding of ER with basal transcription factors on a constitutive promoter (CMV-(HRE)n-CAT, containing hormone response element(s) between the TATA-box and the start site of transcription of the Cytomegalovirus promoter upstream of the chloramphenicol acetyltransferase gene) we were able to examine the DNA binding ability of the human ER in whole cells. We used this promoter interference assay to examine the DNA binding of ER in cell lines containing high and low levels of endogenous ER, as well as in Chinese Hamster Ovary (CHO) cells expressing wild-type and mutant ERs from cotransfected expression vectors. We have found that the ER is capable of binding to reporter templates within intact cells in the absence of ligand; however, ligand enhances this interaction. We provide some evidence that this DNA binding may result in ligand-independent transactivation of transgenes by the receptor, and that DNA binding alone is not sufficient for full receptor activity. Likewise, receptors occupied with estradiol or two classes of antiestrogens were also capable of DNA binding. Receptors occupied with the pure antiestrogen ICI 164,384 bound to DNA in whole cells and were in sufficient quantity to occupy receptor binding sites on reporter templates, indicating that neither a loss of DNA binding of ICI-receptor complexes or reduction of ER protein in target cells could fully explain the antagonistic nature of this compound. Through the analysis of a temperature-sensitive ER mutant (C447A), we provide evidence that the ligand-independent DNA binding observed for the ER is the basis of functional differences observed between the ER and other members of the steroid receptor family.

We have used affinity labeling, site-directed mutagenesis and regional chemical mutagenesis in order to determine regions of the human estrogen receptor (ER) important in hormone binding, ligand discrimination between estrogens and antiestrogens, and transcriptional activation. Affinity labeling studies with the antiestrogen, tamoxifen aziridine and the estrogen, ketononestrol aziridine have identified cysteine 530 in the ER hormone binding domain as the primary site of labeling. In the absence of a cysteine at 530 (i.e. C530 mutant), C381 becomes the site of estrogen-compatible tamoxifen aziridine labeling. Hence these two residues, although far apart in the primary linear sequence of the ER protein, must be close in the three-dimensional structure of the protein, in the ER ligand binding pocket, so that the ligand can reach either site. Site-directed mutagenesis of selected residues in the ER and region-specific chemical mutagenesis of the ER hormone binding domain with initial phenotypic screening in yeast have enabled the identification of a region near C530 important in discrimination between estrogens and antiestrogens and of other residues important in hormone-dependent transcriptional activation. Some ER mutants with alterations in the carboxy-terminal portion of the hormone binding domain are transcriptionally inactive yet bind hormone and also function as potent dominant negative ERs, suppressing the activity of wild-type ER at low concentrations. These studies reveal a separation of the hormone binding and transcription activation functions of the ER. They are also beginning to provide a more detailed picture of the ER hormone binding domain and amino acids important in ligand binding and discrimination between different categories of agonist and antagonist ligands. Such information will be important in the design of maximally effective antiestrogens. In addition, since there is now substantial evidence for a mixture of wild-type and variant ERs in breast cancers, our studies should provide insight about the bioactivities of these variant receptors and their roles in modulating the activity of wild type ER, and should lead to a better understanding of the possible role of variant receptors in altered response or resistance to antiestrogen and endocrine therapy in breast cancer. In addition, some dominant negative receptors may prove useful in examining ER mechanisms of action and in suppressing the estrogen-dependent growth of breast cancer cells.

We have shown that charged amino acids near C530 of the human estrogen receptor (ER) are involved in receptor discrimination between estrogen and antiestrogen. We now examine the role of charged residues, adjacent to the three other cysteines (381, 417, and 447) in the hormone-binding domain of the human ER, in the hormone-binding, DNA-binding, and transcription activation abilities of the receptor. Mutation of the one charged amino acid nearest to C381 gave a mutant receptor (E380Q) requiring two to three times less estradiol (E2) than wild type (WT) ER to achieve maximal activity and having activity in the absence of added estrogen that was 6-fold higher than that of WT receptor. The enhanced ability of this mutant to bind to estrogen response element DNA in the absence and presence of estrogen may, at least in part, explain its elevated, seemingly constitutive trans-activation activity and its increased sensitivity to estrogen. While more sensitive to E2, this E380Q mutant was less sensitive than WT ER to antiestrogen for suppression of transcriptional activity. Mutation of all three charged residues nearest to C381 (the triple mutant D374N, E380Q, and E385Q) resulted in a greatly reduced potency of the receptor in trans-activation with no change in estrogen-binding affinity. When K449 (near C447), highly conserved among steroid receptors, was mutated to Q, 400-fold more E2 was required for maximal reporter gene trans-activation due to an unstable, temperature-sensitive hormone-receptor complex. In contrast, the mutant K416Q (near C417) was unaltered in E2-binding or receptor transcriptional activity. These studies reveal a region in the N-terminal portion of the hormone-binding domain (ca. amino acids 374-385) where alterations in charged residues result in either increases or decreases in receptor transcriptional activity with no change in receptor affinity for hormone. Our findings suggest that this region may be important in DNA binding and protein-protein interactions that modulate transcriptional activity of the ER. In addition, the region near C447, which is well conserved among steroid receptors, appears to be important in maintaining the receptor in a conformation that is stable at physiological (37 C) temperatures. To our knowledge, this is the first report of an ER (E380Q) with a sensitivity to E2 for trans-activation greater than that of WT receptor and having high trans-activation activity in the absence of added hormone.

We have developed a transient transfection system using the Cytomegalovirus (CMV) promoter to express the human estrogen receptor (ER) at very high levels in COS-1 cells and have used it to study the interaction of agonist and antagonist receptor complexes with estrogen response element (ERE) DNA. ER can be expressed to levels of 20-40 pmol/mg or 0.2-0.3% of total soluble protein and all of the soluble receptor is capable of binding hormone. The ER binds estradiol with high affinity (Kd 0.2 nM), and is indistinguishable from native ER in that the receptor is capable of recognizing its cognate DNA response element with high affinity, and of transactivating a transgene in an estradiol-dependent manner. Gel mobility shift assays reveal interesting ligand-dependent differences in the binding of receptor complexes to ERE DNA. Receptors occupied by estradiol or the type I antiestrogen transhydroxytamoxifen bind to DNA response elements when exposed to the ligand in vitro or in vivo. Likewise, receptors exposed to the type II antiestrogen ICI 164,384 in vitro bind to ERE DNA. However, when receptor exposure to ICI 164,384 is carried out in vivo, the ER-ICI 164,384 complexes do not bind to ERE DNA, or do so only weakly. This effect is not reversed by subsequent incubation with estradiol in vitro, but is rapidly reversible by in vivo estradiol exposure of intact COS-1 cells. This suggests there may be some cellular process involved in the mechanism of antagonism by the pure antiestrogen ICI 164,384, which is not observed in cell-free extracts.

In this study we report the first estrogen receptor to be characterized in an oviparous elasmobranch. The skate receptor has high affinity for estradiol (Kd = 0.7 nM), binds both estradiol and the synthetic estrogen DES, and exists in low quantities (50-100 fmol/g oviduct). The receptor displays rapid binding kinetics with half-times of 5 min at 22 degrees and 77 min at 4 degrees. DEAE-Sepharose chromatography reveals one receptor moiety which elutes between 0.13 and 0.14 M KCl. By sucrose gradient ultracentrifugation sedimentation coefficients of 3.6 S under high-salt (0.5 M KCl) and 6.0 S under low salt (0.01 M KCl) conditions were obtained. Using Sephadex G200 gel filtration chromatography, a Stokes radius (Rs) of 2.8 nm and an estimated molecular weight of 43 kDa were calculated. DNA-cellulose elution profiles reveal that the receptor elutes as one peak between 0.34 and 0.36 M NaCl (as compared to 0.20-0.22 M NaCl in mammals and birds and 0.55 M for dogfish). Although some differences are noted between the elasmobranch ER and those of other vertebrates (e.g., dissociation kinetics, DNA affinity), in general it can be said that the skate ER is a "classical" ER in most respects. It is suggested that this steroid receptor has played a key role in the reproductive tract functions of nutrient provision, embryo protection, and as a conduit to the external environment since the earliest chordate era, approximately 400 million years ago.

DNA microarray and genetic studies of Saccharomyces cerevisiae have demonstrated that histone deacetylases (HDACs) are required for transcriptional activation and repression, but the mechanism by which they activate transcription remains poorly understood. We show that two HDACs, RPD3 and HOS2, are required for the activation of DNA damage-inducible genes RNR3 and HUG1. Using mutants specific for the Rpd3L complex, we show that the complex is responsible for regulating RNR3. Furthermore, unlike what was described for the GAL genes, Rpd3L regulates the activation of RNR3 by deacetylating nucleosomes at the promoter, not at the open reading frame. Rpd3 is recruited to the upstream repression sequence of RNR3, which surprisingly does not require Tup1 or Crt1. Chromatin remodeling and TFIID recruitment are largely unaffected in the Deltarpd3/Deltahos2 mutant, but the recruitment of RNA polymerase II is strongly reduced, arguing that Rpd3 and Hos2 regulate later stages in the assembly of the preinitiation complex or facilitate multiple rounds of polymerase recruitment. Furthermore, the histone H4 acetyltransferase Esa1 is required for the activation of RNR3 and HUG1. Thus, reduced or unregulated constitutive histone H4 acetylation is detrimental to promoter activity, suggesting that HDAC-dependent mechanisms are in place to reset promoters to allow high levels of transcription.

The reproductive biology of the chondrichthyan fishes is remarkably sophisticated. Using both oviparous and viviparous reproductive modes, the group in general has adapted the strategy of producing relatively few young at one time. The oviparous species foreshadow the situation common in oviparous reptiles and universal in birds; viviparous species range from internal incubators to species in which the complexity of placentation and egg yolk reduction approaches the eutherian condition. In certain viviparous elasmobranchs histiotrophic nutrition attains an importance not seen in any other vertebrate group. Associated with the elasmobranch priority on these female reproductive adaptations, a typically vertebrate type of reproductive endocrinology is seen for the first time. This laboratory has focused on ovarian endocrine function and the regulation of the reproductive tract. We report on the steroidogenic capacity of theca, granulosa, and luteal elements and their regulation and correlate this with the natural ovarian cycle and plasma hormone levels. In addition, we describe the biochemistry of the ovarian peptide hormone relaxin and some of its actions on the reproductive tract. As in terrestrial species, relaxin effect on the elasmobranch reproductive tract is steroid hormone-dependent. In general, the results support the concept that the basic endocrine regulatory elements for vertebrate reproductive processes were established in the earliest gnathostomes, the elasmobranchs. These species may therefore provide useful models from which to gain insights into the complexities of higher vertebrate systems that may be obscured by subsequent adaptation to a terrestrial environment and homeothermy.

High and low affinity progesterone (P)-binding proteins similar to those described in the chick oviduct were characterized for the first time in liver cytosol in an oviparous turtle, Chrysemys picta. Two forms of high affinity P receptor were separated by diethyl aminoethyl (DEAE)-Sepharose anion exchange chromatography; the A form eluted in low salt buffer, and the B form at a KCl concentration of 0.20 M in a linear gradient. After photoaffinity labeling of crude cytosol with [3H] R5020, two overlapping peaks of radioactivity were detected with sodium dodecyl sulfate-polyacrylamide gel electrophoresis. After separation with DEAE-Sepharose and photoaffinity labeling, the A form migrated as a single peak with a mol wt of 90,000, and the B form as a single peak with a mol wt of 123,000. The affinity (Kd, 2.9 X 10(-9) M), capacity (1 pmol/mg protein), and binding specificity were characteristic of a P receptor. P competed most effectively for [3H]P binding. R5020 and deoxycorticosterone were good competitors; 5 alpha-pregnenolone, 17 alpha-hydroxyprogesterone, and testosterone were quite effective; cortisol, corticosterone, aldosterone, and 5 alpha-dihydrotestosterone were poor competitors. A lower affinity P-binding component (Kd, 1 X 10(-7) M; maximum binding, 15 pmol/mg protein) co-eluted from DEAE-Sepharose columns with the A and B receptor forms. This is the first description of a hepatic P receptor in any vertebrate.

Two progesterone receptors in the oviduct of the freshwater turtle Chrysemys picta: possible homology to mammalian and avian receptor systems. Here we report the characterization of two specific progesterone receptors in nuclear extracts of the turtle oviduct. The receptors differ in dissociation constants (2.8 nM vs 27 nM) which can be separated on DEAE-Sepharose, the former eluting at 0.08 M KCl and the latter at 0.20 M KCl. [3H]R5020 photoaffinity labeling SDS-PAGE revealed that the 2.8 nM moiety migrates with an apparent molecular weight of 80 ± 5 kDa and the 27 nM moiety migrates with an apparent molecular weight of 120 ± 5 kDa. These receptors are termed PR-A and PR-B due to their molecular mass and elution profiles. DNA-cellulose Chromatographic studies show that both bind DNA-cellulose with the PR-A eluting at 0.09 M NaCl and PR-B eluting between 0.20–0.21 M NaCl. In reproductively inactive turtles (from the months of January and February) estradiol is undetectable, and PR-B is absent as determined by Scatchard analysis, [3H]R5020 photoaffinity labeling electrophoretic studies and DEAE-Sepharose and DNA-cellulose chromatography. In these animals PR-B can be replenished by estrogen treatment, suggesting a physiological role for both PR-A and PR-B and dependence of PR-B on estradiol.