DNA structural variation affects complex formation and promoter melting in ribosomal RNA transcription.

Eukaryotic ribosomal RNA promoters exhibit an unusual conservation of non-canonical DNA structure (curvature, twist angle and duplex stability) despite a lack of primary sequence conservation. This raises the possibility that rRNA transcription factors might utilize structural anomalies in their sequence recognition process. We have analyzed in detail the interaction of the polymerase I transcription factor TIF-IB from Acanthmoeba castellanii with the CORE promoter. TIF-IB interacts primarily with the minor groove of the promoter. By correlating the effects on transcription and on DNA structure of promoter point mutations, we show that the TIF-IB interaction is strongly inhibited by increases in minor groove width. This suggests that a particular DNA structure is required for interaction with the transcription factor. In addition, TIF-IB induces a small bend in the promoter upon binding. Modeling of this bend reveals that it requires an additional narrowing of the minor groove, which would favor binding to mutants with narrower grooves. We also discuss how this narrowing would induce a small destabilization of the helix upstream of the transcription start site. Telestability predicts this would result in destabilization of the sequence that melts during initiation, suggesting that TIF-IB may have a role in stimulating melting.

Alternate oscillations in semiconductor ring lasers.

We report on fabrication and characterization of single-longitudinal- and transverse-mode semiconductor ring lasers. A bifurcation from bidirectional stable operation to a regime with alternate oscillations of the counterpropagating modes was observed experimentally and is theoretically explained through a two-mode model. Analytical expressions for the onset and the frequency of the oscillations are derived, and L-I curves numerically evaluated. Good quantitative agreement between theory and measurements made over a large number of tested devices is obtained.

RNA polymerase II and TBP occupy the repressed CYC1 promoter.

Saccharomyces cerevisiae CYC1 gene expression has been studied in great detail with regard to the response to oxygen availability and carbon source. In the absence of oxygen and the presence of glucose, the CYC1 gene is completely repressed. Chromatin structure is thought to play an important role in CYC1 gene regulation, as nucleosome depletion results in 94-fold derepression. In addition, the CYC1 core promoter has been used extensively in hybrid constructs to study activation by heterologous transcription factors. Therefore, we set out to map the chromatin structure of the CYC1 promoter and determine its role in CYC1 gene regulation. We report here that the repressed CYC1 promoter contains no positioned nucleosomes over the core promoter. However, we did find TFIID and RNA polymerase II bound in a complex on the repressed promoter. These results indicate that recruitment of TFIID and RNA polymerase II are not rate-limiting steps in CYC1 activation.

Upstream nucleosomes and Rgr1p are required for nucleosomal repression of transcription.

The mechanisms of transcription repression and derepression in vivo are not fully understood. We have obtained evidence that begins to clarify the minimum requirements for counteracting nucleosomal repression in vivo. Location of the TATA element near the nucleosome dyad does not block RNA polymerase II transcription in vivo if there is a nucleosome-free region located immediately upstream. However, location of the TATA element similarly within the nucleosome does block transcription if the region upstream of it is nucleosome bound. Histone H4 depletion derepresses transcription in the latter case, supporting the idea that the nucleosomes are responsible for the repression. These results raise the intriguing possibility that the minimum requirement for derepression of transcription in vivo is a nucleosome-free region upstream of the core promoter. Importantly, we find that a C-terminal deletion in RGR1, a component of the mediator/holoenzyme complex and a global repressor, can also derepress transcription.

Intrinsic structural disorder of the C-terminal activation domain from the bZIP transcription factor Fos.

The bZIP proto-oncoprotein c-Fos activates transcription of a wide variety of genes involved in cell growth. The C-terminal activation domain of c-Fos is functionally independent of the remainder of the protein. Fos-AD corresponds to the C-terminal activation domain of human c-Fos (residues 216-380). Fos-AD suppresses (squelches) transcription in vitro, as expected for a functional activation domain lacking a DNA-binding domain. Fos-AD is unstructured and highly mobile, as demonstrated by circular dichroism spectra indicative of unfolded proteins, a lack of (1)H chemical shift dispersion, and negative (1)H-(15)N heteronuclear nuclear Overhauser effects. The hydrodynamic properties of Fos-AD are also consistent with an extended structure. We conclude that the C-terminal domain of human c-Fos is biologically active yet intrinsically disordered. Our results suggest that conformational disorder is an integral aspect of the diverse contributions to transcriptional regulation by c-Fos.

Yeast chromatin reconstitution system using purified yeast core histones and yeast nucleosome assembly protein-1.

Transcription regulation in the cell occurs in the context of chromatin. It follows that a thorough investigation of the mechanism of transcription regulation must take into account the role of chromatin structure. Through classical and molecular genetic experiments in yeast, great strides have been made in understanding the role of chromatin in eukaryotic gene regulation. To achieve a more detailed understanding of the biochemical mechanism of transcription regulation, a yeast chromatin reconstitution system is needed. This need drove us to develop a yeast core histone purification procedure for the reconstitution of these histones into chromatin templates using components wholly derived from yeast. We have purified native yeast core histones in milligram quantities and we have shown these histones to be competent for reconstitution of chromatin templates using yeast nucleosome assembly protein-1. This accomplishment sets the stage for studies using the full power of yeast as an experimental organism to investigate the role of chromatin in transcription regulation.

Induction of the rat prodynorphin gene through Gs-coupled receptors may involve phosphorylation-dependent derepression and activation.

Prodynorphin transcription is activated via Gs-coupled receptors through a cyclic AMP (cAMP)-dependent pathway. Four cAMP response elements (CREs) are present within the rat prodynorphin (RD) control region, and all four CREs appear to function in RD regulation. Three CREs located upstream between -1860 and -1504 are critical for receptor-responsive activity, but their function is distance dependent unless they act together with a fourth CRE found in exon 1. Regulation of RD also appears to involve multiple CRE-binding proteins. Both CRE-binding protein (CREB) and activator protein 1 (AP-1) can regulate RD, but their effects are in opposite directions; CREB represses and AP-1 activates RD. CREB-induced repression and AP-1 activation require distinct elements within the control region, but their binding and functions overlap at CRE-3. While CREB repression is dependent on CRE-3, AP-1 activation (and cAMP induction) of RD requires additional CREs (CRE-1, -2, and -4). CREB repression blocks AP-1 activation in unstimulated cells. However, phosphorylation relieves CREB-induced repression and enhances AP-1 activation. Gs-coupled receptor activation of RD may require phosphorylation-dependent derepression and activation steps.

Mechanism of transcriptional antirepression by GAL4-VP16.

Promoter- and enhancer-binding factors appear to function by facilitating the transcription reaction as well as by counteracting chromatin-mediated repression (antirepression). We have examined the mechanism by which a hybrid activator, GAL4-VP16, is able to counteract histone H1-mediated repression by using both H1-DNA complexes and reconstituted H1-containing chromatin templates. The GAL4 DNA binding domain alone was sufficient to disrupt local H1-DNA interactions, but a transcriptional region was additionally necessary for antirepression. GAL4-VP16-mediated antirepression required an auxiliary factor, denoted as a co-antirepressor, which was partially purified from Drosophila embryos. We have found that the co-antirepressor activity was sensitive to digestion with RNase A. Moreover, total RNA from Drosophila embryos could partially substitute for the co-antirepressor fraction, which indicated that the co-antirepressor may function as a histone acceptor ("histone sink"). These findings suggest a model for gene activation in which sequence-specific transcription factors disrupt H1-DNA interactions at the promoter to facilitate transfer of H1 to a histone acceptor, which then allows access of the basal transcription factors to the DNA template.

Threshold phenomena and long-distance activation of transcription by RNA polymerase II.

To explore the underlying mechanisms by which genes are regulated in eukaryotes, long-distance transcriptional activation and threshold effects were reconstituted in vitro. Long-range activation of transcription by GAL4-VP16 protein located 1300 base pairs upstream of the RNA start site was dependent on packaging of the template into histone H1-containing chromatin. A transcriptional threshold effect by GAL4-VP16 was observed with repressed chromatin templates but not naked DNA templates. The experimental data with the chromatin templates were similar to the theoretical activation profile that is predicted if the action of each DNA bound protomer of GAL4-VP16 were independent and additive in terms of free energy.

Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II.

The relation between chromatin structure and transcriptional activity was examined by in vitro transcription analysis of chromatin reconstituted in the absence or presence of histone H1. To maintain well-defined template DNA, purified components were used in the reconstitution of chromatin. Reconstitution of nucleosomal cores to an average density of 1 nucleosome per 200 base pairs of DNA resulted in a mild reduction of basal RNA polymerase II transcription to 25 to 50 percent of that obtained with naked DNA templates. This nucleosome-mediated repression was due to nucleosomal cores located at the RNA start site and could not be counteracted by the sequence-specific transcription activators Sp1 and GAL4-VP16. When H1 was incorporated into the chromatin at 0.5 to 1.0 molecule per nucleosome (200 base pairs of DNA), RNA synthesis was reduced to 1 to 4 percent of that observed with chromatin containing only nucleosomal cores, and this H1-mediated repression could be counteracted by the addition of Sp1 or GAL4-VP16 (antirepression). With naked DNA templates, transcription was increased by a factor of 3 and 8 by Sp1 and GAL4-VP-16, respectively (true activation). With H1-repressed chromatin templates, however, the magnitude of transcriptional activation mediated by Sp1 and GAL4-VP16 was 90 and more than 200 times higher, respectively, because of the combined effects of true activation and antirepression. The data provide direct biochemical evidence that support and clarify previously proposed models in which there is depletion or reconfiguration of nucleosomal cores and histone H1 at the promoter regions of active genes.

An evanescent fluorescence biosensor using ion-exchanged buried waveguides and the enhancement of peak fluorescence.

The principle of an optical molecular sensor using ion-exchanged buried planar waveguides in glass has been demonstrated. We have shown both theoretically and experimentally that the intensity of the peak evanescent fluorescence can be increased by several orders of magnitude with the use of an index-matching material. The method of differential measurement has been used to improve the differentiation between specific and non-specific binding. We used h-IgG (human immunoglobulin G) as the immobilized antibody on the surface of the waveguide and protein A-FITC (fluorescein isothiocyanate) as the fluorescently labelled antigen or anti-antibody to be detected, and have shown that a concentration of protein A as low as 24 nM can easily be detected.

Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription.

The largest subunit of mammalian RNA polymerase II contains at its C terminus an unusual domain consisting of multiple tandem repeats of the seven-amino acid consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. This domain is unphosphorylated in RNA polymerase IIA and extensively phosphorylated in RNA polymerase IIO. To investigate the role of the C-terminal domain and the functional significance of its phosphorylation, changes in the level of phosphorylation were followed as a function of the position of RNA polymerase II in the transcription cycle. Complexes were formed with 32P-labeled RNA polymerase IIA and separated from the free polymerase by gel filtration. The phosphorylation state of the RNA polymerase II largest subunit was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Results indicate that RNA polymerase IIA interacts with the template-committed complex to form a stable preinitiation complex. RNA polymerase IIA associated with such complexes is converted to RNA polymerase IIO in the presence of ATP prior to the formation of the first phosphodiester bond. Furthermore, the observation that purified preinitiation complexes can catalyze the conversion of RNA polymerase IIA to IIO indicates that the protein kinase(s) responsible for phosphorylation of the C-terminal domain is a component of such complexes. The concentration of ATP required for the phosphorylation of RNA polymerase II associated with the preinitiation complex is two to three orders of magnitude lower than that required for the conversion of RNA polymerase IIA to IIO free in solution. These results support the idea that phosphorylation of the C-terminal domain of RNA polymerase subunit IIa occurs subsequent to the association of enzyme with the promoter and prior to the initiation of transcription.

The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIa.

Mammalian cells contain two forms of RNA polymerase II, designated IIO and IIA, that differ in the extent of phosphorylation within the C-terminal domain of their largest subunit. Phosphorylation of this domain, which results in the conversion of RNA polymerase IIA to IIO, may play an important role in the transition from the initiation to the elongation phase of transcription. A third form of the enzyme, RNA polymerase IIB, is found in vitro and lacks the repetitive C-terminal domain. Purified calf thymus RNA polymerase IIA was labeled selectively with casein kinase II in the presence of [gamma-32P]ATP and used as substrate for the identification and partial purification of factors that catalyze the conversion of RNA polymerase IIA to IIO. HeLa cell S-100 transcription extracts contain such an activity that cofractionates with factors essential for promoter-dependent transcription through heparin-Sepharose, DEAE-5PW, and DE52 chromatography. The activity is dependent on either ATP, GTP, or dATP, requires a hydrolyzable beta,gamma-phosphoanhydride bond, and cannot utilize pyrimidine nucleoside triphosphates. This observation supports the idea that the conversion activity is a protein kinase. Transcription of the major late promoter of adenovirus-2 was carried out in the presence of a reconstituted transcription extract containing purified RNA polymerases IIO, IIA, or IIB, and the nature of the elongating enzyme was determined by photoaffinity labeling. When the reaction was initiated with RNA polymerase IIO or IIB, nascent transcripts were found cross-linked to subunit IIo or IIb, respectively. However, when the reaction was initiated with RNA polymerase IIA, nascent transcripts were cross-linked to subunit IIo. Consequently, phosphorylation of the C-terminal domain of subunit IIa must have occurred prior to elongation. The copurification of RNA polymerase IIA to IIO conversion activity with factors essential for promoter-dependent transcription and the observation that RNA polymerase II containing an unphosphorylated C-terminal domain is phosphorylated prior to elongation suggest that protein kinases that phosphorylate the C-terminal domain of subunit IIa may play an essential role in transcription.

Transcription-dependent structural changes in the C-terminal domain of mammalian RNA polymerase subunit IIa/o.

The C-terminal domain of mammalian RNA polymerase subunit IIa consists of 52-tandem repeats of the consensus sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. This C-terminal domain is essentially unmodified in RNA polymerase IIA and extensively phosphorylated in RNA polymerase IIO. A monoclonal antibody directed against the C-terminal domain was shown by kinetic enzyme-linked immunosorbent assay to have a 10-fold higher reactivity with RNA polymerase IIA than with RNA polymerase IIO. The ability of increasing concentrations of this monoclonal antibody to inhibit the initiation and elongation phase of transcription was determined. Although both phases of the transcription reaction were inhibited, a 10-fold higher concentration of antibody was required to inhibit elongation than was required to inhibit initiation. These results support the hypothesis that RNA polymerase IIA, containing an unphosphorylated C-terminal domain, is involved in the formation of an initiated complex, whereas elongation is catalyzed by RNA polymerase IIO, containing a phosphorylated C-terminal domain. Further indication that the C-terminal domain undergoes a structural change during the transcription cycle results from the observation that this domain is 3-fold more sensitive to clostripain cleavage in the elongation enzyme than in the free enzyme.

Fiber-to-waveguide coupling using ion-milled grooves in lithium niobate at 1.3-microm wavelength.

A new method for fiber-Ti:LiNbO(3) waveguide coupling is described. Ion-milled grooves in LiNbO(3) permit repeatable, rigid location of fibers that have been chemically etched and then polished. The constituent loss mechanisms are analyzed and waveguide parameters optimized to minimize insertion loss resulting from modal mismatch by using experimental data on the optical fields. A total insertion loss of -3.1 dB has been measured for the coupler.