Diane K. Hawley - US grants

This research is directed toward understanding the means by which gene expression is regulated in the cells of higher organism. The enzyme, RNA polymerase II is responsible for synthesizing the RNA that serve as messages for protein synthesis. The process of initiation by thus enzyme is intricate but can be broken into a series of simpler, more easily analyzable steps. The components of the transcriptional machinery that act at each of these steps will be identified. Eventually it is hoped to determine how the function of or requirement for these proteins is altered in a cell undergoing a change in its pattern of gene expressions.

The proposed project will be a systematic biochemical characterization in vitro of the mechanism of transcription attenuation by human RNA polymerase II at a site within the adenovirus major late transcription unit. This site has been shown to promote transcriptional blockage at late but not early times during adenovirus infection. Experimental conditions have been found with which efficient termination at this site can be observed and studied in a soluble, cell-free protein extract. A major goal of this research is to identify the proteins that are involved in termination or antitermination at this site and to characterize the role of these proteins in the reaction mechanism. This analysis will be complemented and extended by a localization and dissection of the DNA sequences that contribute to the elongation behavior of the polymerase. In addition, a number of functional properties of the reaction will be examined to provide a better understanding of the molecular mechanism of termination. These properties include the kinetics and extent of transcript release and the role of this research relates to recent evidence from a number of different laboratories that transcription attenuation within genes is an important regulatory mechanism in differential gene expression in eukaryotic cells. The long-term goal of this research is to identify possible ways attenuation of transcription by RNA polymerase II might be regulated in vivo so that future experiments can focus specifically on defining these regulatory mechanisms.*** //

The proposed research will be a systematic biochemical investigation of the proteins and DNA sequences required for transcription initiation in vitro by mammalian RNA polymerase II. The strategy involves a physical and functional characterization of protein-DNA complexes that represent intermediates in the assembly of initiation complexes at the promoter. A major focus of the research will be an extensive analysis of the interaction of the yeast and human TFIID proteins with the TATA box sequence element, as this step has been proposed to be a major determinant of promoter strength both in vitro and in vivo. Using a combination of experimental approaches, including chemical and enzymatic interference methods, gel mobility shift assays, and transcription reactions, the kinetics and stability of TFIID binding to different TATA box sequences will be measured; the role of individual bases within and flanking the TATA box will be probed; and the possible importance of DNA structure to this interaction will be examined. Similar experimental strategies will be used to analyze the protein-protein and protein-DNA interactions that contribute to the binding and function of other general transcription factors in the assembling preinitiation complex. In the initial phases of the research, transcription factors IIA and IIB will be of particular interest, because each of these proteins is capable of forming a complex with TFIID at the promoter in the absence of other proteins. The results from the quantitative and qualitative analyses of protein-DNA complexes formed with different promoter sequences will be correlated with measurements of the ability of these same promoters to function in transcription initiation in the presence and absence of upstream activating proteins. These studies are expected to provide a detailed understanding of the structure and function of the minimal class II promoter, to suggest mechanistic roles for the various proteins required for transcription initiation, and to define the steps that are rate-limiting for transcription. The long-term objective of this research is to identify the mechanistic steps in the assembly and initiation of transcription complexes that are targets of regulation and to determine how this regulation is accomplished.

9317613 Hawley This project will be a biochemical analysis of the proteins and DNA sequences that determine the in vitro elongation behavior of human RNA polymerase II. The major goals of these experiments are to answer questions in three general areas. First, why and how does pol II become transcriptionally blocked at arrest sites and what does the behavior of pol II at such sites reveal about the function and structure of elongation complexes? Initial studies addressing these questions have focused on the mechanism of transcription arrest in vitro at the adenovirus major late arrest site. The DNA sequence elements contributing to arrest at this site are being defined and characterized. These studies will be extended to several additional sites at which arrest and/or termination is observed, with a particular emphasis on understanding what features of the site specify transcript release. The second set of questions addresses the roles of two elongation factors, SII and TFIIF. SII has been shown to promote readthrough of arrest sites and to stimulate a 3' --> 5' exonucleolytic activity of pol II, whereas TFIIF has been shown to enhance the overall rate of elongation. The biochemical characterization of these activities will continue, focusing on several specific questions that address possible physiological roles for the exonuclease activity and the possibility that TFIIF activity is important for moderating that activity to promote efficient elongation. Finally, the ability of pol II elongation complexes to translocate backwards on the template will be used to pose and answer questions about the structure of the elongation complex, focusing particularly on the possibility that RNA secondary structures can inhibit the backing up reaction by inhibiting reformation of the DNA:RNA hybrid and that pol II may respond to termination sites encountered while backing up. %%% One of the most important and fundamental questions in biology is how genetically i dentical cells differentially use the genetic information to become specialized for different functional and structural roles in the organism. The specific morphology and function of a cell are determined by what proteins that cell is making; the information specifying production of all the possible proteins the cell could make is encoded in the genes. Thus, in each cell type, some genes must remain "off" (not expressed), while others are turned on (expressed). The first step in gene expression is the synthesis of a copy of the gene. This copying process, called transcription, produces an RNA molecule that is then used by the cell's machinery to direct production of the protein encoded by that gene. Transcription is performed by an enzyme called RNA polymerase, which must not only select the genes that are to be expressed in a certain cell but then must make a complete copy of that gene. Both the initiation and the completion of transcription are regulated, and this regulation is an important part of the mechanism by which different cells make different sets of proteins. This research will focus on understanding how transcription is regulated at the level of continuation and completion of the copying process. Specifically, there are signals within some genes that cause transcription to stop, and there are proteins that have been identified that alter the ability of the RNA polymerase to respond to or ignore these signals. This project is a biochemical analysis of the interaction of the RNA polymerase with these signals and proteins and is directed at understanding the molecular details of these interactions and their importance to the regulation of gene expression. ***

An Affinity sensors IAys Optical Biosensor will be purchased for studies in assembly and regulatory reactions in replication and transcription, the energetics of assembly of the bacterial chemotaxis signaling complex, the role of SNARE proteins in controlling the specificity of membrane fusion in yeast, assembly and structure of phage and transcription complexes, assembly and function of the RNA polymerase II transcription complexes and the role of chaperones in protein folding.

The long-term goal of this research is to understand, at the molecular level, how transcription elongation is regulated in eukaryotic cells. The importance of appropriate regulation of transcription elongation in human cells has recently been highlighted by the discovery that the gene alterations associated with several forms of cancer alter the function of cellular transcription elongation factors. Research in this laboratory focuses on human and yeast RNA polymerase II, the enzyme that transcribes nuclear protein-encoding genes. The proposed project is a combined biochemical and genetic approach aimed at identifying the physiological role of a recently discovered nuclease activity intrinsic to this and other eukaryotic and prokaryotic RNA polymerases. The conservation of this activity suggests that it is functionally important for transcription. However, whether this activity is required for accuracy of RNA synthesis, efficient RNA chain elongation, transcription termination, and/or regulation of gene expression is not known for any RNA polymerase. Furthermore, mutants that lack this activity have not been described. The proposed investigation will use several strategies to isolate such mutants in the yeast Saccharomyces cerevisiae. Enzymes shown to have an impaired nuclease activity will be assayed in vitro to identify possible alterations in other properties, including the rate and fidelity of transcription elongation and the propensity to pause, arrest, or terminate transcription. The observed biochemical properties and physiological behavior of these mutant enzymes will serve as the basis for proposing and testing specific hypotheses addressing nuclease function in vivo and in vitro. In addition, the physiological role of the 511 protein, which stimulates the nuclease activity, will also be investigated with the proposed experiments. In particular, the re~arch will explore the possibility that the nuclease activity has several functions, perhaps only a subset of which are dependent on SII. Similarly, experiments are proposed to determine whether SII has an additional role in transcription, independent of its stimulation of the nuclease. Together, these experiments will provide insight into the importance of an activity that, until recently, was completely unknown but which is likely to be central to the accurate function and regulation of RNA polymerases.

The project will be a combined genetic and biochemical investigation of the contribution of RNA polymerase (Pol) II to the mechanism of 3' end processing and termination downstream of protein-encoding genes in the yeast Saccharomyces cerevisiae. Termination - the release of the transcribing polymerase complex from the DNA - is an essential, but poorly understood, event in the Pol II transcription cycle. In eukaryotic nuclei, the 3' ends of mature mRNAs are generated by cleavage and polyadenylation. Transcription past the site at which processing occurs signals the Pol II elongation complex to terminate at downstream positions on the DNA. Many proteins required for transcript cleavage and polyadenylation have been identified and characterized, but the mechanism(s) that couple these events to termination are not well-understood. This project will focus on the role of Pol II in the coupling of polyadenylation and termination by characterizing mutated variants of the first and second largest subunits of yeast Pol II that were isolated in a screen for termination defects. This set of mutations identified novel clusters of important residues on the surface of the enzyme that are likely to be interaction sites for other proteins. One specific aim of the project is identification of the protein partners that bind these sites. Standard methods including a yeast two-hybrid approach and a suppressor screen will be used to address this aim. Other mutations altered residues that closely approach the nucleic acids in the elongation complex and so are more likely to affect intrinsic Pol II properties important for the response to termination and/or polyadenylation signals. A second specific aim is to investigate the mechanisms underlying the termination defects for each class of mutants, using a combination of biochemical assays in vitro and functional tests in vivo. Together, results from these experiments will provide a more detailed understanding of the mechanism underlying the drastic changes in the elongation properties of Pol II that occur in response to 3' end processing events.

RNA polymerases transcribe the genetic information stored in DNA into messenger RNA, which is then used as a template for protein synthesis. These enzymes are complex machines that must recognize the encoded signals that flank each gene and specify where transcription should start and stop. This research will provide insight into the mechanism by which an RNA polymerase from a model organism uses encoded information to finish and release the RNA and then fall off the DNA for recycling to another gene. Providing resources and projects suitable for training undergraduates was an important consideration in the design of the experiments. Although some of the experiments would be better suited for graduate students, there are other aspects of the project that are particularly appropriate for the more limited experience and the time constraints of undergraduates. The Principal Investigator's research group has a strong track record of mentoring undergraduates, many of whom have gone on to future scientific contributions and careers in academia and industry.