In order to fully understand the control of gene expression in eukaryotic cells, it is necessary to achieve a much greater understanding of the RNA synthesis machinery, which is one of the most important targets for regulatory pathways. It is now known that RNA polymerase Il, which synthesizes all protein-encoding RNAs, is subject to control at many points: at the assembly of the initiation complex. at the transition into elongation and at discrete arrest sites during the elongation process. Our long-term goal is to provide answers to two fundamental questions: first, what are the molecular events that accompany the transition of RNA polymerase II from the unstable, initiating state to the stable elongation state, and second, what changes in the RNA polymerase II elongation complex are responsible for the loss of elongation competence during arrest? In order for the RNA polymerase to successfully pass from the preinitiation complex to stable transcript elongation, it must escape from an abortive initiation pathway and begin translocation down the template. Simplified systems for transcription initiation will be employed to study the sequence and factor requirements for successful escape from abortive initiation. We will also make a comparison of structural parameters among a series of complexes which are passing through the initiation-elongation transition, in order to identify structural changes which accompany the conversion to elongation competence. A similar series of experiments are proposed to study the transitions that accompany loss of the ability to elongate during arrest; in this case we hope to identify structural features distinctive to the arrested state. To accompany this latter study we will attempt to define more fully the sequence signals that cause arrest. We will also extend earlier studies into the molecular mechanisms of recovery from arrest, in order to better understand the transcript cleavage/resynthesis reaction which is required for recovery.
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