PROJECT SUMMARY Transcription of genes in eukaryotes involves the orchestration of dozens if not hundreds of proteins enabling each step in RNA Polymerase II (Pol II) transcription: initiation, elongation, and termination. These steps occur dynamically on DNA templates packaged into chromatin and coincidentally with a host of cotranscriptional events. The proposed studies broadly involve two main themes – Pol II initiation and Pol II elongation. The first step in transcription, initiation, involves selecting a transcription start site (TSS). Promoters across eukaryotes can have multiple TSSs and these can be used at a wide range of levels. This project will identify comprehensively the determinants of TSS selection in the model organism Saccharomyces cerevisiae and establish the extent to which initiation is sensitive to altered Pol II catalytic activity in other eukaryotes, an important test of distinct mechanisms for initiation in eukaryotes. Such studies utilize massively parallel promoter assays and genome-wide analysis of TSS usage. After initiation occurs, cotranscriptional events run the gamut from RNA processing encompassing capping, splicing, and RNA cleavage, to modification or remodeling of template chromatin. This project will uncover how elongation by Pol II works at a fundamental level and probe connections between Pol II and cotranscriptional splicing; when it occurs and how it is controlled by Pol II elongation rate. The work proposed is uniquely positioned across a wide spectrum of biology, from fundamental mechanisms of Pol II function, to how changes to Pol II result in changes to cellular physiology. The primary S. cerevisiae model employed has several critical advantages to exploit for these purposes – genetics on a scale difficult to match in other systems and amenability to structural and biochemical analyses. Gene expression mechanisms will be probed at many scales, from determining roles of individual amino acids in the Pol II active site that are essential for proper catalytic control, to the changes in transcriptomes caused by distinct genetic or chemical perturbations. Unique among studies on Pol II mechanisms, the coupling of Pol II structural analyses with deep mutational scanning of the Pol II active site will provide novel insights for how these enzymes function and evolve. The conservation of Pol II and its regulatory machinery support the pertinence of results obtained to every eukaryotic cell, including humans where we now recognize a complex syndrome linked to mutations in the large subunit of Pol II itself.