Asf1 and Swi/Snf function in RNA polymerase II elongation and histone dynamics

The conventional view of eukaryotic genomes is that histones are associated with DNA to form a relatively static chromatin structure. In vitro, RNA polymerase II can transcribe across naked DNA templates at physiological rates of elongation. On in vitro chromatin templates, however, Pol II elongation is inhibited. To access DNA, chemical and/or physical methods may alter histone-DNA interactions such as histone acetylation or "chromatin remodeling." This dissertation examines whether and, if so, how histones dissociate from DNA during Pol II elongation. Chromatin immunoprecipitation and real-time PCR are utilized to study such processes in the yeast Saccharomyces cerevisiae. In Chapter 2, data strongly suggest that histones are evicted out of the way, and deposited in the wake of, elongating Pol II. Chapter 3 examines the histone H3/H4 chaperone Asf1. Data strongly suggest that Asf1 functions as an elongation factor, is necessary for histone H3 eviction and deposition at promoters and coding regions, and suppresses internal initiation. Since a defect in histone H3, and not H2B, dynamics is observed, histone H2B and H3 dynamics can be separated. That is, histones are disassembled, as opposed to eviction of the entire octamer at once. Thus, Chapter 2 reveals the dynamic nature of histones and Chapter 3 examines the first factor to mediate histone eviction during Pol II elongation in vivo. Chapter 4 examines the Swi/Snf chromatin remodeling complex. Data presented here demonstrate that Swi/Snf travels with Pol II. Depletion of Swi/Snf suppresses internal initiation in an spt16 mutant and these data suggest that Swi/Snf is necessary for histone eviction within coding regions. Lastly, the first data are presented that Swi/Snf is necessary for histone eviction from the SUC2 promoter in vivo. Thus, Chapter 4 presents novel functions for Swi/Snf in elongation and histone dynamics. This dissertation identifies the phenomenon of histone dynamics during RNA pol II elongation and the roles of Asf1 and Swi/Snf in these processes, in vivo. AM and Swi/Snf are linked to DNA repair and cancer. Understanding the role of these proteins in transcription and histone dynamics may further elucidate the causes of certain cancers.