The Yeast SWI/SNF Complex Structure and Function: A Dissertation

DNA is packaged within the cells ' nucleus as a highly compact chromatin structure ranging between 100-400 nm fibers. The organization and alteration of this structure is mandatory in order to arbitrate DNA-mediated processes of the cell, including transcription, DNA replication, recombination and repair. Many different kinds of enzymes modify chromatin components and, in turn, regulate the accessibility of DNA. These multi-subunited enzymes have emerged as key regulators for several processes of the cell. Central to understanding how DNA-mediated processes are regulated is to comprehend the consequences of these modifications of chromatin, which lead to altered states of either activation or inactivation. One class of factors known to modify chromatin strcture is the A TP-dependent chromatin remodeling enzymes. This class of enzmes encompasses evolutionarily conserved multi-subunited enzymes, which appear to function by using the energy of A TP hydrolysis to disrupt histone-DNA interactions. The prototype of A TP-dependent chromatin remodelers is the Saccharomyces cerevisiae SWI/SNF complex. The yeast SWI/SNF complex is required for the full functioning of several transcriptional activators and for the expression of a subset of yeast genes, a notable number being inducible and mitotic genes. The purified complex is comprised of the following eleven different polypeptides: Swi2p/Snf2p, Swi 1 p, Swi3p, Snf5p, Snf6p, Swp73p, Arp7p, Arp9p, Swp82p, Swp29p and Snf11 p. It has been established that a core of homologous subunits (Swi2p, Swi3p, Swp73p, Snf5p and the Arp proteins) is conserved among the SWI/SNFrelated complexes from several organisms (yRSC , hSWI/SNF , hRSC Drosophila Braha). However, the functional contribution of these polypeptides in the complexes for altering chromatin structure is largely unkown. In this study, biochemistry is used to examine the structure of the complex and function of individual subunits of the yeast SWI/SNF complex to understand better how these proteins are acting in concert to remodel chromatin. In addition, we examine a role for SWI/SNF complex in the process of DNA replication. The relative stoichiometry of the SWI/SNF complex subunits was determined by in vitro biochemical studies. Co-immunoprecipitation has demonstrated that there is only one copy ofSwi2p/Snf2p per complex. Subsequent radioactive labeling of the purified complex revealed that the complex contains one copy of each subunit per complex with the exception of Swi3p and Snf5p, which are present in two copies per complex. The subunit organization of SWI/SNF complex has been more clearly defined by determining direct subunit-subunit interactions in the complex. The Swi3p component has previously been shown to be critical for complex function in vivo and essential for the integrity of the complex in vitro, and this study demonstrates that Swi3p serves as a scaffolding protein that nucleates SWI/SNF complex assembly. In vitro binding studies with Swi3p have revealed that Swi3p displays self-association, as well as direct interactions with the Swi2p, Snf5p, Swp73p, Swilp and Snf6p members of the complex. The direct interactions of the yeast SWI/SNF subunits with transcriptional activators , thought to be important for yeast SWI/SNF targeting, were examined. In vitro binding assays demonstrate that individual SWI/SNF subunits, Snf5p, Snf6p and Swilp, and sub-complexes Swi2p/Swi3p and Swp73p/Swi3p can directly interact with specific domains of transcriptional activators of either the Swi5p zinc-finger DBD or VP 16 acidic activation domain. This work begins to characterize the functional contribution of individual subunits , and cooperative sub-complexes that are critical for the SWI/SNF complex functional activities. The yeast SWI/SNF complex was investigated for the ability to playa role in DNA replication. Interestingly, plasmid stability assays reveal that minichromosomes that contain DNA replication origin ARS121 is weakened when the SWI/SNF complex is non-functional. ARSI21's SWI/SNF dependency is overcome by the over-expression of DNA replication regulatory protein, Cdc6p. Thus , this suggests SWI/SNF may either indirectly effect DNA replication by effecting the expression of Cdc6p, or has a redundant function with Cdc6p. In addition, several crippled derivatives of ARS acquire SWI/SNF dependence , and it is found that the SWI/SNF complex requires a transcriptional activation domain to enhance ARS 1 function. These results reinforce the view that SWI/SNF playa role in two chromatin-mediated processes , transcription and DNA replication.