Chromatin structure is a major determinant of eukaryotic gene expression, and the regulation of chromatin is a fundamental step in all dynamic cellular responses. Improper regulation of chromatin leads to developmental defects and human cancers. The overall goal of this project is to understand how dynamic changes in chromatin structure are encoded in a static genome, and determine how these changes are orchestrated in a condition-specific manner. To begin to achieve this goal, we are modeling condition-specific establishment of nucleosome positions by a transcription factor-targeted chromatin remodeling protein. While sequence-specific transcription factors are widely known to recruit and interact with chromatin remodeling machinery, how these interactions regulate nucleosome positioning outcomes is largely undetermined. Recent studies have shown that Ume6-recruited ISW2 complex leads to highly precise motif-proximal nucleosome positioning. The mechanism of these specific chromatin remodeling events will be dissected using a combination of biochemistry and genomics to answer the following three fundamental questions: 1) How does Ume6 interaction with ISW2 lead to motif-proximal nucleosome selection at Ume6 targets. 2) How is the final nucleosome position achieved through Ume6-ISW2 interactions and ISW2 autoregulation. 3) How do motif- proximal nucleosome positions at Ume6 targets affect transcriptional repression. Answering these questions is critical to elucidating how specific chromatin segments are rearranged in a predictable manner, and will provide a conceptual framework through which condition-specific sequence-targeted chromatin remodeling events can be understood.
Interaction of transcription factors with chromatin remodeling proteins is a conserved phenomenon essential for developmental processes and normal cellular function. Mutations in both chromatin remodeling proteins and their transcription factor partners are associated with various disease and cancer states. Elucidating how regulatory interactions between these factors lead to proper chromatin structure in living systems will be a major advance toward understanding mechanisms governing normal and diseased cellular states.