Nucleosome structure has profound implications for DNA-templated processes and modulation of this structure is of critical importance for replication and transcription. Nucleosome structure must be loosened (reorganized) to facilitate polymerase passage and normal structure must be re-established in the wake of the elongating polymerase. Also, nucleosomes must be translated along DNA (remodeled) to allow access to promoter sequences and replication origins. Our goal is to understand the molecular basis for these activities and other important regulatory interactions. Our proposal is organized into three specific Aims, each of which focuses on a different protein or complex:
Spt6 (Aim 1) promotes reformation of normal nucleosome structure following passage of RNA Pol II. It also makes a myriad of functionally important interactions and provides a link between the machineries for RNA transcription and processing. yFACT (Spt16-Pob3) (Aim 2) is a reorganizing complex that restructures nucleosomes to facilitate transcription initiation and passage of elongating RNA Pol II. It also performs an important (presumably equivalent) role in DNA replication.
RSC (Aim 3) is an ATP driven remodeling complex that functions in the expression of numerous genes by mediating nucleosomal translocation. Our approach is highly collaborative and broad. Because our goal is to achieve detailed molecular understanding we will determine relevant structures by x-ray crystallography (Hill, PI). Because we aim to understand processes in a biological context we are exploiting the strengths of yeast genetics (Formosa, co-I;and Cairns, collaborator). The link between structural and in vivo studies is provided by biochemical analysis, which is ongoing in all three labs. Further strength is added by collaboration with an expert in electron microscopy (Andres Leschziner). We have made considerable progress toward the specific aims. Important structures have been determined and informative biochemical and genetic assays developed. Preliminary data indicate that considerable productivity will ensue and also lay the foundation for longer-term goals that carry more risk but also offer potential for high reward

Public Health Relevance

The proteins/complexes Spt6, yFACT, and RSC mediate nucleosome dynamics and other events that regulate gene expression and DNA replication.
We aim to advance understanding of function by a combination of determining relevant three-dimensional structures, biochemistry, and genetic analysis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BCMB-B (02))
Program Officer
Preusch, Peter C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Utah
Schools of Medicine
Salt Lake City
United States
Zip Code
Kemble, David J; McCullough, Laura L; Whitby, Frank G et al. (2015) FACT Disrupts Nucleosome Structure by Binding H2A-H2B with Conserved Peptide Motifs. Mol Cell 60:294-306
Schubert, Heidi L; Wittmeyer, Jacqueline; Kasten, Margaret M et al. (2013) Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A 110:3345-50
Close, Devin; Johnson, Sean J; Sdano, Matthew A et al. (2011) Crystal structures of the S. cerevisiae Spt6 core and C-terminal tandem SH2 domain. J Mol Biol 408:697-713
McDonald, Seth M; Close, Devin; Xin, Hua et al. (2010) Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. Mol Cell 40:725-35
Johnson, Sean J; Close, Devin; Robinson, Howard et al. (2008) Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J Mol Biol 377:1460-73
VanDemark, Andrew P; Kasten, Margaret M; Ferris, Elliott et al. (2007) Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell 27:817-28
VanDemark, Andrew P; Blanksma, Mary; Ferris, Elliott et al. (2006) The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol Cell 22:363-74