Large eukaryotic genomes must be packaged as chromatin to keep them organized and stable, but this generally inhibits accessibility to the DNA. Controlling transcription and DMA replication therefore requires the ability to selectively overcome this chromatin barrier. We have identified a factor called yFACT in yeast cells that uses a novel mechanism to diminish the inhibitory effects of chromatin. Unlike the better- characterized remodeling factors that use energy derived from ATP hydrolysis to reposition nucleosomes, yFACT changes the structure of individual nucleosomes without hydrolysing ATP or changing the location of the nucleosomes. We call this novel mechanism """"""""nucleosome reorganization"""""""" to distinguish it from remodeling. yFACT is required for both transcription and replication. The goal of this proposal is to analyze the mechanism of nucleosome reorganization and to determine how this reorganizing activity participates in a variety of distinct steps in transcription and replication in living yeast cells. yFACT must interact with many different proteins to accomplish these diverse functions.
The first aim of the proposal is to better characterize the interaction between yFACT and 2 of its known partners, RPA and histones, and then to determine how this binding contributes to the range of yFACT functions. RPA is a key factor in DNA replication and histones compose the protein core of nucleosomes, so these interactions are likely to be central to the diverse functions of yFACT. Models for how these interactions contribute to replication, repair, and transcription are proposed and tested.
The second aim i s to better characterize the mechanism of nucleosome reorganization using purified components. The reorganized state will be probed using nucleases, the stability of reorganized nucleosomes will be tested, and the proximity of components to one another will be mapped. Finally, chromatin immunoprecipitation, tests of genetic stability, and 2-D gels will be used to address how mutations in yFACT components affect key intermediates in transcription and replication in living cells. The ability to make accurate copies of DNA, either as RNA to allow normal cellular metabolism or as DNA for segregation to progeny, is fundamentally important. yFACT is a vital and novel component of both processes, so studying it provides insight into several distinct central pathways simultaneously. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM064649-05A1
Application #
7148488
Study Section
Molecular Genetics A Study Section (MGA)
Program Officer
Carter, Anthony D
Project Start
2002-03-01
Project End
2010-06-30
Budget Start
2006-07-01
Budget End
2007-06-30
Support Year
5
Fiscal Year
2006
Total Cost
$310,213
Indirect Cost
Name
University of Utah
Department
Biochemistry
Type
Schools of Medicine
DUNS #
009095365
City
Salt Lake City
State
UT
Country
United States
Zip Code
84112
McCullough, Laura L; Connell, Zaily; Xin, Hua et al. (2018) Functional roles of the DNA-binding HMGB domain in the histone chaperone FACT in nucleosome reorganization. J Biol Chem 293:6121-6133
Shen, Zuolian; Formosa, Tim; Tantin, Dean (2018) FACT Inhibition Blocks Induction But Not Maintenance of Pluripotency. Stem Cells Dev 27:1693-1701
Sdano, Matthew A; Fulcher, James M; Palani, Sowmiya et al. (2017) A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. Elife 6:
Valieva, Maria E; Armeev, Grigoriy A; Kudryashova, Kseniya S et al. (2016) Large-scale ATP-independent nucleosome unfolding by a histone chaperone. Nat Struct Mol Biol 23:1111-1116
McCullough, Laura; Connell, Zaily; Petersen, Charisse et al. (2015) The Abundant Histone Chaperones Spt6 and FACT Collaborate to Assemble, Inspect, and Maintain Chromatin Structure in Saccharomyces cerevisiae. Genetics 201:1031-45
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
Voth, Warren P; Takahata, Shinya; Nishikawa, Joy L et al. (2014) A role for FACT in repopulation of nucleosomes at inducible genes. PLoS One 9:e84092
Kemble, David J; Whitby, Frank G; Robinson, Howard et al. (2013) Structure of the Spt16 middle domain reveals functional features of the histone chaperone FACT. J Biol Chem 288:10188-94
McCullough, Laura; Poe, Bryan; Connell, Zaily et al. (2013) The FACT histone chaperone guides histone H4 into its nucleosomal conformation in Saccharomyces cerevisiae. Genetics 195:101-13
Formosa, Tim (2012) The role of FACT in making and breaking nucleosomes. Biochim Biophys Acta 1819:247-55

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