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Tim Formosa

Professor of Biochemistry

Tim Formosa

B.S. University of California, Davis

Ph.D. University of California, San Francisco

Research

References

tim@biochem.utah.edu

Tim Formosa's Lab Page

Tim Formosa's PubMed Literature Search

 

Molecular Biology Program

Biological Chemistry Program

Chromatin in DNA Replication

Research

We use yeast to study a highly conserved complex called FACT, which reorganizes nucleosomes and therefore alters the fundamental structure of chromatin. FACT is essential in all eukaryotes, but the nature of its effects on nucleosomes remains poorly understood. We use genetics to ask which processes in living cells make use of FACT, and biochemistry with purified proteins to determine the mechanism of FACT function. In addition, we collaborate with Chris Hill's lab to use X-ray crystallography to probe the structure of reorganized nucleosomes and the FACT complex. This combination of methods takes full advantage of the powerful tools provided by the yeast model system, and provides training in a range of modern methods extending from traditional genetics and biochemistry to bioinformatics.

FACT is a histone chaperone that participates in a broad range of steps in transcription and DNA replication. It promotes transitions between stable and unstable forms of nucleosomes, making it potentially useful both for opening chromatin to allow accessibility and for depositing nucleosomes after they are disrupted or after the DNA is duplicated. The integrity of the chromatin barrier is an essential feature of genomic stability and regulated gene expression, so the processes that FACT promotes affect several fundamentally important processes that remain poorly understood. For example, although several histone chaperones are known to contribute to the deposition of nucleosomes after DNA replication, the mechanism of chromatin formation during this process remains unknown. The role of FACT in forming and maintaining the chromatin barrier is therefore of high interest. Biochemistry tells us how proteins and DNA behave in isolation, but it cannot tell us what is important about their functions in cells.  Genetics tells us what is important about cellular processes, but provides little specific information about mechanisms.  Using biochemistry and genetics together is therefore synergistic and allows insights to be gained into the fundamental workings of cells. We are using this balanced approach to explore the function of FACT in mediating transcription and replication.

Other projects in the lab use the same approaches to study other transcription factors with an emphasis on other histone chaperones like Spt6, with the goal of determining how these chaperones collaborate to maintain chromatin. We also study the role of the proteasome in regulating cellular function, with an emphasis on understanding an emerging connection between proteasomes and the stability of mitochondrial genomes.

Tim Formosa Figure

References

  1. McCullough, L., B. Poe, Z. Connell, H. Xin, and T. Formosa, The FACT Histone Chaperone Guides Histone H4 Into Its Nucleosomal Conformation in Saccharomyces cerevisiae. Genetics, 2013. 195(1): p. 101-113.
  2. Kemble, D.J., F.G. Whitby, H. Robinson, L.L. McCullough, T. Formosa, and C.P. Hill, Structure of the Spt16 Middle Domain Reveals Functional Features of the Histone Chaperone FACT. J Biol Chem, 2013. 288(15): p. 10188-94.
  3. Stadtmueller, B.M., E. Kish-Trier, K. Ferrell, C.N. Petersen, H. Robinson, D.G. Myszka, D.M. Eckert, T. Formosa, and C.P. Hill, Structure of a proteasome Pba1-Pba2 complex: implications for proteasome assembly, activation, and biological function. J Biol Chem, 2012. 287(44): p. 37371-37382.
  4. Formosa, T., The role of FACT in making and breaking nucleosomes. Biochim Biophys Acta, 2012. 1819(3-4): p. 247-255.
  5. McCullough, L., R. Rawlins, A.E. Olsen, H. Xin, D.J. Stillman, and T. Formosa, Insight into the Mechanism of Nucleosome Reorganization from Histone Mutants that Suppress Defects in the FACT Histone Chaperone. Genetics, 2011. 188(4):p. 835-846.
  6. Close, D., S.J. Johnson, M.A. Sdano, S.M. McDonald, H. Robinson, T. Formosa, and C.P. Hill, Crystal Structures of the S. cerevisiae Spt6 Core and C-Terminal Tandem SH2 Domain. J Mol Biol, 2011. 408(4): p. 697-713.
  7. Sadre-Bazzaz, K., F.G. Whitby, H. Robinson, T. Formosa, and C.P. Hill, Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening. Mol Cell, 2010. 37(5): p. 728-735.
  8. McDonald, S.M., D. Close, H. Xin, T. Formosa, and C.P. Hill, Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. Mol Cell, 2010. 40(5): p. 725-35.
  9. Han, J., Q. Li, L. McCullough, C. Kettelkamp, T. Formosa, and Z. Zhang, Ubiquitylation of FACT by the cullin-E3 ligase Rtt101 connects FACT to DNA replication. Genes Dev, 2010. 24(14): p. 1485-1490.
  10. Sadre-Bazzaz, K., F.G. Whitby, H. Robinson, T. Formosa, and C.P. Hill, Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening. Mol Cell, 2010. 37(5): p. 728-735.
  11. Xin, H., S. Takahata, M. Blanksma, L. McCullough, D.J. Stillman, and T. Formosa, yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement. Mol Cell, 2009. 35(3): p. 365-376.
  12. Vandemark, A.P., H. Xin, L. McCullough, R. Rawlins, S. Bentley, A. Heroux, D.J. Stillman, C.P. Hill, and T. Formosa, Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits. J Biol Chem, 2008. 283(8): p. 5058-5068.
  13. Biswas, D., R. Dutta-Biswas, D. Mitra, Y. Shibata, B.D. Strahl, T. Formosa, and D.J. Stillman, Opposing roles for Set2 and yFACT in regulating TBP binding at promoters. Embo J, 2006. 25(19): p. 4479-4489.
  14. VanDemark, A.P., M. Blanksma, E. Ferris, A. Heroux, C.P. Hill, and T. Formosa, 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, 2006. 22(3): p. 363-374.
  15. Rhoades, A.R., S. Ruone, and T. Formosa, Structural Features of Nucleosomes Reorganized by Yeast FACT and Its HMG Box Component, Nhp6. Mol Cell Biol, 2004. 24(9): p. 3907-3917.

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Last Updated: 11/2/16