David J. Stillman, PhD
- Gene Expression Regulation
- Gene Regulation
- Departments: Pathology - Professor Emeritus
- Divisions: Microbiology and Immunology
Dr. Stillman’s laboratory asks questions in three distinct areas of transcriptional regulation.
Promoter specificity of transcriptional factors. Specific gene expression is controlled by transcription factors binding to elements present in promoters and enhancers. Yeast has two transcription factors, Swi5 and Ace2, that show similar patterns of cell cycle regulation, that have nearly identical zinc finger DNA-binding domains, and recognize the same DNA sequences in vitro. Despite these similarities, Swi5 and Ace2 activate transcription of different genes in vivo. We have used DNA Microarrays to identify genes activated by Swi5 and Ace2, and we have combined Chromatin Immunoprecipitations with Promoter Microarrays to identify which genes these proteins bind to in vivo. There are some genes where only Swi5 binds and activates in vivo, although Ace2 can bind in vitro, and for these genes promoter specificity is determined by mechanisms that control factor binding. Experiments are in progress to determine how chromatin structure can prevent one factor from binding while allowing another protein, with the same DNA-binding domain, to bind. Both Swi5 and Ace2 bind to other promoters in vivo, but only Ace2 is able to actually activate transcription of these genes; thus, Swi5 binds to the promoter but fails to activate. We have shown the Fkh proteins bound to these promoter function as a selective “anti-activator,” blocking Swi5 from activating transcription while Ace2 to activate. Current experiments are studying how the Fkh protein function as selective anti-activators. These studies are quite relevant to mammalian gene regulation, because in many cases it has been shown that multiple transcription factors recognize the same sequence, but that simple DNA-binding at a promoter is not sufficient for gene activation in vivo.
Regulation of the Yeast HO gene. The transcriptional regulation of the HO gene is very complex, and has been a prototypic promoter where changes in chromatin structure regulate gene expression. Chromatin Immunoprecipitation experiments show that transcriptional activation of HO involves the sequential binding of various factors, both sequence specific DNA-binding factors and general chromatin factors such as chromatin remodeling factors, histone acetyltransferase complexes, architectural transcription factors, and the Mediator complex. The Swi5 DNA-binding protein is the earliest factor that binds to the HO promoter, and it then recruits other regulatory complexes that remain stably bind long after the unstable Swi5 factor is degraded. Importantly, one can experimentally extend the time between when Swi5 was last bound and when the gene is activated, and the promoter “remembers” the actions of the Swi5 activator. Thus the HO promoter has been described as having a “memory,” and current experiments are defining this molecularly.
yFACT in transcriptional regulation. We are studying the role of yFACT in regulating gene expression in collaboration with Tim Formosa’s laboratory. In addtion to the previously described roles in transcriptional elongation and for replication. We have shown a role for yFACT in regulating transcriptional initiation at the level of stimulating binding of the basal transcription factors TBP and TFIIA to promoters. We also show that the yFACT works in opposition to two chromatin modifying factors, the Chd1 chromodomain protein and the Set2 histone methyl transferase.
|Postdoctoral Fellowship||MRC Laboratory of Molecular Biology
|Doctoral Training||University of California, San Diego
|Undergraduate||University of California, Berkeley
|Postdoctoral Fellowship||MRC Laboratory of Molecular Biology
|Postdoctoral Fellow||United Kingdom|
- Parnell EJ, Stillman DJ (2019). Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to the HO Promoter in Saccharomyces cerevisiae. Genetics, 212(4), 1181-1204.
- McCullough LL, Pham TH, Parnell TJ, Connell Z, Chandrasekharan MB, Stillman DJ, Formosa T (2019). Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae. Genetics, 211(3), 877-892.
- Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, Bell R, Delgado JC, Cox J, Voth W, Brown J, Stillman DJ, OConnell RM, Tebo AE, Round JL (2017). A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med, 9(380).
- Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ (2016). Disruption of promoter memory by synthesis of a long noncoding RNA. Proc Natl Acad Sci U S A, 113(34), 9575-80.
- Yarrington RM, Goodrum JM, Stillman DJ (2016). Nucleosomes Are Essential for Proper Regulation of a Multigated Promoter in Saccharomyces cerevisiae. Genetics, 202(2), 551-63.
- Yarrington RM, Rudd JS, Stillman DJ (2015). Spatiotemporal cascade of transcription factor binding required for promoter activation. Mol Cell Biol, 35(4), 688-98.
- Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, Stillman DJ (2014). The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor. J Biol Chem, 289(51), 35431-7.
- Zapata J, Dephoure N, Macdonough T, Yu Y, Parnell EJ, Mooring M, Gygi SP, Stillman DJ, Kellogg DR (2014). PP2ARts1 is a master regulator of pathways that control cell size. J Cell Biol, 204(3), 359-76.
- Voth WP, Takahata S, Nishikawa JL, Metcalfe BM, Nr AM, Stillman DJ (2014). A role for FACT in repopulation of nucleosomes at inducible genes. PLoS One, 9(1), e84092.
- Stillman DJ (2013). Dancing the cell cycle two-step: regulation of yeast G1-cell-cycle genes by chromatin structure. Trends Biochem Sci, 38(9), 467-75.
- Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, Bai L (2013). Stochastic expression and epigenetic memory at the yeast HO promoter. Proc Natl Acad Sci U S A, 110(34), 14012-7.
- Takahata S, Yu Y, Stillman DJ (2011). Repressive chromatin affects factor binding at yeast HO (homothallic switching) promoter. J Biol Chem, 286(40), 34809-19.
- McCullough L, Rawlins R, Olsen A, Xin H, Stillman DJ, Formosa T (2011). Insight into the mechanism of nucleosome reorganization from histone mutants that suppress defects in the FACT histone chaperone. Genetics, 188(4), 835-46.
- Takahata S, Yu Y, Stillman DJ (2009). The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters. EMBO J, 28(21), 3378-89.
- Takahata S, Yu Y, Stillman DJ (2009). FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter. Mol Cell, 34(4), 405-15.
- Biswas D, Takahata S, Stillman DJ (2008). Different genetic functions for the Rpd3(L) and Rpd3(S) complexes suggest competition between NuA4 and Rpd3(S). Mol Cell Biol, 28(14), 4445-58.
- Voth WP, Yu Y, Takahata S, Kretschmann KL, Lieb JD, Parker RL, Milash B, Stillman DJ (2007). Forkhead proteins control the outcome of transcription factor binding by antiactivation. EMBO J, 26(20), 4324-34.
- Biswas D, Dutta-Biswas R, Stillman DJ (2007). Chd1 and yFACT act in opposition in regulating transcription. Mol Cell Biol, 27(18), 6279-87.
- Biswas D, Dutta-Biswas R, Mitra D, Shibata Y, Strahl BD, Formosa T, Stillman DJ (2006). Opposing roles for Set2 and yFACT in regulating TBP binding at promoters. EMBO J, 25(19), 4479-89.
- Mitra D, Parnell EJ, Landon JW, Yu Y, Stillman DJ (2006). SWI/SNF binding to the HO promoter requires histone acetylation and stimulates TATA-binding protein recruitment. Mol Cell Biol, 26(11), 4095-110.
- Biswas D, Yu Y, Prall M, Formosa T, Stillman DJ (2005). The yeast FACT complex has a role in transcriptional initiation. Mol Cell Biol, 25(14), 5812-22.
- Biswas D, Imbalzano AN, Eriksson P, Yu Y, Stillman DJ (2004). Role for Nhp6, Gcn5, and the Swi/Snf complex in stimulating formation of the TATA-binding protein-TFIIA-DNA complex. Mol Cell Biol, 24(18), 8312-21.
- Eriksson P, Biswas D, Yu Y, Stewart JM, Stillman DJ (2004). TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein. Mol Cell Biol, 24(14), 6419-29.
- Formosa T, Ruone S, Adams MD, Olsen AE, Eriksson P, Yu Y, Rhoades AR, Kaufman PD, Stillman DJ (2002). Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure. Genetics, 162(4), 1557-71.
- Bhoite LT, Yu Y, Stillman DJ (2001). The Swi5 activator recruits the Mediator complex to the HO promoter without RNA polymerase II. Genes Dev, 15(18), 2457-69.
- Formosa T, Eriksson P, Wittmeyer J, Ginn J, Yu Y, Stillman DJ (2001). Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J, 20(13), 3506-17.
- A.W. Meikle, D.J. Stillman, J.M. Orrock, A.H. Terry and T.M. Sandrock (2004). Methods and Compositions for Assaying and Identifying Ligands for Nuclear Hormone Receptors.