Office: Mrb 111
Phone: (970) 491-5068
- Ph.D., University of Rochester
Our research is focused on investigating the regulation of gene expression using budding yeast, S. cerevisiae, as a model system and genetic, genomic, molecular and biochemical approaches. Our work began with studies on the basic machinery for RNA Polymerase II (RNAPII) transcription and has evolved due to a growing appreciation for the chromatin context in which our in vivo studies are performed. The long-term overall goal of our research is to understand how the transcription machinery interfaces with chromatin to regulate gene expression in living cells, and can be divided into two main areas: one stemming from our work on inactive/poised RNAPII complexes and the other on transitions in chromatin states during activation.
Inactive/poised RNAPII complexes.
The initial discovery of RNAPII bound at genes prior to their transcriptional activation occurred a quarter century ago in Drosophila. The preloading of these "poised" complexes in an inactive state is now apparent in many different organisms (yeast, flies, humans) and occurs at a diverse set of genes. We have been characterizing the poised S. cerevisiae CYC1 gene during the inactive to active transition, and find that a multitude of coactivators and chromatin remodeling complexes are essential for this transition. Intriguingly, these same factors play critical roles in pausing of RNAPII in metazoan cells, suggesting that there are universal requirements in the transition of RNAPII from a poised to an actively elongating state.
Transitions in chromatin states during activation in vivo.
RNAPII and the general transcription machinery have restricted access to genes since the eukaroytic genome is assembled and compacted into nucleosomes. The nucleosome is the basic repeating unit of chromatin and consists of 147 base pairs of DNA wrapped around an octamer of four core histones (H2A, H2B, H3 and H4). Histones and additional chromatin architectural proteins cooperate to compact chromosomal DNA 500,000-fold to fit into the cell nucleus. Therein lies the conundrum: genetic material must be organized and compacted while remaining accessible for critical biological functions, like transcription. We are characterizing a collection of cellular factors that actively participate in altering this balance to achieve the necessary outcome. These factors include histone chaperones (proteins that function to assemble and disassemble nucleosomes), and histone acetyltransferases (enzymes that modify the histones covalently).
Biochemistry is Elementary outreach program.
"The scientists are coming!" can be heard echoing down the halls of the elementary school. As part of our work involving yeast genetics, and in collaboration with Dr. Eric Ross (BMB/CSU), we have partnered with fifth graders and their teachers in a novel outreach program. We have created and implemented a highly successful program with seven separate sessions involving hands-on activities designed to introduce genetics and biochemistry to fifth graders. Due to the inexpensive and biologically safe reagents and the detailed instructions and workbooks we have created, many scientists could offer something similar to their local community if interested in achieving broader impact.
- Genome Instability Is Promoted by the Chromatin-Binding Protein Spn1 in Saccharomyces cerevisiae. Genetics, 4, 2018.
- Regulation of Gene Expression Using Lac Z Reporter Gene: Expression of Gal 4-Activater Galactose Metabolism Genes with TATA/CATA Variant Elements at the Core Promoter in Saccaromyces cerevisiae Proceedings of the Association for Biology Laboratory Education Volume 39, Article 79, 2018, 79, 2018.
- The elongation factor Spn1 is a multi-functional chromatin binding protein. Nucleic acids research, 5, 2018.
- The elongation factor Spn1 is a multi-functional chromatin binding protein. Nucleic acids research, 2017.
- DNA-mediated association of two histone-bound complexes of yeast Chromatin Assembly Factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication. eLife, 2017.
- DNA-mediated association of two histone-bound CAF-1 complexes drives tetrasome assembly in the wake of DNA replication eLIFE.
- Histone Chaperone Nap1 Is a Major Regulator of Histone H2A-H2B Dynamics at the Inducible GAL Locus. Molecular and cellular biology, 8, 2016.
- Utilizing targeted mass spectrometry to demonstrate Asf1-dependent increases in residue specificity for Rtt109-Vps75 mediated histone acetylation. PloS one, 3, 2015.
- The head module of Mediator directs activation of preloaded RNAPII in vivo. Nucleic acids research, 22, 2013.
- Chaperone Nap1 shields histone surfaces used in a nucleosome and can put H2A-H2B in an unconventional tetrameric form. Molecular cell, 5, 2013.
- An integrated biochemistry and genetics outreach program designed for elementary school students Genetics, 2, 2012.
- The Transition of Poised RNA Polymerase II to an Actively Elongating State Is a "Complex" Affair. Genetics research international, 2011.
- The transcription factor Spn1 regulates gene expression via a highly conserved novel structural motif. Journal of molecular biology, 1, 2010.
- Histone chaperones, histone acetylation, and the fluidity of the chromogenome. Journal of cellular physiology, 2, 2010.
- The histone chaperone Nap1 promotes nucleosome assembly by eliminating nonnucleosomal histone DNA interactions. Molecular cell, 6, 2010.
- Activation of a poised RNAPII-dependent promoter requires both SAGA and mediator. Genetics, 3, 2010.
- Histone chaperone specificity in Rtt109 activation. Nature structural & molecular biology, 9, 2008.
- Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II. Molecular and cellular biology, 4, 2008.
- Non-optimal TATA elements exhibit diverse mechanistic consequences. The Journal of biological chemistry, 32, 2006.
- TFIIA plays a role in the response to oxidative stress. Eukaryotic cell, 7, 2006.
- Mapping and functional characterization of the TAF11 interaction with TFIIA. Molecular and cellular biology, 3, 2005.
- Protein-protein interaction map for yeast TFIID. Nucleic acids research, 4, 2003.
- SPN1, a conserved gene identified by suppression of a postrecruitment-defective yeast TATA-binding protein mutant. Genetics, 4, 2002.
- The stability of the TFIIA-TBP-DNA complex is dependent on the sequence of the TATAAA element. The Journal of biological chemistry, 32, 2001.
- Transcriptional activity of the TFIIA four-helix bundle in vivo. Proteins, 2, 2001.
- TFIIA interacts with TFIID via association with TATA-binding protein and TAF40. Molecular and cellular biology, 5, 2001.
- TFIIA has activator-dependent and core promoter functions in vivo. The Journal of biological chemistry, 17, 2000.
- Reevaluation of transcriptional regulation by TATA-binding protein oligomerization: predominance of monomers. Biochemistry, 10, 2000.
- Evolutionary stable strategy: a test for theories of retroviral pathology which are based upon the concept of molecular mimicry. Journal of theoretical biology, 3, 2000.
- A TATA-binding protein mutant defective for TFIID complex formation in vivo. Molecular and cellular biology, 6, 1999.
- Molecular interactions between the coactivator CBP and the human T-cell leukemia virus Tax protein. Journal of molecular biology, 3, 1998.
- A new class of activation-defective TATA-binding protein mutants: evidence for two steps of transcriptional activation in vivo. Molecular and cellular biology, 8, 1996.
- Mechanisms of transcriptional activation in vivo: two steps forward. Trends in genetics : TIG, 8, 1996.
- Gene-specific signal transduction between microtubules and tubulin genes in Tetrahymena thermophila. Molecular and cellular biology, 9, 1995.
- The TBP-TFIIA interaction in the response to acidic activators in vivo. Science (New York, N.Y.), 5220, 1995.
- Conserved and nonconserved functions of the yeast and human TATA-binding proteins. Genes & development, 11, 1994.
- TATA-binding protein and nuclear differentiation in Tetrahymena thermophila. Molecular and cellular biology, 1, 1994.
- Temporal and spatial association of histone H2A variant hv1 with transcriptionally competent chromatin during nuclear development in Tetrahymena thermophila. Genes & development, 12B, 1993.
- Drugs affecting microtubule dynamics increase alpha-tubulin mRNA accumulation via transcription in Tetrahymena thermophila. Molecular and cellular biology, 4, 1992.
- Cell-cell interactions trigger the rapid induction of a specific high mobility group-like protein during early stages of conjugation in Tetrahymena. Developmental biology, 2, 1991.
- Transcriptional regulation of gene expression in Tetrahymena thermophila. Nucleic acids research, 22, 1990.