+ Genomics


We use functional genomics tools to study pathways regulated by signalling and transcriptional enzymes through
assessment of genetic redundancy and sensitivity to increased gene dosage.


Post translational modifications (Sara Sharifpoor, Ji-Young Youn, Wendy Liang)
We perform synthetic lethal or synthetic dosage lethal screens using Synthetic Genetic Array (SGA) technology to study genetic interactions of genes encoding a variety of post-translational modification enzymes (e.g. kinases and lysine deacetylases, also known as KDACs). Using colony size as a read-out, we assess increased or reduced fitness that results from a combination of null, hypomorphic or hyperactive alleles. To examine the effects of dosage, our lab has created a variety of yeast collections that can be used in the SGA platform. We use functional genomics to interrogate important signalling pathways, such as those involving phosphorylation and acetylation. As such, we use a variety of computational and statistical methods to assess fitness using accurate measurements of colony size. Our ultimate goal is to unravel the complexity of complex signalling networks through large-scale analysis of genetic interactions.

Genetic redundancy (Elena Kuzmin)
In collaboration with Dr. Charlie Boone, our lab is also assessing combinatorial mutations (e.g. in double and triple mutants) to look for reduced or increased fitness of strains that can be attributed to perturbation of genes involved in similar processes; a phenomenon called genetic buffering. We are making all pair-wise double mutants using all 6000 genes, to assess the overall level of cellular buffering. We are also making triple mutants to fine-tune the degree of redundancy for highly buffered genes in the genome.

Natural Variation (Pierre Cote)
We are also interested in genetic variation, a property that can be used to predict an individual's susceptibility to certain diseases or reaction to drugs. Therefore, we are mapping natural variation in budding yeast to decipher complex genetic traits. Our ultimate goal is to understand the genetic causes of complex diseases, by studying conserved processes from yeast to man.


+ Phenomics



Our lab is interested in the underlying genome-wide changes that arise in cells under genetic or environmental
conditions, an area of research called phenomics. We use high-throughput cell biological assays to look for either
changes in localization and abundance of proteins or defects in subcellular morphology.

Dynamics of proteinlocalization and abundance (Mike Cox, Ben Grys, Helena Friesen)
High-throughput fluorescence microscopy has become a powerful tool in our lab to look for targets of enzymes (e.g. kinases, KDACs). To this end, we are currently screening for changes in the abundance and subcellular distribution of GFP-tagged proteins. We use Synthetic Genetic Array technology coupled with high-content screening (SGA-HCS) for genome-wide analysis of protein localization and abundance, under a variety of genetic, environmental and chemical perturbations.
Changes in protein abundance and localization drive the cell cycle. To understand the dynamics of these properties, we are quantifying and analyzing the expressed yeast proteome in asynchronous and synchronized cell populations.

 

Sub-cellular morphology- "The marker project" (Erin Styles)
We also aim to use SGA-HCS to detect defects in subcellular morphology that are attributed to a genetic or environmental stimulation. The so called "marker project" aims to explore the underlying cell biological causes of drastic phenotypic outcomes (e.g. lethality), as well as to understand the subtle intracellular changes that arise from a combination of genetic and environmental stresses.



+ Cell Cycle regulated transcription


In eukaryotic cells, cell division is primarily controlled in G1 phase of the cell cycle at a regulatory nexus called the
restriction point or Start. The importance of understanding Start and other cell cycle transitions is underscored
by the observation that perturbations of cell cycle regulators appear to be a universal feature of cancer cells. To get an
overall picture of cell-cycle-dependent transcription we are screening for regulators of every class of cell-cycle-
dependent transcript using Reporter-SGA (R-SGA) and identifying the mechanisms of action through directed experiments
that monitor transcript levels at different stages of the cell cycle.

Reporter-SGA (Henny Goettert, Yvonne Tsao)
Our lab has developed a fluorescent reporter system called Reporter Synthetic Genetic Array (R-SGA) that exploits the tools available in budding yeast to assess consequences of genetic perturbations (e.g. gene deletion) on gene expression. In R-SGA, both a control promoter fused to RFP and a test promoter of interest fused to GFP, are introduced into an array of haploid deletion mutants producing an output array where both reporter genes are combined with each deletion mutant. The resulting panel of yeast deletion mutants is then assayed for enhanced or diminished promoter-GFP expression by scanning both fluorescence intensities directly from colonies arrayed from agar plates using a scanning fluoroimager. So far, our R-SGA project has focused largely on applications of the deletion mutant collection, but we are now extending this approach to overexpression collections.

Mechanisms of cell-cycle transcription (Nazareth Bastajian, Christoph Kurat)
We are exploring novel transcriptional regulators identified from our R-SGA screens that regulate histone promoters during S-phase. In addition, we are interested in mechanisms of cell cycle regulation by two transcription factors, SBF and MBF, which coordinately control expression of a massive group of genes at Start. Studies in both yeast and mammalian cells have clearly shown that the periodic activation of transcription is a cornerstone of cell cycle regulation. We have shown that a novel transcriptional repressor, Whi5, controls transcription at Start, by recruiting lysine deacetylases to repress transcription.