Gordon Chua

1.  Deciphering transcriptional and posttranscriptional regulatory networks in the fission yeast Schizosaccharomyces pombe.  Proper regulation of gene expression in all cell types in response to external conditions is fundamental for normal growth and development.  Aberrant gene expression as a result of dysregulation is a major cause of numerous complex diseases.  Gene expression is controlled at the transcriptional and posttranscriptional level by specialized nucleic acid-binding proteins that regulate mRNA synthesis, stability, localization and translation.  Our lab is currently working on two distinct research projects utilizing functional genomic approaches to better understand transcriptional and posttranscriptional regulation in the fission yeast model system.  Project 1 aims to decipher the transcriptional-regulatory network in this organism by the identification of signaling pathways and target genes of transcription factors.  Project 2 focuses on the functional characterization of the Pumilio family of posttranscriptional-regulatory proteins by identification of its target mRNAs and interacting proteins.  We are specifically investigating the network interactions between transcription factors/Pumilio proteins and their targets that regulate flocculation and the cell cycle in fission yeast.

2.  Development of an algal-based bioremediation strategy to reduce toxicity of oil sands process-affected water for eventual release into the environment.   The Athabasca Oil Sands represent the third largest oil reserve in the world.  Bitumen is recovered from surface mining of oil sands by alkaline hot water extraction.  This method generates vast amounts of oil sands process-affected water that contain acid-extractable organics such as naphthenic acids known to be toxic to a variety of aquatic and terrestrial organisms.  Due to a zero-discharge policy, the oil sands process-affected water is stored in settling ponds.  Our lab focuses on the characterization of indigenous algae existing in oil sands process-affected water.  Specifically, we are investigating: (1) the identity of algal species and community; (2) the ability of algae to degrade acid-extractable organics including naphthenic acids in oil sands process-affected water and; (3) the ability of stimulated algal growth to reduce toxicity of oil sands process-affected water.  In addition, we are employing a toxicogenomics approach in fission yeast to elucidate the mode-of-action and toxicity of acid-extractable organics.  This research is a collaborative effort with Suncor Energy Inc. and the Canada’s Oil Sands Innovation Alliance (COSIA-Water).

• Google Scholar Link
• Chatfield-Reed, K., Vachon, L., Kwon, E.J. and Chua, G. (2016) Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast. Genetics 202:1365-1675.
• Quesnel, D.M., Oldenburg, T.B., Larter, S.R., Gieg, L.M. and Chua, G. (2015) Biostimulation of Oil Sands Process-Affected Water with Phosphate Yields Removal of Sulfur-Containing Organics and Detoxification. Environ. Sci. Technol. 49:13012-13020.
• Widdup, E.E., Chatfield-Reed, K., Henry, D., Chua, G., Samuel, M.A. and Muench, D.G. (2015) Identification of detoxification pathways in plants that are regulated in response to treatment with organic compounds isolated from oil sands process-affected water. Chemosphere 139:47-53.
• Renaud-Young, M., Lloyd, D.C., Chatfield-Reed, K., George, I., Chua, G. and Cobb, J. (2015) The NuA4 complex promotes translesion synthesis (TLS) mediated DNA damage tolerance. Genetics 199:1065-1076.
• Chua, G. (2013) Systematic genetic analysis of transcription factors to map the fission yeast transcriptional-regulatory network. Biochem. Soc. Trans. 41:1696-1700.
• Vachon, L., Wood, J., Kwon, G., Laderoute, A., Chatfield-Reed, K., Karagiannis, J. and Chua, G. (2013) Functional characterization of fission yeast transcription factors by overexpression analysis. Genetics 194:873-884. 
• Sankaranarayanan, C., Jamshed, M., Deb, S., Chatfield-Reed, K., Kwon, G., Chua, G. and Samuel, M.A. (2013) Deciphering the stigmatic transcriptional landscape of compatible and self-compatible pollinations in Brassica napus reveals a rapid stigma senescence response following compatible pollination. Molecular Plant 6:1988-1991. 
• Leishman, C., Widdup, E., Quesnel, D.M., Chua, G., Gieg, L., Samuel, M.A. and Muench, D.G. (2013) The effect of oil sands process-affected water and naphthenic acids on the germination and development of Arabidopsis. Chemosphere 93:380-387.
• Kwon, G., Laderoute, A., Chatfield-Reed, K., Vachon, L., Karagiannis, J. and Chua, G. (2012) Deciphering the Transcriptional-Regulatory Network of Flocculation in Schizosaccharomyces pombe. PLoS Genetics 8:e1003104. 
• Koch, E.N., Costanzo, M., Bellay, J., Deshpande, R., Chatfield-Reed, K., Chua, G., D'Urso, G., Andrews, B, Boone, C. and Myers, C.L. (2012) Conserved rules govern genetic interaction degree across species. Genome Biol. 13:R57.  
• Quesnel, D.M., Bhaskar, I.M., Gieg, L.M. and Chua, G. (2011) Naphthenic acid biodegradation by the alga Dunaliella tertiolecta. Chemosphere 84:504-511. 
• Chowdhury, S., Lloyd-Price, J., Smolander, O.P., Baici, W.C., Hughes, T.R., Yli-Harja, O., Chua, G. and Ribeiro, A.S. (2010) Information propagation within the genetic network of Saccharomyces cerevisiae. BMC Syst. Biol. 4:143. 
• Chua, G. (2009) Identification of transcription factors by phenotypic activation and microarray profiling in yeast. Methods Mol. Biol. 548:19-35.
• Chan, E.T., Quon, G.T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R.A., Aubin, J., Ratcliffe, M.J., Wilde, A., Brudno, M., Morris, Q.D. and Hughes, T.R. (2009) Conservation of core gene expression in vertebrate tissues. J. Biol. 8:33.
• Kainth P., Sassi H.E., Peña-Castillo L., Chua G., Hughes T.R. and Andrews B. (2009) Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast. Methods 48:258-264.
• Cheung, V., Chua, G., Batada, N., Landry, C.R., Michnick, S.W., Hughes, T.R. and Winston, F. (2008) Evidence that cryptic promoters occur extensively throughout the Saccharomyces cerevisiae genome and express alternative genetic information. PLoS Biol. 6:e277. 
• Dixon, S.J., Fedyshyn, F., Koh, J.L.Y., Prasad, T.S.K., Chahwan, C., Chua, G., Toufighi, K., Baryshnikova, A., Haynes, J., Hoe, K.-L., Kim, D.-U., Park, H.-O., Myers, C.L., Pandey, A., Durocher, D., Andrews, B.J. and Boone, C. (2008) Significant conservation of synthetic lethal genetic interaction networks between distantly-related eukaryotes. PNAS 105:16653-16658.
• Willis, I.M., Chua, G., Tong, A.H., Brost, R.L. Hughes, T.R, Boone, C. and Moir, R.D. (2008) Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. PLoS Genetics 4:e1000112. 
• Rutherford, J.C., Chua, G., Hughes, T., Cardenas, M.E and Heitman, J (2008) A Mep2-dependent transcriptional profile links permease function to gene expression in pseudohyphal growth in Saccharomyces cerevisiae. Mol. Biol. Cell 19:3028-3039. 
• Marcon, E., Babak, T., Chua, G., Hughes, T.R. and Moens, P.B. (2008) miRNA and piRNA localization in the male mammalian meiotic nucleus. Chromosome Res. 16:243-260.
• Huang, J.C., Babak, T., Corson, T.W., Chua, G., Khan, S., Gallie, B.L., Hughes, T.R., Blencowe, B.J., Frey, B.J. and Morris, Q.D. (2007) Using expression profiling data to identify human microRNA targets. Nat. Methods 4:1045-1049.
• Jeronimo, C., Forget, D., Bouchard, A., Li, Q., Chua, G., Poitras, C., Therien, C., Bourassa, S., Greenblatt, J., Chabot, B., Poirier, G., Hughes, T.R., Blanchette, M., Price, D. and Coulombe, B. (2007) Systematic analysis of the protein interaction network for the human transcriptional machinery reveals the identity of the 7SK capping enzyme. Mol. Cell 27:262-274.
• Chua, G., Morris, Q.D., Sopko, R., Robinson, M., Ryan, O., Chan, E.T., Frey, B.J., Andrews, B.J., Boone, C. and Hughes T.R. (2006) Identifying transcription factor functions and targets by phenotypic activation. PNAS 103:12045-12050.Parsons, A.B., Lopez, A., Givoni, I., Williams, D., Gray, C., Porter, J., Chua, G., Sopko, R., Brost, R.L., Ho, C.-H., Wang, J., Ketela, T., Brenner, C., Brill, J.A., Fernandez, J.E., Lorenz, T.C., Payne, G.S., Ishihara, S., Ohya, Y., Andrews, B., Hughes, T.R., Frey, B., Graham, T.R., Andersen, R.J. and Boone, C. (2006) Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell 126:611-625.
• Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Synder, M., Oliver, S., Cyert, M., Hughes, T., Boone, C. and Andrews, B. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21:319-330.
• Alto, N.M., Shao, F., Lazar, C.S., Brost, R.L., Chua, G., Mattoo, S., McMahon, S.A., Ghosh, P., Hughes, T.R., Boone, C. and Dixon, J. (2006) Identification of a bacterial type III effector family with G protein mimicry functions. Cell 124:133-145.
• Chua, G., Robinson, M.D., Morris, Q. and Hughes T.R. (2004) Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr. Opin. Microbiol. 7:638-46.
• Chua, G., Lingner, C., Frazer, C. and Young P.G. (2002) The sal3+ gene encodes an importin-? homologue implicated in the nuclear import of Cdc25 in Schizosaccharomyces pombe. Genetics 162:689-703.
• Chua, G., Taricani, L., Stangle W. and Young P.G. (2000) Insertional mutagenesis based on illegitimate recombination in Schizosaccharomyces pombe. Nucleic Acids Res. 28: E53

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