Gordon Chua

Exploration of Essential Gene Functions via Titratable Promoter Alleles

Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and subjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.

Using expression profiling data to identify human microRNA targets

We demonstrate that paired expression profiles of microRNAs (miRNAs) and mRNAs can be used to identify functional miRNA-target relationships with high precision. We used a Bayesian data analysis algorithm, GenMiR++, to identify a network of 1,597 high-confidence target predictions for 104 human miRNAs, which was supported by RNA expression data across 88 tissues and cell types, sequence complementarity and comparative genomics data. We experimentally verified our predictions by investigating the result of let-7b downregulation in retinoblastoma using quantitative reverse transcriptase (RT)-PCR and microarray profiling: some of our verified let-7b targets include CDC25A and BCL7A. Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels.

Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome

Previous studies in Saccharomyces cerevisiae have demonstrated that cryptic promoters within coding regions activate transcription in particular mutants. We have performed a comprehensive analysis of cryptic transcription in order to identify factors that normally repress cryptic promoters, to determine the amount of cryptic transcription genome-wide, and to study the potential for expression of genetic information by cryptic transcription. Our results show that a large number of factors that control chromatin structure and transcription are required to repress cryptic transcription from at least 1,000 locations across the S. cerevisiae genome. Two results suggest that some cryptic transcripts are translated. First, as expected, many cryptic transcripts contain an ATG and an open reading frame of at least 100 codons. Second, several cryptic transcripts are translated into proteins. Furthermore, a subset of cryptic transcripts tested is transiently induced in wild-type cells following a nutritional shift, suggesting a possible physiological role in response to a change in growth conditions. Taken together, our results demonstrate that, during normal growth, the global integrity of gene expression is maintained by a wide range of factors and suggest that, under altered genetic or physiological conditions, the expression of alternative genetic information may occur.

Identifying transcription factor functions and targets by phenotypic activation

Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes and pathways induced by individual TFs that does not require knowledge of their normal activation cues. Microarray analysis of 55 yeast TFs that caused a growth phenotype when overexpressed showed that the majority caused increased transcript levels of genes in specific physiological categories, suggesting a mechanism for growth inhibition. Induced genes typically included established targets and genes with consensus promoter motifs, if known, indicating that these data are useful for identifying potential new target genes and binding sites. We identified the sequence 5′-TCACGCAA as a binding sequence for Hms1p, a TF that positively regulates pseudohyphal growth and previously had no known motif. The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology.

Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes

Synthetic lethal genetic interaction networks define genes that work together to control essential functions and have been studied extensively in Saccharomyces cerevisiae using the synthetic genetic array (SGA) analysis technique (ScSGA). The extent to which synthetic lethal or other genetic interaction networks are conserved between species remains uncertain. To address this question, we compared literature-curated and experimentally derived genetic interaction networks for two distantly related yeasts, Schizosaccharomyces pombe and S. cerevisiae. We find that 23% of interactions in a novel, high-quality S. pombe literature-curated network are conserved in the existing S. cerevisiae network. Next, we developed a method, called S. pombe SGA analysis (SpSGA), enabling rapid, high-throughput isolation of genetic interactions in this species. Direct comparison by SpSGA and ScSGA of ∼220 genes involved in DNA replication, the DNA damage response, chromatin remodeling, intracellular transport, and other processes revealed that ∼29% of genetic interactions are common to both species, with the remainder exhibiting unique, species-specific patterns of genetic connectivity. We define a conserved yeast network (CYN) composed of 106 genes and 144 interactions and suggest that this network may help understand the shared biology of diverse eukaryotic species.

miRNA and piRNA localization in the male mammalian meiotic nucleus

During mammalian meiosis, transcriptional silencing of the XY bivalent is a necessary event where defects may lead to infertility in males. While not well understood, the mechanism of meiotic gene silencing is believed to be RNA-dependent. In this study, we investigated the types and localization of non-coding RNAs in the meiotic nucleus of the male mouse using a microarray screen with different cell isolates as well as FISH. We report that the dense body, a component of the murine spermatocyte sex body similar to that of a dense body in Chinese hamster spermatocytes, is DNA-negative but rich in proteins and RNA including miRNAs (micro RNAs) and piRNAs (PIWI associated small RNAs), or their precursors. Selective miRNAs and piRNAs localize to chromosome cores, telomeres and the sex body of spermatocytes. These RNAs have not previously been detected in meiotic nuclei. These RNAs appear to associate with the nucleolus of the Sertoli cells as well as with the dense body. While in MIWI-null male mice the nucleolar signal from miRNA and piRNA probes in Sertoli cells is largely diminished, a differential regulation must exist in meiotic nuclei since the localization of these two components appears to be unaffected in the null animal.

Naphthenic acid biodegradation by the unicellular alga Dunaliella tertiolecta.

Naphthenic acids (NAs) are a major contributor to toxicity in tailings waste generated from bitumen production in the Athabasca Oil Sands region. While investigations have shown that bacteria can biodegrade NAs and reduce tailings toxicity, the potential of algae to biodegrade NAs and the biochemical mechanisms involved remain poorly understood. Here, we discovered that the marine alga Dunaliella tertiolecta is able to tolerate five model NAs (cyclohexanecarboxylic acid, cyclohexaneacetic acid, cyclohexanepropionic acid, cyclohexanebutyric acid and 1,2,3,4-tetrahydro-2-naphthoic acid) at 300mgL(-1), a level which exceeds that of any single or combination of NAs typically found in tailings ponds. Moreover, we show that D. tertiolecta can metabolize four of the model NAs. Analysis of NA-amended cultures of D. tertiolecta via low resolution gas chromatography-mass spectrometry allowed us to quantify decreasing NA levels, identify metabolites, and formulate putative mechanisms of biodegradation. Degradation of cyclohexanebutyric acid and cyclohexanepropionic acid proceeded via β-oxidation and resulted in the transient accumulation of cyclohexaneacetic acid and cyclohexanecarboxylic acid, respectively. Cyclohexanecarboxylic acid was metabolized via 1-cyclohexenecarboxylic acid suggesting that further degradation may occur by step-wise β-oxidation. When D. tertiolecta was inoculated in the presence of oil sands tailings water from the Athabasca region, biodegradation of single-ring NAs was observed relative to controls. This result corroborates the trend we observed with the single-ring model NAs.

A Mep2-dependent Transcriptional Profile Links Permease Function to Gene Expression during Pseudohyphal Growth in Saccharomyces cerevisiae

The ammonium permease Mep2 is required for the induction of pseudohyphal growth, a process in Saccharomyces cerevisiae that occurs in response to nutrient limitation. Mep2 has both a transport and a regulatory function, supporting models in which Mep2 acts as a sensor of ammonium availability. Potentially similar ammonium permease-dependent regulatory cascades operate in other fungi, and they may also function in animals via the homologous Rh proteins; however, little is known about the molecular mechanisms that mediate ammonium sensing. We show that Mep2 is localized to the cell surface during pseudohyphal growth, and it is required for both filamentous and invasive growth. Analysis of site-directed Mep2 mutants in residues lining the ammonia-conducting channel reveal separation of function alleles (transport and signaling defective; transport-proficient/signaling defective), indicating transport is necessary but not sufficient to sense ammonia. Furthermore, Mep2 overexpression enhances differentiation under normally repressive conditions and induces a transcriptional profile that is consistent with activation of the mitogen-activated protein (MAP) kinase pathway. This finding is supported by epistasis analysis establishing that the known role of the MAP kinase pathway in pseudohyphal growth is linked to Mep2 function. Together, these data strengthen the model that Mep2-like proteins are nutrient sensing transceptors that govern cellular differentiation.

Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast.

The development and application of genomic reagents and techniques has fuelled progress in our understanding of regulatory networks that control gene expression in eukaryotic cells. However, a full description of the network of regulator-gene interactions that determine global gene expression programs remains elusive and will require systematic genetic as well as biochemical assays. Here, we describe a functional genomics approach that combines reporter technology, genome-wide array-based reagents and high-throughput imaging to discover new regulators controlling gene expression patterns in Saccharomyces cerevisiae. Our strategy utilizes the synthetic genetic array (SGA) method to systematically introduce promoter-GFP (green fluorescent protein) reporter constructs along with a control promoter-RFP (red fluorescent protein) gene into the array of approximately 4500 viable yeast deletion mutants. Fluorescence intensities from each reporter are assayed from individual colonies arrayed on solid agar plates using a scanning fluorimager and the ratio of GFP to RFP intensity reveals deletion mutants that cause differential GFP expression. We are exploiting this screening approach to construct a detailed map describing the interplay of regulators controlling the eukaryotic cell cycle. The method is extensible to any transcription factor or signalling pathway for which an appropriate reporter gene can be devised.

The effect of oil sands process-affected water and naphthenic acids on the germination and development of Arabidopsis

Oil sands mining in the Athabasca region of northern Alberta results in the production of large volumes of oil sands process-affected water (OSPW). We have evaluated the effects of OSPW, the acid extractable organic (AEO) fraction of OSPW, and individual naphthenic acids (NAs) on the germination and development of the model plant, Arabidopsis thaliana (Arabidopsis). The surrogate NAs that were selected for this study were petroleum NAs that have been used in previous toxicology studies and may not represent OSPW NAs. A tricyclic diamondoid NA that was recently identified as a component of OSPW served as a model NA in this study. Germination of Arabidopsis seeds was not inhibited when grown on medium containing up to 75% OSPW or by 50mgL(-1) AEO. However, simultaneous exposure to three simple, single-ringed surrogate NAs or a double-ringed surrogate NA had an inhibitory effect on germination at a concentration of 10mgL(-1), whereas inhibition of germination by the diamondoid model NA was observed only at 50mgL(-1). Seedling root growth was impaired by treatment with low concentrations of OSPW, and exposure to higher concentrations of OSPW resulted in increased growth inhibition of roots and primary leaves, and caused bleaching of cotyledons. Treatment with single- or double-ringed surrogate NAs at 10mgL(-1) severely impaired seedling growth. AEO or diamondoid NA treatment was less toxic, but resulted in severely impaired growth at 50mgL(-1). At low NA concentrations there was occasionally a stimulatory effect on root and shoot growth, possibly owing to the broad structural similarity of some NAs to known plant growth regulators such as auxins. This report provides a foundation for future studies aimed at using Arabidopsis as a biosensor for toxicity and to identify genes with possible roles in NA phytoremediation.