Transcription profiling of S. cerevisiae sua5D and wildtype BY4742 strains
Ontology highlight
ABSTRACT: To decipher the function of SUA5, we compare the expression profiles of sua5D and wildtype BY4742. We also compared the expression profile changed during the passage of sua5D strain. Experiment Overall Design: Sua5 disruptioin strains were obtained by tetrad dissection of a sua5D/SUA5 diploid strain. The spores were restreaked on YPD plate for 12 times. Each restreaking is suggested to 25 generaions. The first restreaking, 12th restreaking and wildtype strains were compared. Experiment Overall Design: Four indepedent clones (First restreaking), three independent clones (12th restreaking), and three independent clones (wildtype control) were used.
Project description:We reprocessed a recently published microarray compendium of 269 regulator knockouts that contains most known TFs and many epigenetic regulators for the yeast \italic{Saccharomyces cerevisiae} (Hu et al 2007). Using sensitive microarray analysis tools, we gained nearly 10 times more differentially expressed genes and recovered 90\% of previously described targets. We validated our analysis using Gene Ontology (GO), DNA-protein interactions, TF binding sites and protein-protein interactions. Our validation underlines the advantages of our sensitive analysis. The original data files for this submission can be found in E-MTAB-109.additional.zip
Project description:NET-seq was performed on yeast strains carrying deletions of mRNA decay factors (plus a control) in order to assess the effect of their deletion on RNA polymerase II occupancy at genetic loci. This is in pursuit of understanding the process of mRNA buffering which links mRNA synthesis and decay.
Project description:Using gene expression changes at mid-log phase data from microarray experiments, we investigated the roles of global transcription regulators in D. vulgaris. Comparison of cells treated with DVU2097, DVU3111, DVU0379, DVU2547 Mutant to untreated Wildtype cells at times of 0 min
Project description:Purpose: Understand the synergistic relationship between the methyltransferases Set1 and Set5 in the regulation of gene expression. Methods: Total mRNA was obtained from two independent biological replicates each of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ S. cerevisiae strains. Libraries were generated and sequenced using an Illumina HiSeq2000 platform. The sequence reads that passed quality filters were mapped using TopHat and expression levels were quantified using Cufflinks. Results: We generated FPKM expression values for each transcript and identified the differentially expressed genes using an FDR-adjusted p-value of 0.05. Subsequent data analysis was restricted to genes with fold-change greater than 1.7 relative to WT. Our results show that Set1 and Set5 have roles primarily in transcription repression. Moreover, lack of both Set1 and Set5 results in a synergistic exhacerbation of the transcriptional derepression observed in the single mutants. Further analysis revealed a specific enrichment of the Set5/Set1-repressed genes near repetitive DNA sequences of the genome. Conclusions: Our study uncovers an unexpected synergistic role of Set1 and Set5 in transcription repression of telomeric regions and Ty retrotransposons. mRNA profiles of wildtype (WT), set1∆, set5∆, SET5 Y402A and set1∆set5∆ were generated by sequencing using an Illumina HiSeq2000 platform. Two biological replicates of each strain were used.
Project description:Systemic infection with Cryptococcus neoformans, a dangerous and contagious pathogen found throughout the world, frequently results in lethal cryptococcal pneumonia and meningoencephalitis, and no effective treatments of cryptococcosis are available. Here, we describe Prm1, a novel regulator of virulence in C. neoformans. C. neoformans prm1 cells exhibit extreme sensitivity to various environmental stress conditions. Furthermore, prm1 cells show deficiencies in the biosynthesis of chitin, chitosan, and mannoprotein, which in turn result in impairment of cell wall integrity. Treatment of mice with heat-killed prm1 cells was found to facilitate the host immunological defence against infection with wild-type C. neoformans. Further investigation demonstrated that prm1 cells strongly promote pulmonary production of interferon- and Th1 responses, leading to activation of macrophage M1 differentiation and inhibition of M2 polarization. Therefore, our findings suggest that C. neoformans Prm1 may be a viable target for the development of anti-cryptococcosis medications and, cells lacking Prm1 represent a promising candidate for a vaccine.
Project description:To identify the direct targets of the Paf1/RNA polymerase II complex we compared expression profiles of isogenic wild type and paf1 and ctr9 mutant strains. We also created a Tet-regulated form of Paf1 and monitored expression patterns after shut off of Paf1. Samples were isolated at one hour intervals from 1 to 8 hours after shut off. Experiment Overall Design: Transcripts were compared on Affymetrix microarrays using standard protocols.
Project description:We are investigating the transcriptional response of Anc1 deficient yeast under basal and MMS exposed conditions; We used microarrays to detail the global programme of gene expression underlying the MMS response in WT and Anc1 deficient yeast Experiment Overall Design: Yeast strains either WT or Anc1 deficient were exposed or unexposed to MMS
Project description:Yeast remains an important model for systems biology and for evaluating proteomics strategies. In-depth shotgun proteomics studies have reached nearly comprehensive coverage, and rapid, targeted approaches have been developed for this organism. Recently, we demonstrated that single LC-MS/MS analysis using long columns and gradients coupled to a linear ion trap Orbitrap instrument had an unexpectedly large dynamic range of protein identification (Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell Proteomics 10, 10.1074/mcp.M110.003699). Here we couple an ultra high pressure liquid chromatography system to a novel bench top Orbitrap mass spectrometer (Q Exactive) with the goal of nearly complete, rapid, and robust analysis of the yeast proteome. Single runs of filter-aided sample preparation (FASP)-prepared and LysC-digested yeast cell lysates identified an average of 3923 proteins. Combined analysis of six single runs improved these values to more than 4000 identified proteins/run, close to the total number of proteins expressed under standard conditions, with median sequence coverage of 23%. Because of the absence of fractionation steps, only minuscule amounts of sample are required. Thus the yeast model proteome can now largely be covered within a few hours of measurement time and at high sensitivity. Median coverage of proteins in Kyoto Encyclopedia of Genes and Genomes pathways with at least 10 members was 88%, and pathways not covered were not expected to be active under the conditions used. To study perturbations of the yeast proteome, we developed an external, heavy lysine-labeled SILAC yeast standard representing different proteome states. This spike-in standard was employed to measure the heat shock response of the yeast proteome. Bioinformatic analysis of the heat shock response revealed that translation-related functions were down-regulated prominently, including nucleolar processes. Conversely, stress-related pathways were up-regulated. The proteomic technology described here is straightforward, rapid, and robust, potentially enabling widespread use in the yeast and other biological research communities. Data analysis: The raw files were processed using MaxQuant version 1.2.0.34. The fragmentation spectra were searched against the yeast ORF database (release date of February 3, 2011; 6752 entries) using the Andromeda search engine with the initial precursor and fragment mass tolerances set to 7 and 20 ppm, respectively, and with up to two missed cleavages. Carabamidomethlyation of cysteine was set as a fixed modification, and oxidation of methionine and protein N-terminal acetylation were chosen as variable modifications for database searching. Both peptide and protein identifications were filtered at 1% false discovery rate and thus were not dependent on the peptide score. Bioinformatics analysis was performed using the Perseus tools available in the MaxQuant environment.
Project description:Expression microarrays of WT vs. hog1D cells in aerobic or 5 hours of hypoxic growth (100% nitrogen gas). Two strains (WT vs. hog1 deletion), two conditions (aerobic vs. 5 hours hypoxic), two biological replicates each strain/condition.
Project description:Using data from microarray experiments, we investigated the transcriptional changes in evolved and ancestor D. vulgaris strains. gene expression changes in evolved salt-stressed DvH strain (ES, evolved in LS4D + 100 mM NaCl for 1200 generations), evolved control DvH strain (EC, evolved in LS4D for 1200 generations) and ancestor DvH strain grown in non-stress (LS4D), low salt stress (LS4D + 100 mM NaCl) or high salt stress (LS4D + 250 mM NaCl) conditions Comparison of gene expression in evolved salt-stressed strain (ES, 1200g) to ancestor (An) or evolved control (EC, 1200g) strains at mid-logarithmic phase under standard growth condition with defined medium LS4D, salt stress conditions LS4D+100 mM NaCl or LS4D+250 mM NaCl.