Project description:Purpose: ATG41 is involved both in autophagy and zinc-deficient growth. The goal of this study is to compare transcriptomic profiles of wild-type and atg41Δ strains to discover autophagy-independent molecular phenotypes for the mutant. The atg1Δ mutant is a control for autophagy activity. Methods: Wild-type and mutant yeast were grown to mid-log phase in replete medium and shifted to zinc-deficient medium for 8 hours, after which, cells were harvested for RNA sequencing to detect differential gene expression. Results: Gene expression data for virtually every gene (~6,000) was obtained with ~12,000,000 reads per sample. Differential gene expression analysis showed that several hundred genes were differentially experessed in the atg41Δ mutant (greater than 2-fold) at an FDR of 0.5. Conclusions: Most strikingly, we found that the atg41Δ mutant transcriptome shows signs that sulfur metabolism is distrupted during zinc-deficinet growth. Expression of Met4 gene targets is increased.
Project description:Sequencing of mononucleosomal DNA during G1 and S phases in Saccharomyces cerevisiae Samples from mononucleosomal DNA from WT and rpd3 mutant strains (W303-1a background) in G1 or in S phase in the presence of 0.2 M HU were sequenced (Illumina Genome Analyzer IIx) using the single-end read protocol
Project description:Yeast sensor checkpoint kinase Mec1 is phosphorylated at Ser1991 upon HU replication stress. The phospho-accepter mutant (mec1-S1991A) confers HU sensitivity and synthetic sickness with the mutants that aggravate replication and transcription collision. To understand how the entire chromatin proteome (chromatome) responds to replication stress, we first investigated the global chromatin-bound proteins in S-phase yeast cells in the presence and absence of HU. Second, we performed phospho-proteome analysis in wild-type and mec1-S1991A mutant to find the S1991-phospho-dependent targets of Mec1 in the presence and absence of HU. Samples were duplicated in chromatome and triplicated in phospho-proteome analysis.
Project description:To understand the gene expression in Saccharomyces cerevisiae under fermentative and respiraotry conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of S. cerevisiae wild type, sef1 deletion, and hyperactive SEF1-VP16 mutants under the YPD and YPGly conditions.
