Project description:The transcription factor Cst6p in Saccharomyces cerevisiae has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and the mechanisms for its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p with ChIP-exo at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol, but hardly binds to the genome on glucose. The growth deficiency of CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of carbonic anhydrase gene NCE103, which is a direct target of Cst6p. The target genes of Cst6p have a large overlap with those of stress-responsive transcription factors, such as Sko1p and Skn7p. In addition, the CST6 deletion mutant growing on ethanol shows hypersensitivity to oxidative stress and ethanol stress, assigning Cst6p as a new member of the stress-responsive transcriptional regulatory network. These results show that genome-wide binding site mapping is able to provide new insights into the function of transcription factors, and highlight the highly connected and condition-dependent nature of the transcriptional regulatory network in S. cerevisiae. The binding sites of Cst6p when cells were grown in glucose or ethanol were measured in biological duplicates, so there are four samples in total.

2016-04-04 | E-GEOD-76154 | biostudies-arrayexpress

The Paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae

Project description:The polymerase associated factor 1 complex (Paf1C) is a multifunctional epigenetic regulator of RNA polymerase II (Pol II) transcription. Paf1C controls gene expression by stimulating the placement of co-transcriptional histone modifications, influencing nucleosome occupancy in coding regions, facilitating transcription termination, and regulating nuclear export of RNAs. In this study, we investigate the extent to which these functions of Paf1C combine to influence the Saccharomyces cerevisiae transcriptome. Using conditions that enrich for unstable transcripts, we show that deletion of PAF1 affects all classes of Pol II-transcribed RNAs including multiple classes of noncoding transcripts. Gene ontology analysis revealed that mRNAs encoding genes involved in iron and phosphate homeostasis were differentially affected by deletion of PAF1. We further investigated these two groups of mRNAs with the goal of identifying overarching mechanisms of up and down-regulation in cells lacking Paf1. Our results indicate that only a subset of the observed changes result from loss of Paf1C-promoted histone modifications. We also found that transcription of the FET4 gene is differentially regulated by Paf1 and an upstream CUT. Together these data highlight the complexity of the epigenetic regulation of Pol II transcription imposed by Paf1C and identify a role for Paf1C in promoting CUT transcription.

2019-06-11 | GSE122704 | GEO

Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae

2016-04-04 | GSE76154 | GEO

Saccharomyces cerevisiae

Project description:Competition and cooperativity determine transcription factor binding and regulation

| PRJNA131843 | ENA

Saccharomyces cerevisiae

Project description:Transcription Factor Regulation and Chromosome Dynamics in Pseudohyphal Growth

| PRJNA237777 | ENA

Saccharomyces cerevisiae

Project description:Transcriptional profiling of the yeast forkhead transcription factor Hcm1

| PRJNA125583 | ENA