Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA306490 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome.
2013-06-21 | GSE39566 | GEO
Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae.
2013-01-10 | GSE40110 | GEO
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.
2016-04-04 | GSE76154 | GEO
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
Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae. Experimental benchmark of five different protocols (3tfill, bpmI, internal, rnaseq and yoon) for genome-wide identification of polyadenylation sites in Saccharomyces cerevisiae and transcript quantification. RNA was extracted from WT cells grown in glucose (ypd) or galactose (ypgal) as carbon source. The same RNA was used for 3 independent library constructions (technical replicates, rep).
2013-01-10 | E-GEOD-40110 | biostudies-arrayexpress
Project description:Genome wide Mms1-binding sites in S. cerevisiae
| PRJNA385333 | ENA
Project description:Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome. RPC128-FLAG ChIP-seq single end seqquencing on Illumina GAII. 2 replicates of IP samples and 1 MOCK sample. Done in under normal growth and nutrient deprivation (4 hours).
2013-06-21 | E-GEOD-39566 | biostudies-arrayexpress
Project description:We report the genome-wide localization of Sgo1p in mitosis of Saccharomyces cerevisiae using ChIP-seq. The high resolution mapping clearly shows a tripartite domain of Sgo1p in each mitotic chromosome. This domain requires the wildtype tension sensing motif (TSM) of histone H3.
2018-09-01 | GSE110953 | GEO
Project description:Genome-wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
| PRJNA149379 | ENA
Project description:Genome-wide binding of THO and Sub2 in Saccharomyces cerevisiae
| PRJNA132001 | ENA