scholarly journals Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae

Yeast ◽  
2017 ◽  
Vol 34 (11) ◽  
pp. 447-458 ◽  
Author(s):  
Lydia P. Morris ◽  
Andrew B. Conley ◽  
Natalya Degtyareva ◽  
I. King Jordan ◽  
Paul W. Doetsch
Keyword(s):  
Oxidative Stress ◽  
Saccharomyces Cerevisiae ◽  
Binding Sites ◽  
Genome Wide

scholarly journals Genome-Wide Redistribution of Meiotic Double-Strand Breaks in Saccharomyces cerevisiae

2006 ◽  
Vol 27 (5) ◽  
pp. 1868-1880 ◽  
Author(s):  
Nicolas Robine ◽  
Norio Uematsu ◽  
Franck Amiot ◽  
Xavier Gidrol ◽  
Emmanuel Barillot ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Meiotic Recombination ◽  
Binding Sites ◽  
Chromosomal Region ◽  
Double Strand Breaks ◽  
Dna Binding Domain ◽  
Dna Double Strand Breaks ◽  
Strand Breaks ◽  
Genome Wide ◽  
Local Stimulation

ABSTRACT Meiotic recombination is initiated by the formation of programmed DNA double-strand breaks (DSBs) catalyzed by the Spo11 protein. DSBs are not randomly distributed along chromosomes. To better understand factors that control the distribution of DSBs in budding yeast, we have examined the genome-wide binding and cleavage properties of the Gal4 DNA binding domain (Gal4BD)-Spo11 fusion protein. We found that Gal4BD-Spo11 cleaves only a subset of its binding sites, indicating that the association of Spo11 with chromatin is not sufficient for DSB formation. In centromere-associated regions, the centromere itself prevents DSB cleavage by tethered Gal4BD-Spo11 since its displacement restores targeted DSB formation. In addition, we observed that new DSBs introduced by Gal4BD-Spo11 inhibit surrounding DSB formation over long distances (up to 60 kb), keeping constant the number of DSBs per chromosomal region. Together, these results demonstrate that the targeting of Spo11 to new chromosomal locations leads to both local stimulation and genome-wide redistribution of recombination initiation and that some chromosomal regions are inherently cold regardless of the presence of Spo11.

scholarly journals The Genome-Wide Early Temporal Response of Saccharomyces cerevisiae to Oxidative Stress Induced by Cumene Hydroperoxide

PLoS ONE ◽  
2013 ◽  
Vol 8 (9) ◽  
pp. e74939 ◽  
Author(s):  
Wei Sha ◽  
Ana M. Martins ◽  
Reinhard Laubenbacher ◽  
Pedro Mendes ◽  
Vladimir Shulaev
Keyword(s):  
Oxidative Stress ◽  
Saccharomyces Cerevisiae ◽  
Cumene Hydroperoxide ◽  
Temporal Response ◽  
Genome Wide

scholarly journals Ash1 and Tup1 Dependent Repression of the Saccharomyces cerevisiae HO promoter Requires Activator-Dependent Nucleosome Eviction

2020 ◽  
Author(s):  
Emily J. Parnell ◽  
Timothy J. Parnell ◽  
Chao Yan ◽  
Lu Bai ◽  
David J. Stillman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Dna Sequences ◽  
Binding Sites ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Mother Cells ◽  
Activation Cycle

ABSTRACTTranscriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle.

scholarly journals Ash1 and Tup1 dependent repression of the Saccharomyces cerevisiae HO promoter requires activator-dependent nucleosome eviction

PLoS Genetics ◽  
2020 ◽  
Vol 16 (12) ◽  
pp. e1009133
Author(s):  
Emily J. Parnell ◽  
Timothy J. Parnell ◽  
Chao Yan ◽  
Lu Bai ◽  
David J. Stillman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Dna Sequences ◽  
Binding Sites ◽  
Genome Wide ◽  
Intergenic Regions ◽  
Mother Cells ◽  
Activation Cycle

Transcriptional regulation of the Saccharomyces cerevisiae HO gene is highly complex, requiring a balance of multiple activating and repressing factors to ensure that only a few transcripts are produced in mother cells within a narrow window of the cell cycle. Here, we show that the Ash1 repressor associates with two DNA sequences that are usually concealed within nucleosomes in the HO promoter and recruits the Tup1 corepressor and the Rpd3 histone deacetylase, both of which are required for full repression in daughters. Genome-wide ChIP identified greater than 200 additional sites of co-localization of these factors, primarily within large, intergenic regions from which they could regulate adjacent genes. Most Ash1 binding sites are in nucleosome depleted regions (NDRs), while a small number overlap nucleosomes, similar to HO. We demonstrate that Ash1 binding to the HO promoter does not occur in the absence of the Swi5 transcription factor, which recruits coactivators that evict nucleosomes, including the nucleosomes obscuring the Ash1 binding sites. In the absence of Swi5, artificial nucleosome depletion allowed Ash1 to bind, demonstrating that nucleosomes are inhibitory to Ash1 binding. The location of binding sites within nucleosomes may therefore be a mechanism for limiting repressive activity to periods of nucleosome eviction that are otherwise associated with activation of the promoter. Our results illustrate that activation and repression can be intricately connected, and events set in motion by an activator may also ensure the appropriate level of repression and reset the promoter for the next activation cycle.

scholarly journals Genome-Wide Mapping of Binding Sites Reveals Multiple Biological Functions of the Transcription Factor Cst6p in Saccharomyces cerevisiae

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Guodong Liu ◽  
David Bergenholm ◽  
Jens Nielsen
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Sites ◽  
Regulatory Network ◽  
Deletion Mutant ◽  
Transcriptional Regulatory Network ◽  
Biological Processes ◽  
Genome Wide ◽  
Transcriptional Regulatory

ABSTRACT In the model eukaryote Saccharomyces cerevisiae , the transcription factor Cst6p has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p 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 promoter at any gene when cells are grown on glucose. The retarded growth of the CST6 deletion mutant on ethanol is attributed to the markedly decreased expression of NCE103 , encoding a carbonic anhydrase, 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, a 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 mapping of genome-wide binding sites can 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 . IMPORTANCE Transcription factors regulate the activity of various biological processes through binding to specific DNA sequences. Therefore, the determination of binding positions is important for the understanding of the regulatory effects of transcription factors. In the model eukaryote Saccharomyces cerevisiae , the transcription factor Cst6p has been reported to regulate several biological processes, while its genome-wide targets remain unknown. Here, we mapped the genome-wide binding sites of Cst6p at high resolution. We show that the binding of Cst6p to its target promoters is condition dependent and explain the mechanism for the retarded growth of the CST6 deletion mutant on ethanol. Furthermore, we demonstrate that Cst6p is a new member of a stress-responsive transcriptional regulatory network. These results provide deeper understanding of the function of the dynamic transcriptional regulatory network in S. cerevisiae .

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