Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA348730 | ENA |
REPOSITORIES: ENA
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Project description:Break-chip (microarray-based double strand break mapping) analysis of mec1 cells recovering from 200 mM hydroxyurea in the presence or absence of 0.8 micromolar bathophenanthroline sulfonate (BPS). We asked if the presence of an iron chelator, BPS, during cell recovery from transient exposure to 200 mM hydroxyurea changes the global patterns of DNA double strand breaks (DSBs). We used a yeast checkpoint mutant, mec1, which has been shown to produce DSBs at replication forks after hydroxyurea was removed from the cell culture. We synchronously released cells from the G1/S transition into S phase in the presence of 200 mM hydroxyurea. After 1h treatment, the drug was removed and cells were allowed to recover in fresh medium for 1h in the presence or absence of 0.8 micromolar BPS. Recover (R) samples, R-1h-BPS and R-1h+BPS, as well as the G1 control samples were collected. Break-chip analysis was performed as previously described (Feng et al., G3(Bethesda) 2011 Oct;1(5):327-35. doi: 10.1534/g3.111.000554).
2015-01-12 | E-GEOD-64446 | biostudies-arrayexpress
Project description:Background: Chromatin remodeling complexes facilitate the access of enzymes that mediate transcription, replication or repair of DNA by modulating nucleosome position and/or composition. Ino80 is the DNA-dependent Snf2-like ATPase subunit of a complex whose nucleosome remodeling activity requires actin-related proteins, Arp4, Arp5 and Arp8, as well as two RuvB-like DNA helicase subunits. Budding yeast mutants deficient for Ino80 function are not only hypersensitive to reagents that induce DNA double strand breaks, but also to those that impair replication fork progression. Results: To understand why ino80 mutants are sensitive to agents that perturb DNA replication, we used chromatin immunoprecipitation to map the binding sites of the Ino80 chromatin remodeling complex on four budding yeast chromosomes. We found that Ino80 and Arp5 binding sites coincide with origins of DNA replication and tRNA genes. In addition, Ino80 was bound at 67% of the promoters of genes that are sensitive to ino80 mutation. When replication forks were arrested near origins in the presence of hydroxyurea (HU), the presence of the Ino80 complex at stalled forks and at unfired origins increased dramatically. Importantly, the resumption of DNA replication after release from a HU block was impaired in the absence of Ino80 activity. Mutant cells accumulated double-strand breaks as they attempted to restart replication. Consistently, ino80-deficient cells, although proficient for checkpoint activation, delay recovery from the checkpoint response. Conclusions: The Ino80 chromatin remodeling complex is enriched at stalled replication forks where it promotes the resumption of replication upon recovery from fork arrest. Keywords: ChIP-chip • The goal of the experiment Genome-wide localization of Ino80 on chromosome in Saccharomyces cerevisiae • Keywords DNA replication, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI) • Experimental factor Distribution of Ino80 in random culture Distribution of Ino80 in G1 phase Distribution of Ino80 in early S phase • Experimental design ChIP analyses: W303 background cells expressing Myc-tagged Ino80 were used for the ChIP using anti-Myc monoclonal antibody (9E11). ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI) was used. • Quality control steps taken Confirmation of several loci by quantitative real time PCR.
2008-04-10 | E-GEOD-9420 | biostudies-arrayexpress
Project description:Break-chip (microarray-based double strand break mapping) analysis of mec1 cells recovering from 200 mM hydroxyurea in the presence or absence of 0.8 micromolar bathophenanthroline sulfonate (BPS).
2015-01-12 | GSE64446 | GEO
Project description:ChIP-chip of DSB factors in the presence and absence of S phase checkpoint induction
| PRJNA202450 | ENA
Project description:Background: Chromatin remodeling complexes facilitate the access of enzymes that mediate transcription, replication or repair of DNA by modulating nucleosome position and/or composition. Ino80 is the DNA-dependent Snf2-like ATPase subunit of a complex whose nucleosome remodeling activity requires actin-related proteins, Arp4, Arp5 and Arp8, as well as two RuvB-like DNA helicase subunits. Budding yeast mutants deficient for Ino80 function are not only hypersensitive to reagents that induce DNA double strand breaks, but also to those that impair replication fork progression. Results: To understand why ino80 mutants are sensitive to agents that perturb DNA replication, we used chromatin immunoprecipitation to map the binding sites of the Ino80 chromatin remodeling complex on four budding yeast chromosomes. We found that Ino80 and Arp5 binding sites coincide with origins of DNA replication and tRNA genes. In addition, Ino80 was bound at 67% of the promoters of genes that are sensitive to ino80 mutation. When replication forks were arrested near origins in the presence of hydroxyurea (HU), the presence of the Ino80 complex at stalled forks and at unfired origins increased dramatically. Importantly, the resumption of DNA replication after release from a HU block was impaired in the absence of Ino80 activity. Mutant cells accumulated double-strand breaks as they attempted to restart replication. Consistently, ino80-deficient cells, although proficient for checkpoint activation, delay recovery from the checkpoint response. Conclusions: The Ino80 chromatin remodeling complex is enriched at stalled replication forks where it promotes the resumption of replication upon recovery from fork arrest. Keywords: ChIP-chip • The goal of the experiment Genome-wide localization of Ino80 and Arp5 on chromosome in Saccharomyces cerevisiae • Keywords DNA replication, Saccharomyces cerevisiae, Genome tilling array (chromosome III, IV, V, VI) • Experimental factor Distribution of Ino80 and Arp5 in wild type in random culture Distribution of Ino80 in G1 cells Distribution of Ino80 in early S phase cells • Experimental design ChIP analyses: W303 background cells expressing Myc tagged Ino80 were used for the ChIP using anti-Myc monoclonal antibody (9E11). ChIP analyses: W303 background cells expressing Myc tagged Ino80 were used for the ChIP using anti-Arp5 polyclonal antibody. ChIP-chip analyses: In all cases, hybridization data for ChIP fraction was compared with WCE (whole cell extract) fraction. Saccharomyces cerevisiae affymetrix genome tiling array (SC3456a520015F for chromosome III, IV, V, VI) was used. • Quality control steps taken Confirmation of several loci by quantitative real time PCR.
2008-04-10 | E-GEOD-9233 | biostudies-arrayexpress
Project description:Interfering with once-per-cell-cycle regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered different systems in budding yeast to induce over-replication in G1 and investigated its characteristics and consequences within the same cell cycle. To study replisome composition, we immunopurified replisomes via a GFP-tag on the Psf2 subunit of the GINS complex from S phase in the presence and absence of hydroxyurea and after unscheduled replication initiation in G1.
2022-11-09 | PXD028308 | Pride
Project description:Interfering with once-per-cell-cycle regulation of DNA replication initiation generates genome instability through over-replication and has been linked to early stages of cancer development. Here, we engineered different systems in budding yeast to induce over-replication in G1 and investigated its characteristics and consequences within the same cell cycle. To study replisome composition, we immunopurified replisomes via a GFP-tag on the Psf2 subunit of the GINS complex from S phase in the presence and absence of hydroxyurea and after unscheduled replication initiation in G1.
2023-03-11 | PXD035629 | Pride
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: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.
2024-03-25 | GSE262043 | GEO
Project description:Genome-wide Ifh1p occupancy at the OX growth phase and RC quiescent phase of the yeast metabolic cycle
| PRJNA170091 | ENA