Rad51 binding in meiosis after undergoing S phase with different replication programs.
Ontology highlight
ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
SUBMITTER: Pei-Yun Jenny Wu
PROVIDER: E-GEOD-53880 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion. Comparison of H3 and H3k4Me3 in diploid pat1-114 cells grown in -N and +N conditions.
2014-02-20 | E-GEOD-53878 | biostudies-arrayexpress
Project description:Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase. Experiments were performed in the following strains and conditions for mitotic cells: cdc25-22 (temperature-sensitive mutation arrests cells at G2/M for synchrony, otherwise wild type), nitrogen-rich conditions; wild type, haploid and diploid, nitrogen-depletion conditions. Experiments were performed in the following strains and conditions for meiotic cells: pat1-114 diploid (temperature-sensitive mutation induces a synchronous meiosis, otherwise wild type), nitrogen-depletion and nitrogen-rich conditions; pat1-114 diploid with altered Cdc45 levels, nitrogen-depletion conditions. Comparison of samples before and after S phase entry; dye-swap experiments were performed and averaged.
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-02-20 | E-GEOD-53921 | biostudies-arrayexpress
Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.
2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress
Project description:Crossovers formed by recombination between homologous chromosomes are important for proper homolog segregation during meiosis and for generation of genetic diversity. Optimal molecular analysis of DNA intermediates of recombination requires synchronous cultures. We previously described a mutant, pat1-as2, of the fission yeast Schizosaccharomyces pombe that undergoes synchronous meiosis at 25°C when an ATP analog is added to the culture. Here, we compare recombination intermediates in pat1-as2 at 25°C with those in the widely used pat1-114 temperature-sensitive mutant at 34°C, a temperature higher than optimal. DNA double-strand breaks at most hotspots are similarly abundant in the two conditions but, remarkably, a few hotspots are distinctly deficient at 25°C. In both conditions Holliday junctions at DNA break hotspots form more frequently between sister chromatids than between homologs, but a novel species, perhaps arising from invasion by only one end of broken DNA, is more readily observed at 25°C. Our results confirm the validity of previous assays of recombination intermediates in S. pombe and provide new information on the mechanism of meiotic recombination. DNA double-strand break analysis by immunoprecipation of Rec12-FLAG covalently linked to DNA (without exogenous crosslinking agent used) following meiotic induction via pat1-114 or pat1-as2 alleles
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Project description:We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1 and pat1 mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in WT. These mRNAs show reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
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Project description:Identification of sites of replication initiation by copy number analysis, comparing samples before and after entry into S phase. Experiments were performed in the following strains and conditions for mitotic cells: cdc25-22 (temperature-sensitive mutation arrests cells at G2/M for synchrony, otherwise wild type), nitrogen-rich conditions; wild type, haploid and diploid, nitrogen-depletion conditions. Experiments were performed in the following strains and conditions for meiotic cells: pat1-114 diploid (temperature-sensitive mutation induces a synchronous meiosis, otherwise wild type), nitrogen-depletion and nitrogen-rich conditions; pat1-114 diploid with altered Cdc45 levels, nitrogen-depletion conditions.
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Project description:ARF is a tumour suppressor activated by oncogenic stress, which stabilizes p53. Although p53 is a key component of the response to DNA damage, a similar function for ARF has not been ascribed. In this work we show that homologous recombination (HR) -deficient primary mouse and human cells accumulate DNA damage, which triggers checkpoint signalling and ARF activation. We also show that in the absence of ARF p53 is induce in response to DNA damage, but surprisingly fails to trigger senescence. The hypothesis tested in this study was that ARF deficiency alters the spectrum of genes activated by p53 in response to HR deficiency. Using mRNA microarray analysis and expression profiling, we identified genes upregulated in wild type primary MEFs treated with RAD51 shRNA, whose expression was not induced in similarly treated Arf -/- primary MEFs. Clustering analysis of p53 transcriptional targets with increased expression in RAD51-depleted cells revealed three groups: genes requiring functional ARF for their expression, genes transcribed in an ARF-independent manner and genes that are upregulated in both ARF-proficient and ARF-deficient cells. Among the genes in the last group we found Cdkn1a(p21), encoding the p21 inhibitor of cyclindependent kinases and well-characterized effector of the p53 role in promoting senescence. The subset of p53 targets requiring ARF for their transcription was specifically upregulated in response to RAD51 inhibition in wild type, but not Arf -/- MEFs. Among these genes, two encoded the dual specificity phosphatase (DUSP) family members DUSP4 and DUSP7, which act as ERK phosphatases and negative regulators of the MAPK kinase pathway in mammalian cells. Four samples were analysed (WT or ARF negative cells transfected with GFP or RAD51 shRNAs) in duplicate. Samples treated with GFP shRNA are the reference samples and the ones treated with RAD51 shRNA are the experimental ones (RAD51 depletion leads to HR deficiency). The WT cell line is our control cell line to study the effect of HR deficiency on the transcription of p53 target genes
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Project description:Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements, collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, which is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq datasets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as well as alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation, by functional assays including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin are generally (on chromosome 2) associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
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Project description:We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using a combination of ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors.
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