Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA307181 | ENA |
REPOSITORIES: ENA
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Project description:The Saccharomyces cerevisae RAD3 gene is homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Mutant alleles of RAD3 have been identified (rad3-101 and rad3-102) that have partial defects in DNA repair associated with a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. We have further characterized these events using a system in which the reciprocal products of mitotic recombination between homologs are recovered as red and white sectored colonies. Both rad3-101 and rad3-102 elevate the frequency of sectored colonies about 100-fold. Subsequent mapping of these events shows that three-quarters of crossovers between homologs induced in hyper-Rec rad3 mutants reflect DSBs formed in at the same positions in both sister chromatids (double sister-chromatid breaks, DSCBs). The remainder reflects DSBs formed in single chromatids (single chromatid breaks, SCBs). The ratio of DSCBs to SCBs is similar to that observed for spontaneous recombination events in wild-type cells. In addition to examining crossovers on chromosome V, we mapped 216 unselected genomic alterations throughout the genome including crossovers, gene conversions, deletions, and duplications. We found a significant association between the location of these recombination events and regions with elevated gamma-H2AX. In addition, there was a hotspot for deletions and duplications at the IMA2 and HXT11 genes near the left end of chromosome XV. A comparison of these data with our previous analysis of spontaneous mitotic recombination events suggests that a sub-set of spontaneous events in wild-type cells may be initiated by incomplete NER reactions, and that DSCBs, which cannot be repaired by sister-chromatid recombination, are a major source of mitotic recombination between homologous chromosomes.
2015-12-30 | GSE76395 | GEO
Project description:High-resolution mapping of heteroduplex DNA formed in UV-induced and spontaneous mitotic recombination events in yeast
| PRJNA391954 | ENA
Project description:Transcriptome analysis of isolated hyper-producer carotenoids mutants
| PRJNA224097 | ENA
Project description:Mapping physiological double strand breaks (DSBs) in cancer cells uncovers transcription-coupled repair mechanism at oncogenic super-enhancers in which RAD51 of the homologous recombination pathway plays a key role supporting the hyper-transcription of related oncogenes.
2019-08-27 | GSE136365 | GEO
Project description:In the yeast Saccharomyces cerevisiae, cleavage factor I (CFI) and cleavage and polyadenylation factor (CPF) build the core of the transcription termination machinery. CFI comprises the Rna14, Rna15, Pcf11, and Clp1 proteins, as well as the associated Hrp5 RNA-binding protein. We found that CFI participates in the DNA damage response and that rna14-1 shows synthetic growth defects with mutants of different repair pathways, including homologous recombination, non-homologous end joining, post replicative repair, mismatch repair, and nucleotide excision repair, implicating that impaired RNAPII termination and 3’-end processing decreases the cellular tolerance for DNA damage. Beyond replication progression defects, we found that bypass of the G1/S checkpoint in rna14-1 cells leads to synthetic sickness, accumulation of phosphorylated H2A, as well as increase in Rad52-foci and in recombination. Our data provide evidence that CFI dysfunction impairs RNAPII turnover, leading to replication hindrance and lower tolerance to exogenous DNA damage. These findings underscore the importance of coordination between transcription termination, DNA repair and replication in the maintenance of genomic stability.
2014-03-31 | GSE50947 | GEO
Project description:The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination
| PRJNA378431 | ENA
Project description:In the yeast Saccharomyces cerevisiae, cleavage factor I (CFI) and cleavage and polyadenylation factor (CPF) build the core of the transcription termination machinery. CFI comprises the Rna14, Rna15, Pcf11, and Clp1 proteins, as well as the associated Hrp5 RNA-binding protein. We found that CFI participates in the DNA damage response and that rna14-1 shows synthetic growth defects with mutants of different repair pathways, including homologous recombination, non-homologous end joining, post replicative repair, mismatch repair, and nucleotide excision repair, implicating that impaired RNAPII termination and 3â-end processing decreases the cellular tolerance for DNA damage. Beyond replication progression defects, we found that bypass of the G1/S checkpoint in rna14-1 cells leads to synthetic sickness, accumulation of phosphorylated H2A, as well as increase in Rad52-foci and in recombination. Our data provide evidence that CFI dysfunction impairs RNAPII turnover, leading to replication hindrance and lower tolerance to exogenous DNA damage. These findings underscore the importance of coordination between transcription termination, DNA repair and replication in the maintenance of genomic stability. S. cerevisiae strains were grown in YPAD liquid culture at 30°C, total RNA was isolated and hybridized on Affymetrix microarrays.
2014-03-31 | E-GEOD-50947 | biostudies-arrayexpress
Project description:The diploid isolate EM93 is the main ancestor to the widely used Saccharomyces cerevisiae haploid laboratory strain, S288C. In this study, we first hybridise DNA from eight EM93 segregants from two tetrads to Affymetrix genechip S. cerevisiae Tiling 1.0R Arrays to generate a high-resolution overview of the genetic differences between EM93 and S288C. We show that EM93 is heterozygous for many polymorphisms, including large sequence polymorphisms, such as deletions and a Saccharomyces paradoxus introgression. We also find that many of the large sequence polymorphisms are associated with Ty-elements and sub-telomeric regions. We next utilize the hybridization profiles of the 3.2 million Tiling Array probes to identify 2,965 genetic markers, which we then used to design an EM93 genotyping array. By genotyping 120 EM93 tetrads, we deduced the structures of all EM93 chromosomes and found that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 57 non-crossover events; we also identified 203 recombination hot-spots and provide evidence for crossover interference. We find that the effect of heterozygous large sequence polymorphisms on recombination is chromosome position-dependent, with sub-telomeric large sequence polymorphisms having no discernable effect on recombination but non-sub-telomeric large sequence polymorphisms reducing recombination. Finally, we find that recombination hotspots show limited conservation, with some but not all strain-specific hotspots being due to heterozygous non-sub-telomeric large sequence polymorphisms.
2012-06-08 | E-MEXP-3246 | biostudies-arrayexpress
Project description:High-resolution genome-wide mapping of histone modifications.
| PRJNA99305 | ENA