Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA99281 | ENA |
REPOSITORIES: ENA
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Project description:Band-array detection of chromosomal rearrangements in diploid yeast cells exposed to ionizing radiation
| PRJNA99265 | ENA
Project description:At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instability that can be rectified by various repair processes. Homologous recombination (HR) is highly effective at protecting the genome from DSBs and provides for accurate repair between sister chromatids and homologous chromosomes. Here we show that although random DSBs induced by ionizing radiation in yeast chromosomes are repaired efficiently by HR in G-2 diploid cells, rearrangements are frequent. The chromosome aberrations (ABs) primarily resulted from recombination between Ty retrotransposable elements, the most abundant class of dispersed repetitive DNAs in the genome, while some rearrangements involved other classes of repetitive DNA. Few, if any, of the ABs could be attributed to nonhomologous end-joining (NHEJ). We conclude that only those few DSBs that fall at or near the 3-5% of the genome composed of repetitive DNA elements are effective at generating rearrangements, while other lesions that appear in unique (single copy) sequences are correctly repaired. Thus, by successfully competing with repair that normally occurs between large homologous chromosomal DNAs, the combination of repetitive elements and DSBs provides genome plasticity and a rich source of evolutionary opportunities. Keywords: CGH-array Diploid G-2 yeast cells were exposed to 80 krad of ionizing radiation and plated on rich media to obtain survivor colonies. Genomic DNA from each of 37 survivors (Cy5/red; JW1 to JW13, and A1 to A24) was competitively hybridized to DNA from the parent diploid strain (Cy3/green). Gains of genomic segments in the survivors were detected as continuous regions of positive Log2 Red:Green ratios, while losses were detected as negative Log2 Red:Green ratios.
2010-06-11 | E-GEOD-6984 | biostudies-arrayexpress
Project description:At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instability that can be rectified by various repair processes. Homologous recombination (HR) is highly effective at protecting the genome from DSBs and provides for accurate repair between sister chromatids and homologous chromosomes. Here we show that although random DSBs induced by ionizing radiation in yeast chromosomes are repaired efficiently by HR in G-2 diploid cells, rearrangements are frequent. The chromosome aberrations (ABs) primarily resulted from recombination between Ty retrotransposable elements, the most abundant class of dispersed repetitive DNAs in the genome, while some rearrangements involved other classes of repetitive DNA. Few, if any, of the ABs could be attributed to nonhomologous end-joining (NHEJ). We conclude that only those few DSBs that fall at or near the 3-5% of the genome composed of repetitive DNA elements are effective at generating rearrangements, while other lesions that appear in unique (single copy) sequences are correctly repaired. Thus, by successfully competing with repair that normally occurs between large homologous chromosomal DNAs, the combination of repetitive elements and DSBs provides genome plasticity and a rich source of evolutionary opportunities. Keywords: CGH-array
2007-02-08 | GSE6984 | GEO
Project description:At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instability that can be rectified by various repair processes. Homologous recombination (HR) is highly effective at protecting the genome from DSBs and provides for accurate repair between sister chromatids and homologous chromosomes. Here we show that although random DSBs induced by ionizing radiation in yeast chromosomes are repaired efficiently by HR in G-2 diploid cells, rearrangements are frequent. The chromosome aberrations (ABs) primarily resulted from recombination between Ty retrotransposable elements, the most abundant class of dispersed repetitive DNAs in the genome, while some rearrangements involved other classes of repetitive DNA. Few, if any, of the ABs could be attributed to nonhomologous end-joining (NHEJ). We conclude that only those few DSBs that fall at or near the 3-5% of the genome composed of repetitive DNA elements are effective at generating rearrangements, while other lesions that appear in unique (single copy) sequences are correctly repaired. Thus, by successfully competing with repair that normally occurs between large homologous chromosomal DNAs, the combination of repetitive elements and DSBs provides genome plasticity and a rich source of evolutionary opportunities. Keywords: Band-array Each array in this series corresponds to the DNA of a yeast chromosomal band excised from a pulse-field gel (CHEF). Chromosomal aberrations identified in radiation survivors were analyzed by microarray to reveal which regions of the genome were present in the new chromosomes. The DNA enriched in the specific band appears in the arrays as continuos segments of spots with highly positive Log2 Red/Green ratios.
2010-06-11 | E-GEOD-6991 | biostudies-arrayexpress
Project description:Ionizing radiation, released during accidents at nuclear power plants or after atomic bomb explosions, is a potentially serious health threat for the exposed human population. This type of high-energy radiation causes DNA damage including single- and double-strand breaks and induces chromosomal rearrangements and mutations, but it is not known if ionizing radiation directly induces changes in the epigenome of irradiated cells. We treated normal human fibroblasts and normal human bronchial epithelial cells with different doses of gamma-radiation emitted from a cesium 137 (137Cs) radiation source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a small number of potential methylation changes with low fold-difference ratios in the irradiated cells. These minor methylation differences seen on the microarrays could not be verified by COBRA (combined bisulfite restriction analysis) or bisulfite sequencing of selected target loci. Our study shows that acute gamma-radiation treatment of two types of human cells had no appreciable effect on DNA cytosine methylation patterns in exposed cells.
2012-11-29 | GSE39038 | GEO
Project description:Ionizing radiation, released during accidents at nuclear power plants or after atomic bomb explosions, is a potentially serious health threat for the exposed human population. This type of high-energy radiation causes DNA damage including single- and double-strand breaks and induces chromosomal rearrangements and mutations, but it is not known if ionizing radiation directly induces changes in the epigenome of irradiated cells. We treated normal human fibroblasts and normal human bronchial epithelial cells with different doses of gamma-radiation emitted from a cesium 137 (137Cs) radiation source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a small number of potential methylation changes with low fold-difference ratios in the irradiated cells. These minor methylation differences seen on the microarrays could not be verified by COBRA (combined bisulfite restriction analysis) or bisulfite sequencing of selected target loci. Our study shows that acute gamma-radiation treatment of two types of human cells had no appreciable effect on DNA cytosine methylation patterns in exposed cells. DNA methylation patterns in gamma-irradiated cells and non- treated cells analyzed by microarrays
2012-11-29 | E-GEOD-39038 | biostudies-arrayexpress
Project description:<p>Long-term low-dose ionizing radiation (LLIR) widely exists in human life and has been confirmed to have potential pathogenic effects on cancer and cardiovascular diseases. However, it is technically and ethically unfeasible to explore LLIR-induced phenotypic changes in the human cohort, leading to slow progress in revealing the pathogenesis of LLIR. In this work, we recruited 32 radiation workers and 18 healthy non-radiation workers from the same city with the same eating habits for radiation damage evaluation and metabolomics profiling. It was found that clear metabolic phenotypic differences existed between LLIR and non-LLIR exposed participants. Moreover, LLIR exposed workers can be further divided into 2 types of metabolic phenotypes, corresponding to high and low damage types, respectively. 3-hydroxypropanoate and glycolaldehyde were identified as sensitive indicators to radiation damage, which specific response to the chromosomal aberration of workers and may be potential monitoring markers for LLIR protection. Taurine metabolism-related pathways were identified as the main differential metabolic pathway under LLIR inducing, which had been confirmed to have a response to acute or chronic radiation exposure. We expect our study can be helpful to LLIR damage monitoring and symptomatic intervention in the future.</p>
2022-04-07 | MTBLS3854 | MetaboLights
Project description:At the organismal level, genome rearrangements are usually deleterious and are often associated with disease. Yet, on an evolutionary scale, they can be beneficial as they provide for rapid genetic diversification. DNA lesions, particularly double-strand breaks (DSBs), are sources of genome instability that can be rectified by various repair processes. Homologous recombination (HR) is highly effective at protecting the genome from DSBs and provides for accurate repair between sister chromatids and homologous chromosomes. Here we show that although random DSBs induced by ionizing radiation in yeast chromosomes are repaired efficiently by HR in G-2 diploid cells, rearrangements are frequent. The chromosome aberrations (ABs) primarily resulted from recombination between Ty retrotransposable elements, the most abundant class of dispersed repetitive DNAs in the genome, while some rearrangements involved other classes of repetitive DNA. Few, if any, of the ABs could be attributed to nonhomologous end-joining (NHEJ). We conclude that only those few DSBs that fall at or near the 3-5% of the genome composed of repetitive DNA elements are effective at generating rearrangements, while other lesions that appear in unique (single copy) sequences are correctly repaired. Thus, by successfully competing with repair that normally occurs between large homologous chromosomal DNAs, the combination of repetitive elements and DSBs provides genome plasticity and a rich source of evolutionary opportunities. Keywords: Band-array
2007-02-10 | GSE6991 | GEO
Project description:We investigated the effects of the ploidy on cellular response in strains carrying various types of gross chromosomal rearrangements. Fourteen mutated strains (6 haploid strains and 8 diploid strains) were compared to their associated parental strain (haploid or diploid parental strain). For each comparison, 2 microarray experiments implying biological replicates were performed.
2011-06-17 | E-GEOD-28285 | biostudies-arrayexpress
Project description:We explored how Cas9-induced double-strand breaks (DSBs) on Ty1 produce genomic alterations in the diploid yeast Saccharomyces cerevisiae. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements (large deletions and duplications), loss of heterozygosity (gene conversions, crossovers, and break-induced replication), and aneuploidy. Almost all of the chromosomal rearrangements reflect the repairing of DSBs at Ty1 elements by homologous recombination.
2022-06-01 | GSE205199 | GEO