Array CGH with DNA extracted from Candida albicans strains and its derivatives, which is monosomic for chromosome 5
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE48093 | GEO | 2013/11/04
SECONDARY ACCESSION(S): PRJNA208920
REPOSITORIES: GEO
Similar Datasets
Project description:Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the derivatives Pair-wise comparison of genomic content between parental strains and their derivatives.
2013-11-04 | E-GEOD-48093 | biostudies-arrayexpress
Project description:Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the mutant Sor55
2010-06-14 | GSE21616 | GEO
Project description:Goal of this experiment was to confirm the proposed monosomy condition of chromsome 5 genes in the mutant Sor55 Different batches of total DNA were prepared from the parental strain 3153A and its derivative Sor55. Hybridization included different combinations of two independent batches of DNA from 3153A or Sor55, as well as one dye-swap. Parental/mutant ratio data was analyzed.
2010-06-14 | E-GEOD-21616 | biostudies-arrayexpress
Project description:Differential expression between monosoic derivative and parental strain of Candida albicans. The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, assuring survival. In the absence of the adverse environment, the altered portion of the genome can be restored to its normal condition. One major question is how C. albicans copes with gene imbalance arising by transitory aneuploid states. Here, we compared transcriptomes from two copies of chromosome 5 (Ch5) in a normal diploid strain 3153A and from a single copy of Ch5 in representative derivative Sor55. Statistical analysis revealed that at least 40% of transcripts from the monosomic Ch5 are fully compensated to a disomic level, thus, indicating the existence of a genome-wide mechanism maintaining cell homeostasis. However, a minor portion of transcripts diminished twofold in accordance with what would be expected for Ch5 monosomy. Another minor portion of transcripts, unexpectedly, increased up to twofold and higher then the disomic level, demonstrating indirect control by monosomy. We suggest that C. albicans unusual regulation of gene expression by the loss and gain of entire chromosomes is coupled with widespread compensation of gene dosage at the transcriptional level.
2010-06-09 | GSE18779 | GEO
Project description:The purpose of this review is to describe the tools used to detect genome changes, to highlight recent advances in our understanding of large scale chromosome changes that arise in C. albicans and to discuss the role of specific stresses in eliciting these genome changes. The types of genomic diversity that have been characterized suggest C. albicans can undergo extreme genomic changes in order to survive stresses in the human host. We propose that C. albicans and other pathogens may have evolved mechanisms not only to tolerate, but also to generate, large-scale genetic variation as a means of adaptation.
2010-06-01 | GSE21643 | GEO
Project description:Aneuploidy and the evolution of aneuploid karyotypes of Candida albicans strains was identified using aCGH. Whole chromosome and segmental aneuploidies, (specifically on the left arm of chromosome 5 - shown to be due to isochromosome formation) are associated with the appearance of resistance to the antifungal drug fluconazole. Keywords: Comparative Genomic Hybridization
2006-06-30 | GSE4995 | GEO
Project description:Phenotypic diversity can arise rapidly through loss of heterozygosity (LOH) or by the acquisition of copy number variations (CNV) spanning whole chromosomes or shorter contiguous chromosome segments. In Candida albicans, a heterozygous diploid yeast pathogen with no known meiotic cycle, homozygosis and aneuploidy alter clinical characteristics, including drug resistance. Here, we developed a high-resolution microarray that simultaneously detects ?39,000 single nucleotide polymorphism (SNP) alleles and ?20,000 copy number variation loci across the C. albicans genome. An important feature of the array analysis is a computational pipeline that determines SNP allele ratios based upon chromosome copy number. Using the array and analysis tools, we constructed a haplotype map (hapmap) of strain SC5314 to assign SNP alleles to specific homologs, and we used it to follow the acquisition of loss of heterozygosity (LOH) and copy number changes in a series of derived laboratory strains. This high-resolution SNP/CGH microarray and the associated hapmap facilitated the phasing of alleles in lab strains and revealed detrimental genome changes that arose frequently during molecular manipulations of laboratory strains. Furthermore, it provided a useful tool for rapid, high-resolution, and cost-effective characterization of changes in allele diversity as well as changes in chromosome copy number in new C. albicans isolates.
| S-EPMC3276171 | biostudies-literature
Project description:The purpose of this review is to describe the tools used to detect genome changes, to highlight recent advances in our understanding of large scale chromosome changes that arise in C. albicans and to discuss the role of specific stresses in eliciting these genome changes. The types of genomic diversity that have been characterized suggest C. albicans can undergo extreme genomic changes in order to survive stresses in the human host. We propose that C. albicans and other pathogens may have evolved mechanisms not only to tolerate, but also to generate, large-scale genetic variation as a means of adaptation. Strains included in this series are described in a Eukaryotic Cell review of genomic plasticity of Candida albicans. These strains are well-characterized and some of them are frequently utilized by the Candida community to generate mutant strains. Each strain was analyzed once and all strains were competed against the same reference strain, SC5314 (the first sequenced C. albicans strain).
2010-06-01 | E-GEOD-21643 | biostudies-arrayexpress
Project description:Aneuploidy and the evolution of aneuploid karyotypes of Candida albicans strains was identified using aCGH. Whole chromosome and segmental aneuploidies, (specifically on the left arm of chromosome 5 - shown to be due to isochromosome formation) are associated with the appearance of resistance to the antifungal drug fluconazole. Keywords: Comparative Genomic Hybridization Hybridization of all strains was compared to the hybridization of SC5314, the sequenced laboratory strain.
2006-06-30 | E-GEOD-4995 | biostudies-arrayexpress
Project description:Chromosome loss that results in monosomy has detrimental consequences for human cells, but the underlying molecular mechanisms remain enigmatic. Using p53 deficient monosomic cell lines, we found that chromosome loss impairs proliferation and genomic stability. Transcriptome and proteome analysis revealed a partial compensation of the gene dosage changes that mitigates the effects of chromosome loss. Monosomy triggers global gene expression changes that differ from the effects of trisomy. Strikingly, ribosome biogenesis and translation were commonly downregulated in monosomic cells. Polysome profiling and translation analysis suggest that the defects arise due to haploinsufficiency of ribosomal genes. The ensuing ribosome biogenesis stress triggers the p53 pathway and G1 arrest when TP53 is reintroduced into monosomic cells. Accordingly, impaired ribosome biogenesis and p53 inactivation are associated with monosomy in cancer. Our first systematic study of monosomy in human cells demonstrates that haploinsufficiency of ribosomal genes presents a dominant negative phenotype of monosomy.
2021-06-17 | PXD018440 | Pride