Natural genetic variation in yeast longevity
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE37590 | GEO | 2012/07/18
SECONDARY ACCESSION(S): PRJNA161891
REPOSITORIES: GEO
Similar Datasets
Project description:A quantitative genetic analysis of the yeast replicative life span was carried out by sampling the natural genetic variation Genomic DNA was extracted from 39 recombinant lines from a cross between strains S96 and YJM 789.
2012-07-17 | E-GEOD-37590 | biostudies-arrayexpress
Project description:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross between a common laboratory strain (S288c) and a clinically derived strain (YJM145) were subjected to quantitative trait locus (QTL) analysis, using 3048 molecular markers across the genome. Five significant, replicative lifespan QTL were identified. Among them, QTL 1 on chromosome IV has the largest effect and contains SIR2, whose product differs by five amino acids in the parental strains. Reciprocal gene swap experiments showed that this gene is responsible for the majority of the effect of this QTL on lifespan. The QTL with the second-largest effect on longevity was QTL 5 on chromosome XII, and the bulk of the underlying genomic sequence contains multiple copies (100-150) of the rDNA. Substitution of the rDNA clusters of the parental strains indicated that they play a predominant role in the effect of this QTL on longevity. This effect does not appear to simply be a function of extrachromosomal ribosomal DNA circle production. The results support an interaction between SIR2 and the rDNA locus, which does not completely explain the effect of these loci on longevity. This study provides a glimpse of the complex genetic architecture of replicative lifespan in yeast and of the potential role of genetic variation hitherto unsampled in the laboratory.
| S-EPMC3460191 | biostudies-literature
Project description:Natural genetic variation is the raw material of evolution and influences disease development and progression. To analyze the effect of the genetic background on protein expression in the nematode C. elegans (Caenorhabditis elegans), the two genetically highly divergent wild-type strains N2 (Bristol) and CB4856 (Hawaii) were compared quantitatively. In total, we quantified 3,238 unique proteins in three independent SILAC (stable isotope labeling by amino acids in cell culture) experiments. The differentially expressed proteins were enriched for genes that function in insulin-signaling and stress response pathways.
2016-03-11 | PXD002010 | Pride
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221025 | GEO
Project description:Histone modification affects life span in various organisms. The loss of Histone H3K36 methylation can shorten replicative life span in Saccharomyces cerevisiae. However, budding yeast, as a model organism for aging research, has replicative life span (RLS) and chronological life span (CLS). In this study, we showed that the loss of Histone H3K36 methylation can shorten CLS in Saccharomyces cerevisiae. We identified Ubc3/Bre1 mediates polyubiquitination of Set2 K25 and K530 at log phase and stationary phase, and Bre1 interacts with Ubc3 and Rad6 simultaneously. BRE1 knockout can stabilize Set2 protein to maintain H3K36me3 and regulate the transcription of aging related genes, such as DSE1/DSE2/SUN4/EGT2/SCW11. We also proved that Gcn5-mediated Set2 acetylation regulates Set2 protein stability and chronological aging. Altogether, our study showed that knockout of BRE1 and GCN5 regulate Set2 protein level by mediating the polyubiquitination of Set2 to influence the level of H3K36me3 and the transcription level of aging related genes enriched by H3K36me3, thereby extending the chronological life span.
2023-09-29 | GSE221024 | GEO
Project description:Natural Genetic Variation in the Human Genome
| PRJNA736763 | ENA
Project description:Natural Genetic Variation in the Human Genome
| PRJNA736764 | ENA
Project description:Our understanding of the genetic basis of phenotypic diversity is limited by the paucity of examples in which multiple, interacting loci have been identified. We show that natural variation in the efficiency of sporulation, the program in yeast that initiates the sexual phase of the life cycle, between oak tree and vineyard strains is due to allelic variation between four nucleotide changes in three transcription factors: IME1, RME1, and RSF1. Furthermore, we identified that selection has shaped quantitative variation in yeast sporulation between strains. These results illustrate how genetic interactions between transcription factors are a major source of phenotypic diversity within species.
| S-EPMC4984536 | biostudies-literature
Project description:Here, we analyzed 76 ecologically diverse wild yeast isolates and discovered a wide diversity of replicative lifespan. Phylogenetic analyses pointed to genes and environmental factors that strongly interact to modulate the observed aging patterns. We then identified genetic networks causally associated with natural variation in replicative lifespan across wild yeast isolates, as well as genes, metabolites and pathways, many of which have never been associated with yeast lifespan in laboratory settings. In addition, a combined analysis of lifespan-associated metabolic and transcriptomic changes revealed unique adaptations to interconnected amino acid biosynthesis, glutamate metabolism and mitochondrial function in long-lived strains. Overall, our multi-omic and lifespan analyses across diverse isolates of the same species shows how gene-environment interactions shape cellular processes involved in phenotypic variation such as lifespan.
2021-11-07 | GSE188294 | GEO
Project description:Natural variation in gene expression among healthy human individuals has been largely unexplored. In order to understand the genetic basis of variation in gene expression between normal human individuals, we need to obtain genome-wide expression data from various populations. Studies in monozygotic twins could enable us to estimate the size of the contribution of genetic and environmental factors to the natural variation in gene expression. In this work, we report the gene expression analysis of 5 pairs of monozygotic twins and 3 unrelated individuals Normal healthy twin pairs were recruited for the study. Three more normal individuals including two females and one male were recruited. First, labeled products were hybridized with the Affymetrix GeneChip Test3 arrays. If the results were judged satisfactory, hybridization was subsequently carried out with the HG U95A arrays as per manufacturer's instructions. Arrays were hybridized at 45°C for 16 hours. The array was then washed using an automated Gene Chip Fluidics Station 400. After washing, the array was stained with streptavidin-phycoerythrin and scanned with a HP Gene Array Scanner. The data was analyzed using Gene Chip Software for expression analysis (MAS 5). All Gene Chip experiments were performed at the Weizmann Institute of Science, Rehovot, Israel. Following comparisons were carried out: 1. Between female identical twin pair (GSM14480 and GSM14481; GSM29053 and GSM 29054; GSM 29055 and GSM 29056) 2. Between male identical twin pair (GSM14478 and GSM14479; GSM 29057 and GSM 29058) 3. Between unrelated female individuals (include GSM14483, GSM20645 also but exclude comparisons within same twin pairs) 4. Between unrelated male individuals (include GSM14477 but exclude comparisons between same twin pairs) Keywords: repeat sample
2004-12-31 | GSE928 | GEO