Effect of aging on the meiotic cell cycle
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE15570 | GEO | 2009/06/16
SECONDARY ACCESSION(S): PRJNA115743
REPOSITORIES: GEO
Similar Datasets
Project description:Identify which stages of meiosis are impaired in replicative aging cells Transcriptional profile of aging yeast cells (young and old) incubated in sporulation-inducing conditions compared to new-born cells grown in vegetative conditions. Two conditions experiments. Young and Old cells incubated in sporulation-inducing conditions. Control strain was same strain used for the experimental samples but grown in vegetative conditions.
2010-05-08 | E-GEOD-15570 | biostudies-arrayexpress
Project description:Ray2013 - Meiotic initiation in S. cerevisiae
A mathematical representation of early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signalling molecules for regulating protein activities, is described here
This model is described in the article:
Dynamic modeling of yeast meiotic initiation.
Ray D, Su Y, Ye P.
BMC Syst Biol. 2013 May 1;7:37
Abstract:
BACKGROUND:
Meiosis is the sexual reproduction process common to eukaryotes. The diploid yeast Saccharomyces cerevisiae undergoes meiosis in sporulation medium to form four haploid spores. Initiation of the process is tightly controlled by intricate networks of positive and negative feedback loops. Intriguingly, expression of early meiotic proteins occurs within a narrow time window. Further, sporulation efficiency is strikingly different for yeast strains with distinct mutations or genetic backgrounds. To investigate signal transduction pathways that regulate transient protein expression and sporulation efficiency, we develop a mathematical model using ordinary differential equations. The model describes early meiotic events, particularly feedback mechanisms at the system level and phosphorylation of signaling molecules for regulating protein activities.
RESULTS:
The mathematical model is capable of simulating the orderly and transient dynamics of meiotic proteins including Ime1, the master regulator of meiotic initiation, and Ime2, a kinase encoded by an early gene. The model is validated by quantitative sporulation phenotypes of single-gene knockouts. Thus, we can use the model to make novel predictions on the cooperation between proteins in the signaling pathway. Virtual perturbations on feedback loops suggest that both positive and negative feedback loops are required to terminate expression of early meiotic proteins. Bifurcation analyses on feedback loops indicate that multiple feedback loops are coordinated to modulate sporulation efficiency. In particular, positive auto-regulation of Ime2 produces a bistable system with a normal meiotic state and a more efficient meiotic state.
CONCLUSIONS:
By systematically scanning through feedback loops in the mathematical model, we demonstrate that, in yeast, the decisions to terminate protein expression and to sporulate at different efficiencies stem from feedback signals toward the master regulator Ime1 and the early meiotic protein Ime2. We argue that the architecture of meiotic initiation pathway generates a robust mechanism that assures a rapid and complete transition into meiosis. This type of systems-level regulation is a commonly used mechanism controlling developmental programs in yeast and other organisms. Our mathematical model uncovers key regulations that can be manipulated to enhance sporulation efficiency, an important first step in the development of new strategies for producing gametes with high quality and quantity.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000626
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000626 | BioModels
Project description:To investigate the dynamics of the meiotic transcriptome and to ensure meiotic synchrony of our samples, we measured RNA abundance in vegetative cells, respiratory (pre-meiotic) cells and in synchronously sporulating cells at various times after transfer to sporulation media (SM).
2009-09-23 | GSE18181 | GEO
Project description:To investigate the dynamics of the meiotic transcriptome and to ensure meiotic synchrony of our samples, we measured RNA abundance in vegetative cells, respiratory (pre-meiotic) cells and in synchronously sporulating cells at various times after transfer to sporulation media (SM). SK1 yeast strain SHy002 (MATa/MATα ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3)<br> Meiotic Time Course with samples collected during vegetative growth (YPD), respiratory growth (pre-meiotic/YPA 8 hours) and 0 hr, 1.5hr, 3hr, 4.5hr, 6hr, 9hr and 12hr after transfer to sporulation media (SM).<br> 3 separate biological replicates were used for each condition/time-point.<br> Total RNA from each sample was hybridized competitively with a genomic DNA common reference.<br> The expression analysis was carried out from the same biological samples as the FAIRE analysis.<br>
2010-05-22 | E-GEOD-18181 | biostudies-arrayexpress
Project description:Inactivation of the yeast IME4 gene, the yeast homologue of METTL3, was shown to result in the loss of m6A in mRNA of mutant cells grown in sporulation medium. We attempted to characterize the effects of ime4 deletion on gene expression under vegetative and meiosis-inducing conditions. The results show that in vegetatively-growing ime4-/- cells there is an increased expression of the RME1 gene (repressor of meiosis) which prevents precocious entry into the meiotic program. Mutant yeast cells showed reduced expression levels of genes involved in ribosome biogenesis and gene expression processes. Surprisingly, despite the fact that a diploid strain was analyzed, there was also a striking change in the expression level of haploid-specific genes, suggesting that RNA methylation may be used to enforce the sexual identity of diploid cells, required for the implementation of the gametogenesis program. Consistently, when cells were induced to undergo meiosis, ime4-/- diploids failed to undergo the meiotic divisions. Among the genes showing reduced expression in the mutant were IME1 and IME2, the two known inducers of meiosis. Thus, the yeast IME4 gene plays an important role in the regulation of the developmental switch from vegetative cells into gametogenesis. WT and ime4 -/- yeast cells were grown vegetatively in YPD (Yeast extract, Peptone, Dextrose) medium, and transferred to sporulation medium(1% Kacetate) for induction of sporulation for 4 hrs. RNA was purified from the cells and hybridized to Affymetrix microarrays. Experiments were conducted in biological replicates.
2012-04-24 | E-GEOD-36958 | biostudies-arrayexpress
Project description:Ray2013 - S.cerevisiae meiosis-specific metabolic network
Meiosis is a strongly concerved cell division program that generates haploid gametes from a diploid parental cell. Successful meiosis is the fundamental basis of sexual reproduction. Multiple lines of evidence suggest a tight link between meiosis and metabolism. Here, yeast meiosis is studied to elucidate the link between reproduction and metabolism. Network flux is obtained using GLPK (GNU Linear Programming Kit) supported by the COBRA Toolbox for Matlab.
This model is described in the article:
Characterization of the metabolic requirements in yeast meiosis.
Ray D, Ye P.
PLoS One. 2013 May 8;8(5):e63707.
Abstract:
The diploid yeast Saccharomyces cerevisiae undergoes mitosis in glucose-rich medium but enters meiosis in acetate sporulation medium. The transition from mitosis to meiosis involves a remarkable adaptation of the metabolic machinery to the changing environment to meet new energy and biosynthesis requirements. Biochemical studies indicate that five metabolic pathways are active at different stages of sporulation: glutamate formation, tricarboxylic acid cycle, glyoxylate cycle, gluconeogenesis, and glycogenolysis. A dynamic synthesis of macromolecules, including nucleotides, amino acids, and lipids, is also observed. However, the metabolic requirements of sporulating cells are poorly understood. In this study, we apply flux balance analyses to uncover optimal principles driving the operation of metabolic networks over the entire period of sporulation. A meiosis-specific metabolic network is constructed, and flux distribution is simulated using ten objective functions combined with time-course expression-based reaction constraints. By systematically evaluating the correlation between computational and experimental fluxes on pathways and macromolecule syntheses, the metabolic requirements of cells are determined: sporulation requires maximization of ATP production and macromolecule syntheses in the early phase followed by maximization of carbohydrate breakdown and minimization of ATP production in the middle and late stages. Our computational models are validated by in silico deletion of enzymes known to be essential for sporulation. Finally, the models are used to predict novel metabolic genes required for sporulation. This study indicates that yeast cells have distinct metabolic requirements at different phases of meiosis, which may reflect regulation that realizes the optimal outcome of sporulation. Our meiosis-specific network models provide a framework for an in-depth understanding of the roles of enzymes and reactions, and may open new avenues for engineering metabolic pathways to improve sporulation efficiency.
This model is hosted on BioModels Database
and identified
by: MODEL1303140001
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1303140001 | BioModels
Project description:In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery, such as Rdp1, is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, andwe argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that expression of mid-meiotic genes is kept tightly off in vegetative cells by two independent ways: antisense transcription and Fkh2 repression.
2011-11-01 | E-MEXP-3414 | biostudies-arrayexpress
Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination.
2015-12-07 | GSE59004 | GEO
Project description:Meiotic recombination hotspots are associated with histone post-translational modifications and open chromatin. However, it remains unclear how histone modifications and chromatin structure directly regulate meiotic recombination. Here, we identify acetylation of histone H4 at Lys44 (H4K44ac) as a new histone modification, occurring on the nucleosomal lateral surface. We show that H4K44ac is specific to yeast sporulation, rising during yeast meiosis and displaying genome-wide enrichment at recombination hotspots in meiosis. The H4K44 residue is required for normal meiotic recombination, for normal levels of double strand breaks during meiosis, and for optimal sporulation. Non-modifiable substitution H4K44R results in reduced MNase digestion and decreased binding of recombination-associated proteins at hotspots. Our results show that H4K44ac creates an accessible chromatin environment for key proteins to facilitate meiotic recombination.
2015-12-07 | GSE59003 | GEO
Project description:Bromodomain and Extra-terminal motif (BET) proteins play a central role in transcription regulation and chromatin signalling pathways. In yeast, Bdf1 and its homologous protein Bdf2 are partially redundant and the deletion of both genes is lethal. Most of Bdf1 functions have been investigated in vegetative cells even if this protein is essential for sporulation. In this study, we explored for the first time the functional role of the Bdf1 bromodomains during the sporulation program. Extensive purification of Bdf1 partners identified two independent complexes with Bdf2 or the Swr1 complex. However, none of them are required for meiotic gene regulation or to complete sporulation. Taken together, our results unveil a new role for Bdf1 as a meiotic-specific gene transcriptional regulator independently of its predominant protein partners.
2017-01-11 | PXD005227 | Pride