Telomere behavior in a hybrid yeast
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PROVIDER: PRJNA117033 | ENA |
REPOSITORIES: ENA
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Project description:Telomeres and the protein/RNA complexes involved in maintaining them are rapidly evolving systems across eukaryotes. Using two Saccharomyces species, S. cerevisiae and S. bayanus, we provide evidence that the telomere systems of these two closely related yeasts have evolved significantly apart and that the gene in one species can not maintain the set-point of telomere length of the other species in the hybrid. Each array has co-hybridized RNA vs DNA for the indicated species (BB9=S. bayanus, CC5=S. cerevisiae) or hybrid (BC11). The cultures for RNA preparation were grown to midlog phase at the indicated temperature.
2010-05-19 | E-GEOD-15877 | biostudies-arrayexpress
Project description:Telomeres and the protein/RNA complexes involved in maintaining them are rapidly evolving systems across eukaryotes. Using two Saccharomyces species, S. cerevisiae and S. bayanus, we provide evidence that the telomere systems of these two closely related yeasts have evolved significantly apart and that the gene in one species can not maintain the set-point of telomere length of the other species in the hybrid.
2009-05-01 | GSE15877 | GEO
Project description:This experiment is the analysis of the transcriptomes of several hybrid yeast strains obtained by crossing natural (from wine) isolates of S. cerevisiae and S. uvarum. All isolations have been done from hybrid strains growing in exponential phase in YPD. Keywords: Strain comparison
2008-07-15 | GSE9888 | GEO
Project description:Histones of heterochromatin are deacetylated in yeast and methylated in more complex eukaryotes to regulate heterochromatin structure and gene silencing. Here, we report that histone H2A phosphorylated at serine 129 (γH2A) in Saccharomyces cerevisiae is a conceptually new type of heterochromatin modification that functions downstream of silent chromatin assembly. We show that γH2A is enriched throughout yeast telomeric and silent mating locus (HM) heterochromatin where γH2A results from the action of kinases Tel1 and Mec1. Interestingly, mutation of γH2A has no apparent effect on the binding of Sir (silent information regulator) complex or on gene silencing. In contrast, deletion of SIR3 abolishes the formation of γH2A at heterochromatin. To address the function of γH2A, we used a ∆rif1 mutant strain in which telomeres are excessively elongated to show that γH2A is required for the optimal recruitment of Cdc13, a regulator of telomere elongation, and for telomere elongation itself. Thus, a histone modification that parallels Sir3 protein binding is shown here to be dispensable for the formation of a silent structure but is important for a crucial heterochromatin-specific downstream function in telomere homeostasis.
2011-01-05 | GSE21814 | GEO
Project description:This experiment is the analysis of the transcriptomes of several hybrid yeast strains obtained by crossing natural (from wine) isolates of S. cerevisiae and S. uvarum. All isolations have been done from hybrid strains growing in exponential phase in YPD. Keywords: Strain comparison Transcriptomic analysis of three independent replicates of each yeast strain growing in exponential phase. Each replicate has been hybridized on a different macroarray (F19-F22-F24) as indicated in the sample files. A single DNA (S. cerevisiae 3002 wine strain) genomic hybridization, from the same labeling reaction, was done on the same macroarrays for normalization.
2010-06-25 | E-GEOD-9888 | biostudies-arrayexpress
Project description:Changes in gene regulation rapidly accumulate between species and may contribute to reproductive isolation through misexpression of genes in interspecific hybrids. Hybrid misexpression, defined by expression levels outside the range of both parental species, is thought to be a result of cis- and trans-acting regulatory changes that interact in the hybrid, or arise from changes in the relative abundance of various tissues or cell types due to defects in developmental. Here, we show that misexpressed genes in a sterile interspecific Saccharomyces yeast hybrid result from a heterochronic shift in the timing of the normal meiotic gene expression program. By tracking nuclear divisions, we find that S. cerevisiae initiates meiosis earlier than its closest known relative, S. paradoxus, yet both species complete meiosis at the same time. Although the hybrid up- and down-regulates genes in a similar manner to both parents, the hybrid meiotic program occurs earlier than both parents. The timing shift results in a heterochronic pattern of misexpression throughout meiosis I and the beginning of meiosis II. Coincident with the timing of misexpression, we find an increase in the relative abundance of opposing cis and trans-acting changes and compensatory changes, as well as a transition from predominantly trans-acting to cis-acting expression divergence over the course of meiosis. However, misexpression does not appear to be a direct consequence of cis- and trans-acting regulatory divergence. Our results demonstrate that hybrid misexpression in yeast results from a heterochronic shift in the meiotic gene expression program.
2013-10-31 | GSE51809 | GEO
Project description:We compared the genome-wide expression profiles of two yeast species (S. cerevisiae and S. paradoxus) using a two-species microarray that contain species-specific probes and can thus measure the expression levels of the two species simultaneosly. In Addition, we used the array to measure expression levels of the interspecific hybrid of these yeast species, while discriminating between the alleles that correspond to the two parental species. Comparison of the between-species differences and the within-hybrid allele differences allows us to separate cis from trans effects. Also, comparison of the overall expression in the hybrids (both alleles) with their parental species allows us to analyze hybrid over-expression and under-expression. Keywords: comparative transcriptome analysis, hybrid gene expression
2009-04-01 | GSE14708 | GEO
Project description:CGH arrays for Smukowski Heil, et al MBE 2017. Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we address these questions using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae x Saccharomyces uvarum and their parentals. We evolved these strains in nutrient limited conditions for hundreds of generations and sequenced the resulting cultures to identify genomic changes. Analysis of 16 hybrid clones and 16 parental clones identified numerous point mutations, copy number changes, and loss of heterozygosity events, including species biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated loss of heterozygosity at the high affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the loss of heterozygosity is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity, and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
2017-02-21 | GSE95086 | GEO