Yeast three hybrid experiment
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ABSTRACT:
PROVIDER: PRJNA639454 | ENA |
REPOSITORIES: ENA
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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: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:Expanding the binding specificity for RNA recognition by a PUF domain
2021-07-28 | GSE152452 | GEO
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. We analyzed three biological replicates of the parental yeast strains, S. cerevisiae and S. paradoxus, and four replicates of their hybrid over four developmental time points. Two hybrid replicates contain MATa from S. cerevisiae and MATalpha from S. paradoxus. The other two hybrid replicates are reciprocal crosses. The developmental time points are T0, which serves as a control, and is the moment cells enter sporulation media. M1 is the beginning of meiosis I. M1/M2 is the overlap of the end of meiosis I and the beginning of meiosis II. M2 is the end of meiosis II.
2013-10-31 | E-GEOD-51809 | biostudies-arrayexpress
Project description:Hybrid sterility is one of the earliest postzygotic isolating mechanisms to evolve between two recently diverged species. Uncovering the mechanisms of hybrid sterilitynot only provides insight into the origins of species but also potentially revealsnovel causes of intra-species infertility.Here we identify causes underlying hybrid infertilityofSchizosaccharomyces pombeand S. kambucha, two fission yeast species that are 99.5% identical at the nucleotide level.These yeasts mate to form viable diploids that efficiently complete meiosis. However,S. kambucha/S. pombe hybrids generate few viable gametes, most of which are either aneuploid or diploid.We find that chromosomal rearrangements and related recombination defectsare major causes of hybrid infertility. Surprisingly, using experiments in which we eliminate meiotic recombination, we find thatrecombination defects cannot completely explain the hybrid infertility. Instead, we find that a significant fraction of hybrid infertility is caused by the action of at least three distinct meiotic drive alleles, one on each S. kambucha chromosome,that “cheat” to be transmitted to more than half (up to 90%) of viable gametes.Two of these driving lociare linked by a chromosomal translocation and thus constitute a novel type of paired meiotic drive complex. We find that all three S. kambuchadrive loci independently contribute to hybrid infertility by causing nonrandom spore death. This study reveals how quickly multiple barriers to fertility can arise.In addition, it provides further support for models in which genetic conflicts, such as those caused by meiotic drive alleles, can drive speciation.
2014-05-15 | GSE57039 | GEO
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:This SuperSeries is composed of the following subset Series:; GSE9504: Expression data from hybrid female Xenopus sex reversal experiment; GSE9505: Expression data from hybrid male Xenopus sex reversal experiment Experiment Overall Design: Refer to individual Series
2008-06-16 | E-GEOD-9507 | biostudies-arrayexpress
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 We analyzed four conditions (rich media, glycerol, heat shock and TSA). For each conditions, we hybridized the pooled sample of both species dyed with cy3/cy5 and a sample of the hybrid dyed with the alternate fluorescent color. Each experiment was done with 2 biological repeats, except for the rich media experiments done with 4 biological repeats.
2010-06-20 | E-GEOD-14708 | biostudies-arrayexpress
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