Cross species differential gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces paradoxus NRRL Y-17217 Saccharomyces mikatae IFO 1815 Saccharomyces cerevisiae S288C Saccharomyces uvarum CLIB 533
PROVIDER: GSE32679 | GEO | 2011/12/31
SECONDARY ACCESSION(S): PRJNA146911
REPOSITORIES: GEO
Similar Datasets
Project description:AB SOLID sequencing of ribosome-depleted RNA from S. Cerevisiae, S. Paradoxus, S. Mikatae, and S. Bayanus These four yeast species were grown in complete media and total RNA was sequenced. Cross-Species Gene Expression using RNA-Seq Data was examined. Eight samples examined: two biological replicates of each species
2011-12-31 | E-GEOD-32679 | biostudies-arrayexpress
Project description:We profiled the transcriptomes of four Saccharomyces species, as well as pairwise hybrids between three of the species with S. cerevisiae For pairwise comparisons between Saccharomyces cerevisiae and each of S. paradoxus, S. mikatae, and S. bayanus, we performed 3'-end RNA-seq on RNA from each parent species and each interspecific hybrid.
2013-10-21 | E-GEOD-38875 | biostudies-arrayexpress
Project description:A fundamental problem in biology is the molecular basis for divergence among related organisms. We have investigated the level of divergence of transcription factor binding sites for two key factors that regulate developmental processes in the budding yeasts. The genomic binding locations for the Ste12 and Tec1 transcription factors in S. cerevisiae, S. mikatae and S. bayanus were mapped by chromatin immunoprecipitation combined with microarrays (chIP chip)1, 2 and compared to one another. While there was a large core network which was conserved in all three species, there were many instances of binding events whose relative levels differ significantly quantitatively in one species relative to another and as well as species-specific binding events. One interesting class of genes were identified that were bound only in S. mikatae and S. bayanus; many of these genes are targets of Ste12 in haploid strains of S. cerevisiae, suggesting that S. cerevisiae has uniquely acquired the ability to differentially regulate these genes in haploid and diploid cells in these species. To extend these studies, the transcriptional network for the Ste12 homologue (Cph1) in Candida albicans was also mapped and compared to the Saccharomyces species. Again, there were several genes bound by Cph1 which are involved in mating in S. cerevisiae, suggesting that the precise delineation between many mating and pseudohyphal targets by Ste12 may be specific to S. cerevisiae. Overall our results demonstrate that transcription binding sites differ faster than gene content indicating that gene regulation at the level of transcription factor binding is likely to be a major mode of evolutionary divergence between related species. We expect that this divergence is essential for the distinct ecological niches inhabited by these organisms. Keywords: chIP-chip ChIP-chip was performed on Ste12 and Tec1 from S. cerevisiae, S. mikatae and S. bayanus in addition to Cph1 from S. cerevisiae. Three biological replicates were performed for each factor in each species with one replicate representing a dye swap.
2007-09-06 | E-GEOD-5421 | biostudies-arrayexpress
Project description:We sequenced non-ribosomal RNA from a upf1 deletion mutant of S. cerevisiae, and from wild type S. mikatae and S. bayanus, and identified a new class of yeast introns.
2018-01-01 | GSE90105 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE22191: Absolute expression level of Debaryomyces hansenii genes GSE22192: Absolute expression level of Yarrowia lipolytica genes GSE22193: Absolute expression level of Saccharomyces paradoxus genes GSE22194: Absolute expression level of Candida glabrata genes GSE22197: Absolute expression level of Candida albicans genes GSE22198: Absolute expression level of Kluyveromyces lactis genes GSE22199: Absolute expression level of Kluyveromyces waltii genes GSE22200: Absolute expression level of Saccharomyces castellii genes GSE22201: Absolute expression level of Saccharomyces mikatae genes GSE22202: Absolute expression level of Saccharomyces kluyveryii genes GSE22204: Absolute expression level of Saccharomyces cerevisiae genes GSE22205: Absolute expression level of Saccharomyces bayanus genes GSE22211: Genome-wide nucleosome position data for 12 yeast species Refer to individual Series
2010-07-05 | E-GEOD-21960 | biostudies-arrayexpress
Project description:A fundamental problem in biology is the molecular basis for divergence among related organisms. We have investigated the level of divergence of transcription factor binding sites for two key factors that regulate developmental processes in the budding yeasts. The genomic binding locations for the Ste12 and Tec1 transcription factors in S. cerevisiae, S. mikatae and S. bayanus were mapped by chromatin immunoprecipitation combined with microarrays (chIP chip)1, 2 and compared to one another. While there was a large core network which was conserved in all three species, there were many instances of binding events whose relative levels differ significantly quantitatively in one species relative to another and as well as species-specific binding events. One interesting class of genes were identified that were bound only in S. mikatae and S. bayanus; many of these genes are targets of Ste12 in haploid strains of S. cerevisiae, suggesting that S. cerevisiae has uniquely acquired the ability to differentially regulate these genes in haploid and diploid cells in these species. To extend these studies, the transcriptional network for the Ste12 homologue (Cph1) in Candida albicans was also mapped and compared to the Saccharomyces species. Again, there were several genes bound by Cph1 which are involved in mating in S. cerevisiae, suggesting that the precise delineation between many mating and pseudohyphal targets by Ste12 may be specific to S. cerevisiae. Overall our results demonstrate that transcription binding sites differ faster than gene content indicating that gene regulation at the level of transcription factor binding is likely to be a major mode of evolutionary divergence between related species. We expect that this divergence is essential for the distinct ecological niches inhabited by these organisms. Keywords: chIP-chip
2007-09-06 | GSE5421 | GEO
Project description:DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function. Measurement of genome replication time from 4 budding yeast species (Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus) and a hybrid (between Saccharomyces cerevisiae and S. bayanus). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase) The reference genome sequences for each yeast species are available as Series supplementary file [sac*.fa]
2012-06-19 | E-GEOD-36045 | biostudies-arrayexpress
Project description:Comparison of translation efficiency in S. cerevisiae, S. paradoxus, and their F1 hybrid. SRA submission number SRP028552; BioProject number PRJNA213844; Ribosome profiling was used to compare mRNA abundance, ribosome occupancy, and translation efficiency in two yeast species and their F1 hybrid.
2013-12-04 | E-GEOD-52119 | biostudies-arrayexpress
Project description:Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for 200-500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfur transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution.
2016-09-30 | GSE87401 | GEO
Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation.
2013-11-29 | GSE50049 | GEO