Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA169603 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We identify the cis and trans determinants of nucleosome positioning using a functional evolutionary approach involving S. cerevisiae strains containing large genomic regions from other yeast species. In a foreign species, nucleosome depletion at promoters is maintained over poly(dA:dT) tracts, whereas internucleosome spacing and all other aspects of nucleosome positioning tested are not. Interestingly, the locations of the +1 nucleosome and RNA start sites shift in concert. Strikingly, in a foreign species, nucleosome-depleted regions occur fortuitously in coding regions, and they often act as promoters that are associated with a positioned nucleosome array linked to the length of the transcription unit. nucleosome mapping for 3 strains bearing yeast artificial chromosomes from Kluyveromyces lactis and 2 strains with Debaryomyces hansenii artificial chromosomes in Saccharomyces cerevisiae
2012-06-30 | E-GEOD-39011 | biostudies-arrayexpress
Project description:MNase-seq Experiments from Calorie Restricted and Non-Restricted Yeast from WT, ISW2DEL and ISW2K215R strains We used MNase-seq to study genome-wide nucleosome positions under Calorie Restricted and Non-restricted Saccharomyces cerevisiae
2014-09-15 | E-GEOD-53718 | biostudies-arrayexpress
Project description:We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression. Examination of nucleosome positions and transcriptional output through metabolic oscillations in budding yeast.
2016-03-15 | E-GEOD-77631 | biostudies-arrayexpress
Project description:We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of yeast strains that were grown in raffinose and galactose containing media (synthetic complete).
2019-05-14 | GSE116337 | GEO
Project description:We present Micrococcal Nuclease digestion maps of S. cerevisiae through the progression of the Yeast Metabolic Cycle. We demonstrate that nucleosome positions at many promoters are dynamic, and remodeling events at promoters have significant consequences with respect to gene expression.
2016-03-15 | GSE77631 | GEO
Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains.
2015-03-30 | GSE48117 | GEO
Project description:We developed an artificial genome evolution system, which we termed ‘TAQing’, by introducing multiple genomic DNA double-strand breaks using a heat-activatable endonuclease in mitotic yeast. The heat-activated endonuclease, TaqI, induced random DSBs, which resulted in diverse types of chromosomal rearrangements including translocations. Array comparative genomic hybridization (aCGH) analysis was performed with cell-fused Saccharomyces cerevisiae strains induced genome evolution by TAQing system. Some of copy number variations (CNVs) induced by massive genome rearrangements were detected in the TAQed yeast strains.
2018-05-02 | GSE90025 | GEO
Project description:We analyed the nucleosome positions by using 2 concentrations of micrococcal nuclease of haploid yeast strains that were grown in galactose containing synthetic complete media. Strains contained AID-tags at the endogeous TOP1 and TOP2 genes. One strain contained OsTIR1 and these cells were either untreated or treated for 60 min with 500 uM auxin.
2023-04-28 | GSE196945 | GEO
Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains. aCGH analysis of parental and hybrid strains.
2015-03-30 | E-GEOD-48117 | biostudies-arrayexpress
Project description:Abstract: In the yeast S. pombe, multiple chromatin-modifying enzymes are required for heterochromatin formation, yet how their actions alter chromatin structure to block access to DNAby the transcriptional machinery is unknown. We constructed high-resolution nucleosome occupancy maps of heterochromatic regions in wild-type strains and in mutants lacking the H3K9 methyltransferase Clr4 or one of the two activities of the silencing effector complex SHREC. Fourier analysis reveals that these enzymes do not increase the regularity of nucleosome spacing. Rather, their principal effect was to induce the elimination of nucleosome-free regions (NFRs). Both NFRs associated with transcription initiation sites as well as those not associated with promoters are affected. As in S. cerevisiae, repressed genes in euchromatin retain their NFRs. Thus, NFR elimination cannot be explained as a secondary consequence of repression. The maps also show that TFIIIC boundary elements have NFRs resistant to silencing, suggesting a potential role in preventing lateral spread of heterochromatin. NFR elimination offers a mechanism by which heterochromatin restricts access of the transcriptional machinery to DNA. Nucleosome positions in either heterochromatin or euchromatin were mapped in various mutants to determine whether chromatin structure is altered upon heterochromatic silencing. Eight strains were assayed for nucleosome positioning in heterochromatin while two strains were assayed for nucleosome positioning in euchromatin. Two biological replicates were assayed for each strain. No dye swaps were done. RNA transcripts were also mapped using the heterochromatin tiling arrays to determine where RNA transcripts accumulate in heterochromatin. Three strains were assayed for transcripts in heterochromatin by hybridizing cy5-labeled cDNA created from total RNA against cy3-labeled cDNA created from RNA synthesized from sonicated genomic DNA. Two biological replicates were assayed for each strain.
2010-11-24 | E-GEOD-19596 | biostudies-arrayexpress