E-MEXP-1551
Ontology highlight
ABSTRACT:
PROVIDER: E-MEXP-1551 | ExpressionAtlas | 2015-10-22
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Telomeres are nucleoprotein complexes that protect the ends of eukaryotic chromosomes from being recognised as double strand breaks. When telomere structure is perturbed, a co-ordinated series of events to promote arrest of the cell cycle is rapidly initiated so that cells carrying damaged telomeres do not continue to divide. In order to better understand the eukaryotic response to telomere damage, we employed budding yeast strains harbouring a temperature sensitive allele of an essential telomere capping gene (cdc13-1) and conducted a transcriptomic study of the genome-wide response to uncapped telomeres. We show that telomere uncapping in cdc13-1 strains is associated with the differential expression of over 1100 genes and has features in common with the responses to DNA damage, diverse environmental stresses and, as expected, the absence of telomerase. The transcriptomic response to telomere uncapping includes many genes with known roles in telomere function and some features that appear to be unique. BNA2 is the second most highly up-regulated gene upon telomere uncapping in cdc13-1 strains and is required for the biosynthesis of NAD+. We have shown that deletion of BNA2 and other genes involved in NAD+ synthesis, suppresses the temperature sensitivity of cdc13-1 strains. NAD+ synthetic genes may therefore play previously unknown roles in the cellular response to telomere uncapping.
2010-02-24 | E-MEXP-1551 | biostudies-arrayexpress
Project description:We analyzed the effect of deleting the gene encoding putative RNA helicase DBP1 in budding yeast on translational efficiencies (TEs) genome wide in wild-type or ded1-ts (temperature-sensitive allele of DED1) strains by combining ribosome footprint profiling with RNA-seq analysis of mRNA abundance. This study includes a total of 32 samples comprised of 16 RNA-Seq samples (mRNA) and 16 ribosome footprint profiling samples (ribo). Experiment 1 includes 8 samples, comprised of 4 RNA-Seq samples and 4 ribosome footprint profiling samples, derived from 2 biological replicates each of the dbp1Δ and ded1-ts dbp1Δ mutant strains, cultured in synthetic complete (SC) medium, following shifts in growth temperature from 30°C to 37°C for 2h. Experiment 2 examines the effect of overexpression of DBP1 in rescuing genome-wide translational defects of a ded1-cs mutant (cold-sensitive allele of DED1) and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1 (dubbed DED1-CS), ded1-cs and ded1-cs overexpressing DBP1 (ded1-cs_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 15°C for 10 min. Experiment 3 examines rescue of translational defects of ded1-ts by DBP1 overexpression and includes 12 samples, 6 RNA-Seq samples and 6 ribosome footprint profiling samples, derived from 2 biological replicates each of WT DED1(DED1-TS), ded1-ts and ded1-ts overexpressing DBP1 (ded1-ts_hcDBP1) strains, cultured in SC-Leu-His medium, following shifts in growth temperature from 30°C to 37°C for 2h.
2018-03-01 | GSE111255 | GEO
Project description:Assessment of synthetic lethality between a temperature-sensitive allele of CDC102 and Yeast Deletion mutations Keywords: repeat sample
2004-11-05 | GSE1758 | GEO
Project description:We report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 maps of fission yeast mutants with either deletions of non-essential kinetochore genes or conditional inactivation (temperature sensitive, ts) mutations in essential ones. We find that the impairment of the kinetochore componnets cause various levels (from no to prominent) of heterochroamatin spreading into centromeric core regions. Hence, we conclude that the integrity of the inner kinetochore is required to maintain normal centromeric chromatin organization as well as distinct centromere identity.
2019-09-28 | GSE117948 | GEO
Project description:eIF5A is an essential translation elongation factor present in all eukaryotes, and the only known protein to follow a post-translational modification called hypusination. Here, we performed a wide analysis of ribosome dynamics in S. cerevisiae eIF5A depleted cells using 5Pseq (Pelechano et al. 2015 PMID 26046441). This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Since eIF5A is an essential protein in yeast, we used two eIF5A temperature-sensitive strains containing a single Pro83 to Ser mutation (tif51A-1) and double Cys39 to Tyr and Gly118 to Asp mutations (tif51A-3) in the highly expressed gene TIF51A (HYP2) that encodes eIF5A protein (Li et al. 2011 PMID: 24923804).
2017-05-16 | GSE91064 | GEO
Project description:TFIID plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TAF subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse. Yeast (Saccharomyces cerevisiae) TAF1 reportedly possesses at least four distinct activities including a histone acetyltransferase, and TBP, TAF, and promoter binding. Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability. To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature sensitive taf1ts2 yeast strain. After galactose-induction and temperature inactivation of the temperature-sensitive allele, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription. Virtually all TAF1-dependent genes, which comprise ~90% of the yeast genome, displayed a strong dependency upon all regions of TAF1 that were tested. This might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or that all TAF1-dependent genes require the many activities of TAF1. Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes. Keywords: genetic modification
2006-01-10 | GSE3006 | GEO
Project description:Here, we report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. We generated genome-wide H3K9me2 maps of fission yeast mutants in swo1-26 (temperature sensitive, ts) cells at 25℃ and 37℃. We find that H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects.
2020-06-18 | GSE140617 | GEO
Project description:To identify conditional alleles which disrupt the splicing pathway, we screened a collection of ~2000 chemically mutagenized temperature-sensitive fission yeast isolates for intron accumulation in three introns, including a naturally occurring U2-dependent AT-AC intron. We identified 54 strains which accumulate unspliced message at the non-permissive temperature. A combination of mutation effect prediction and genetic mapping techniques revealed missense mutations in core splicing genes which function at various steps of spliceosome assembly and activation including: prp10, prp28, sap61, ntr1, spp42, sap114, cwf22, and prp22. Interrogation of structural data and genome-wide analysis of the splicing defects in these mutations revealed intron-specific defects which suggest the biochemical basis for these mutations’ effects on splicing.
2020-11-13 | GSE161333 | GEO
Project description:The Mediator is composed of multiple of proteins in the head, body, tail and CDK subunits conserved from yeast to humans. However, not all the components are required for transcription. Components of the tail subunit are not essential but to varying degrees are required for changes in transcription to stress. While some stresses are familiar such as heat, desiccation, and starvation, others are exotic yet elicit a physical stress response. MCHM is a hydrotrope that induces growth arrest in yeast. By exploiting genetic variation, specifically in Med15, between yeast strains, we found that Med15 with the polyQ expansion conferred MCHM sensitivity. This sensitivity was not from a loss of function as the reciprocal hemizygous hybrids were all sensitive, suggesting that there is an incompatibility between Mediator complexes from genetic divergent yeast strains. Transcriptomics from yeast expressing the incompatible Med15 changed expression in diverse pathways. Expansion of polyQ tracts in Med15 resulted in multiple isoforms which were mostly from likely post-translational modifications. Stability of Med15 was dependent on Ydj1, a chaperone and the incompatible Med15 allele was expressed at lower levels and less stable than the compatible Med15 allele. Med15 is tethered to the rest of the Mediator complex via Med2 and 3. Deletion of either Med2 or Med3 changes the Med15 isoform patterns in the in a similar manner whereas deletion of Med5, a distal component of the tail did not change the pattern. The med2 and 3 mutants are similarly sensitive to MCHM while med5 mutants are not. Differences between the Med15 alleles extend to responses to different stresses. Whereas the incompatible allele of Med15 improved growth to chemicals that produce free radicals, and the compatible allele of Med15 improved growth to reducing agents, caffeine, and hydroxyurea. This may reflect the positive and negative role that Med15 has in transcription.
2020-04-06 | GSE129898 | GEO
Project description:Elucidation of the mechanism of temperature tolerance in yeast is essential for enhancing cellular robustness of strains, providing more economically and sustainable sound industrial processes. We investigated the differential responses of three distinct Saccharomyces cerevisiae strains, an industrial wine strain, ADY5, a laboratory strain, CEN.PK113-7D and an industrial bioethanol strain, Ethanol Red, grown at sub- (12 ºC) and-supra (39 ºC) optimal temperatures under chemostat conditions, in which specific growth rate–dependent changes are eliminated. In contrast to previous studies, we employed anaerobic conditions, mimicking the industrial processes. The proteomic profile of these strains was performed by SWATH-MS, allowing the quantification of 997 proteins. Our analysis revealed that temperature response differs between the strains, highlighting the precision with which each strain responds to changes in its environment; however, we also found some common responsive proteins among the strains, revealing that the response to temperature involves general stress and specific mechanisms. Overall, sub-optimal temperature conditions involved a higher remodeling of the proteome than supra-optimal temperature. Further, the proteomic data evidenced that the cold response involves a strong repression of translation related proteins as well as induction of amino acid metabolism, together with components related to protein folding and degradation. On the other hand, the high temperature response mainly recruits amino acid metabolism. Our study provides a global and thorough insight into how growth temperature affects yeast proteome, which can be a step forward for research regarding the comprehension and the improvement of yeast thermotolerance.
2021-01-04 | PXD016567 | Pride