Sequencing of rapamycin-treated yeast strains across genetic backgrounds, with and without U18
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE315721 | GEO | 2026/01/14
REPOSITORIES: GEO
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Project description:This analysis correspond to the transcripts of four different yeast strains (NA, WA, WE, and SA) untreated and treated with the Ncr1p inhibitor U18666A
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Project description:Sequencing of rapamycin-treated yeast strains across genetic backgrounds, with and without U18
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Project description:Purpose: We develop a multivariate polynomial temporal genetic association (MPTGA) approach for detecting temporal genetic loci of quantitative traits monitored over time in a population. To dissect causal regulators under each temporal genetic locus, we develop a temporal genetic causality test (TGCT) for inferring causal relationships between traits linked to the locus. We applied MPTGA and TGCT to simulated data sets and a yeast population that was molecularly profiled over six time points in response to treatment with the drug rapamycin. We demonstrate significantly increased power to detect genetic loci modulating gene expression traits over time in this population and to resolve the causal regulators of dynamic expression quantitative loci hot spots, thereby increasing the power to elucidate regulatory networks. We experimentally validated a teQTL (temporal expression Quantitative Trait Locus) hot spot locus interacting with rapamycin treatment over time, which could only be identified using our temporal genetic association procedure. We experimentally validated RRD1, a cis regulated gene in this locus, as the causal regulator for this teQTL hot spot. Methods: The wild type strain BY4730 and RRD1 knockout strain YSC6273-201925697 were obtained from Thermo Scientific Open Biosystems. Yeast was grown in YPD medium to log-phase in shaken flasks at 30°C. Total RNA was extracted as described previously. For rapamycin treatment, 100nM rapamycin (Cayman Chemical, Ann Arbor, MI) was added to the medium after yeast grew to log-phase. After culture for 50 minutes, total RNA was extracted the same as above. All experiments were repeated 3 times on three different days. Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions. Sequence reads were aligned to yeast genome assembly using Tophat . Total 6,932 yeast transcripts were quantified using Cufflinks, and 5,542 of them overlap with transcripts on Yeast Genome 2.0 Arrays from Affymatrix, which was used for generating the yeast F2 time course data. The 5,542 transcripts were used in further analysis. Differentially expressed genes were defined by CuffDiff. At q-value <0.01, 64 and 581 were in RRD1 ko signature without rapamycin (RRD1 ko no treatment vs. wild type no treatment) and RRD1 ko signature with rapamycin (RRD1 ko with rapamycin vs. wild type with rapamycin), respectively. Conclusions: Integration of temporal and genetic data has the potential to enhance the power to resolve causal relationships and to provide a more accurate view of regulatory networks in complex biological systems.
2018-12-21 | GSE86786 | GEO
Project description:We obtained RNA polymerase II occupancy profile across the genome of S.cerevisiae in several strains, Wild type at 25 and 37 degrees C, RNA15-1 at 25 and 37 degrees C, anchor-away parental strain plus rapamycin, Reb1 anchor-away plus rapamycin, Rap1 anchor-away plus rapamycin, Nrd1-AID plus auxin, and nrd1-AID without auxin. This allowed us to compare polymerase profiles when these proteins are depleted from the nucleus.
2018-01-10 | GSE97913 | GEO
Project description:Determination of RNAPII, Rrd1-Myc, RNAPII-Ser2-P, RNAPII-Ser5-P abundance between wildtype and rrd1 deletion strains under rapamycin or control treatments.Rapamycin is an anticancer agent and immunosuppressant that acts by inhibiting the TOR signaling pathway. In yeast, rapamycin mediates a profound transcriptional response for which the RRD1 gene is required. To further investigate this connection, we performed genome-wide association studies of RNA polymerase II (RNAPII) and Rrd1 in response to rapamycin and demonstrate that Rrd1 colocalizes with RNAPII on actively transcribed genes and both are recruited to rapamycin responsive genes. Strikingly, when Rrd1 is lacking, RNAPII remains inappropriately associated to ribosomal genes and fails to be recruited to rapamycin responsive genes. This occurs independently of TATA box binding protein recruitment. Furthermore, Rrd1 modulates the phosphorylation status of RNAPII CTD and additional evidence suggests that Rrd1 is involved in various transcriptional stress responses. We propose that Rrd1 is a novel transcription elongation factor that fine-tunes the transcriptional stress response of RNAPII.
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Project description:p73 is a p53 family transcription factor that plays critical roles during development and tumor suppression. We analyzed p73 activity using a combination of ChIP-on-Chip and gene expression profiling, both at baseline and after treatment with the mTOR inhibitor rapamycin. We report the first comprehensive analysis of p73 binding across the genome. Furthermore, we re-analyzed this p73 cistrome after perturbation with rapamycin, an inhibitor of mTOR and inducer of p73. Multiple determinants of p73 binding, activity, and function were evident, and were modulated by mTOR.
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Project description:A diploid yeast strain was grown at 30C in YPD medium. At an OD of 0.6 (600nm) rapamycin was added to a final concentration of 0.20 ug/ml and the incubation continued for 90 min. A control culture was treated with an equal amount of DMSO vehicle. Cells were harvested at an OD of 0.9 rapamycin and 1.1 control.
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Project description:Compound CID 3538206 inhibits yeast TORC1 activity and functionally mimic rapamycin. We used microarrays to compare the global gene expression with the treatment of CID 3528206 and rapamycin.
2012-05-01 | GSE33320 | GEO
Project description:We are interested in the study of the sensitivity of yeast cells lacking either the type 1 protein phosphatase Ptc6 or Ptc1 and Ptc6 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in wild type, ptc6 mutant and ptc1 ptc6 double mutant cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells and characterized an notable attenuation of the transcriptional response in cells lacking either PTC6 or PTC1 and PTC6 genes.
2013-04-19 | GSE38256 | GEO
Project description:We are interested in the study of the already reported sensitivity of yeast cells lacking the type 1 protein phosphatase Ptc1 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in both, wild type and ptc1 cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells. Under our working conditions rapamycin increased, in wild type cells, at least 2-fold the expression of 667 genes, whereas it decreased the mRNA level of 721 genes (13.8% and 14.9% of genes with measurable expression level, respectively). Gene ontology analysis shows that, as previously documented, many induced genes falls into the NCR, Msn2/Msn4 regulated stress response or Retrograde response categories, whereas genes encoding cytoplasmic, but not mitochondrial, ribosomal proteins and the so called RIBI regulon where largely repressed. Deletion of PTC1 decreases the number of genes induced or repressed at least 2-fold by rapamycin treatment. Remarkably, lack of Ptc1 seems to lead to a general attenuation of changes triggered by rapamycin.
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