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Effects of temperature change within the readily tolerated range on transcription and DNA accessibility in the Drosophila S2R+ cell line

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE159174 | GEO | 2021/09/13

REPOSITORIES: GEO

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Effects of temperature change within the readily tolerated range on transcription and DNA accessibility in the Drosophila S2R+ cell line

Project description:Effects of temperature change within the readily tolerated range on transcription and DNA accessibility in the Drosophila S2R+ cell line

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Effects of ambient temperature on DNA accessibility in nuclear chromatin of Drosophila S2R+ cells [ATAC-seq]

Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation, including the transcriptional level. To study effects of changes in ambient temperature on chromatin accessibility, we performed ATAC-Seq with S2R+ cells, a line derived from embryos of the ectothermic organism Drosophila melanogaster. Aliquots of S2R+ cells were exposed to different temperatures (14, 25 and 29°C) within the readily tolerated range before analysis with ATAC-Seq.

2021-09-13 | GSE159221 | GEO

Temporal dynamics of transcriptome change in Drosophila S2R+ cells after a temperature shift from 25 to 14°C

Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to distinct temperatures is predicted to involve complex regulation. To assess the effects of a temperature downshift from 25 to 14°C, i.e. from the optimal temperature to the lower limit of the readily tolerated range, on the transcriptome in a time-resolved manner, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.

2021-09-13 | GSE159172 | GEO

Temperature dependence of the transcriptome in cultured Drosophila S2R+ cells

Project description:Cells in ectothermic organisms often maintain homeostatic function over a considerable range of ambient temperatures. However, as temperature has pronounced effects on all biological processes, but not necessarily in a uniform manner on each of the myriad of distinct processes, cellular acclimation to ambient temperature change is predicted to involve complex regulation. To assess the effects of temperature change within the readily tolerated temperature range on the transcriptome, we have performed expression profiling with S2R+ cells, which are derived from the ectothermic organism Drosophila melanogaster.

2021-09-13 | GSE159170 | GEO

Effects of ambient temperature on DNA accessibility in nuclear chromatin of Drosophila S2R+ cells [ATAC-seq]

Project description:Effects of ambient temperature on DNA accessibility in nuclear chromatin of Drosophila S2R+ cells [ATAC-seq]

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Large diurnal temperature range increases bird sensitivity to climate change.

Project description:Climate variability is changing on multiple temporal scales, and little is known of the consequences of increases in short-term variability, particularly in endotherms. Using mortality data with high temporal resolution of zebra finches living in large outdoor aviaries (5 years, 359.220 bird-days), we show that mortality rate increases almost two-fold per 1°C increase in diurnal temperature range (DTR). Interestingly, the DTR effect differed between two groups with low versus high experimentally manipulated foraging costs, reflecting a typical laboratory 'easy' foraging environment and a 'hard' semi-natural environment respectively. DTR increased mortality on days with low minimum temperature in the easy foraging environment, but on days with high minimum temperature in the semi-natural environment. Thus, in a natural environment DTR effects will become increasingly important in a warming world, something not detectable in an 'easy' laboratory environment. These effects were particularly apparent at young ages. Critical time window analyses showed that the effect of DTR on mortality is delayed up to three months, while effects of minimum temperature occurred within a week. These results show that daily temperature variability can substantially impact the population viability of endothermic species.

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Effect of histone H2Av depletion on temperature dependence of the Drosophila S2R+ cell transcriptome

Project description:The histone H2A variant H2A.Z has a crucial role in the regulation of temperature-dependent gene expression in the plant Arabidopsis thaliana. To evaluate whether the Drosophila homolog histone H2Av has a similar role in the control of the transcriptional response to temperature change, we depleted this histone variant by RNA interference in S2R+ cells and analyzed the effect on the transcriptome after temperature shifts to different temperatures (14, 25 and 30°C). For control, we performed analogous experiments using treatment with lacZ dsRNA instead of His2Av dsRNA.

2021-09-13 | GSE159171 | GEO

Drosophila S2R+ / TSC1 / TSC2 mutant phosphoproteomics

Project description:The tuberous sclerosis complex (TSC) family of tumor suppressors, TSC1 and TSC2, function together in an evolutionarily conserved protein complex that is a point of convergence for major cell signaling pathways that regulate mTOR complex 1 (mTORC1). Mutation or aberrant inhibition of the TSC complex is common in various human tumor syndromes and cancers. The discovery of novel therapeutic strategies to selectively target cells with functional loss of this complex is therefore of substantial clinical relevance to TSC and sporadic cancers. We developed a CRISPR-based method to generate homogenous mutant Drosophila cell lines. By combining TSC1 and TSC2 mutant cell lines with RNAi screens against all kinases and phosphatases, we identified synthetic interactions with TSC1 and TSC2. Knockdown of three candidate genes (mRNA-cap, Pitslre and CycT; orthologs of RNGTT, CDK11 and CCNT1 in humans) reduced the population growth rate of both Drosophila TSC1 and TSC2 mutant cells but not that of wild-type cells. Moreover, knockdown of all three genes displayed similar selective effects in mammalian TSC2-deficient cell lines, including human tumor-derived cells, illustrating the power of this cross species screening strategy to identify potential drug targets.

2018-10-24 | PXD002670 | Pride

De novo genome assemblies for the Drosophila melanogaster cell line Schneider 2 (S2R+) and the inbred fly strain A4

Project description: Not available

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CRISPR-based engineering of gene knockout cells by homology-directed insertion in polyploid Drosophila S2R+ cells.

Project description:Precise and efficient genome modifications provide powerful tools for biological studies. Previous CRISPR gene knockout methods in cell lines have relied on frameshifts caused by stochastic insertion/deletion in all alleles. However, this method is inefficient for genes with high copy number due to polyploidy or gene amplification because frameshifts in all alleles can be difficult to generate and detect. Here we describe a homology-directed insertion method to knockout genes in the polyploid Drosophila S2R+ cell line. This protocol allows generation of homozygous mutant cell lines using an insertion cassette which autocatalytically generates insertion mutations in all alleles. Knockout cells generated using this method can be directly identified by PCR without a need for DNA sequencing. This protocol takes 2-3 months and can be applied to other polyploid cell lines or high-copy-number genes.

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