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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation

ABSTRACT: This SuperSeries is composed of the following subset Series: GSE18240: Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min GSE18241: S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min GSE18605: Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress Refer to individual Series

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Benjamin Pina

PROVIDER: E-GEOD-18242 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.

Joshi Ricky S RS Piña Benjamin B Roca Joaquim J

The EMBO journal 20100107 4

How DNA helical tension is constrained along the linear chromosomes of eukaryotic cells is poorly understood. In this study, we induced the accumulation of DNA (+) helical tension in Saccharomyces cerevisiae cells and examined how DNA transcription was affected along yeast chromosomes. The results revealed that, whereas the overwinding of DNA produced a general impairment of transcription initiation, genes situated at <100 kb from the chromosomal ends gradually escaped from the transcription sta ...[more]

PMID: 20057354

Similar Datasets

Saccharomyces cerevisiae cells: control vs positive supercoiling accumulation after 0, 30 and 120 min

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Îtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation. Two-condition experiment: delta top1-TOPA vs delta top1 top2-ts-TOPA. 3 time points: 0min, 30min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2010-05-19 | E-GEOD-18240 | biostudies-arrayexpress

S. cerevisiae cells: control vs positive supercoiling accumulation in absence of telomere silencing after 0 and 120 min

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in M-NM-^Ttop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Keywords: Time course of positive helical tension accumulation in absence of telomere silencing. Two-condition experiment: delta top1 delta sir3-TOPA vs delta top1 delta sir3 top2-ts-TOPA. 2 time points: 0min, 120min. 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2009-12-01 | E-GEOD-18241 | biostudies-arrayexpress

Saccharomyces cerevisiae cells: effect of Top2 depletion without accumulation of positive superhelical stress

Project description:Positive DNA helical stress accumulates in vivo by the unbalanced relaxation of positive and negative DNA supercoils in Îtop1, top2ts, pGPD:TopA yeast cells. The resulting overwinding of DNA greatly diminishes overall RNA synthesis. Here we show that whereas most genes reduce their transcript levels by several fold, genes situated at less than 100 kb from the chromosomal ends (near 15% of the genome) are gradually unaffected. This positional effect denotes that chromosomal ends are topologically open, thus precluding the accumulation of DNA helical stress in telomere-proximal regions. The progressive escape from the transcription stall observed in all the chromosome extremities indicates also that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, suffice to confine DNA helical tension along eukaryotic chromatin. Two-condition experiment, JCW25 vs top2-ts-TOPA (JCW26). 3 biological replicates per condition and time point, independently grown in leu- selective media and harvested.

2010-05-18 | E-GEOD-18605 | biostudies-arrayexpress

Profiling thimet oligopeptidase-mediated proteolysis in Arabidopsis thaliana

Project description:Plant stress caused by pathogens or though abiotic means (e.g. drought or temperature) reduces agricultural yields, causing substantial economic losses while reducing food security at the global level. It is critical to recognize how plants perceive stress signals to elicit responses for survival. Endogenous plant peptidases and their peptide products play an important role in the signaling of plant immune processes. Thimet oligopeptidases (TOPs) are zinc-dependent peptide hydrolases with a conserved HEXXH active site motif. These metallopeptidases are critical components in plant response to oxidative stress triggered by pathogens or abiotic factors and are required for a fully functioning immune response to certain pathogens. Further characterization of plant TOPs and their peptide substrates would provide insights into their contribution to defense signaling, stress perception, and plant adaptation pathways. Herein, a quantitative mass spectrometry-based peptidomics approach was implemented to characterize the Arabidopsis thaliana plant peptidome and in the context TOPs (Fig. 1). A comparison between wild type (Col-0) and top1top2 null mutant revealed putative direct and indirect TOPs substrates in vivo.

2021-01-25 | PXD019928 | Pride

ssa1/2 deletion mutant

Project description:Yeast strain lacking the two genes SSA1 and SSA2, which encode cytosolic chaperones, acquires thermotolerance as well as the mild heat-shocked wild-type yeast strain. Series containes 3 independent experiments.

2010-06-30 | E-GEOD-3315 | biostudies-arrayexpress

Proteome-wide analysis of cysteine reactivity in Arabidopsis associated with biotic stress response

Project description:We used a method for the enrichment of proteins with oxidative post-translational modifications that enabled the comprehensive identification and label-free quantification of reversibly oxidized thiols across the plant proteome. The redoxomes were characterized in wild-type and the top1top2 null mutants in the early stages of effector-triggered immunity.

2019-03-19 | PXD010104 | Pride

Genome-wide nucleosome position data for 3 yeast species

Project description:Genome-wide nucleosome position data for wildtype and mutant strains in S. cerevisiae, C. albicans, and S. pombe Illumina sequencing of mononucleosomal DNA isolated from mid-log cultures grown in rich medium (abbreviated CM, in house recipe). S. pombe samples were grown in YES medium at permissive temperature (30C) and restrictive temperature (35C)

2011-08-01 | E-GEOD-28839 | biostudies-arrayexpress

Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress

Project description:An integrated genomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcase chilling in cold air. The response of E. coli during exponential growth at 25°C aw 0.985, 14°C aw 0.985, 25°C aw 0.967 and, 14°C aw 0.967 was compared to that of a reference culture (35°C aw 0.993).

2011-12-29 | E-MTAB-623 | biostudies-arrayexpress

TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts

Project description:Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate - a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc) - is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase, TDP1, which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3’ phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. We find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.

2020-03-13 | PXD017239 | Pride

non-M1 covRS-intact and -mutant GAS vs M1 controls

Project description:Microarray was performed on RNA extracted from mid-logarithmic phase in vitro grown non-M1 Streptococcus pyogenes isolates, with either intact or mutant covRS operons. These isolates were compared with corresponding M1 covRS intact and mutant forms to link the expression prolfiles of these non-M1 isolates with invasive pathogenesis. A dye-swapped cyclic design was used in this study in order that each strain could be compared across all samples in silico. For each strain treated, 2 biological replicates were each analysed in dye-swapped technical replicates, giving a total of n=4 peplicates for each strain.

2010-08-27 | E-GEOD-23825 | biostudies-arrayexpress

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