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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of S. cerevisiae rrp6 delta vs. controls

ABSTRACT: BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30Â°C to OD 0.6 in YPD. BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30Â°C to OD<0.6 in YPD.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Alain Jacquier

PROVIDER: E-GEOD-2579 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase.

Wyers Françoise F Rougemaille Mathieu M Badis Gwenaël G Rousselle Jean-Claude JC Dufour Marie-Elisabeth ME Boulay Jocelyne J Régnault Béatrice B Devaux Frédéric F Namane Abdelkader A Séraphin Bertrand B Libri Domenico D Jacquier Alain A

Cell 20050601 5

Since detection of an RNA molecule is the major criterion to define transcriptional activity, the fraction of the genome that is expressed is generally considered to parallel the complexity of the transcriptome. We show here that several supposedly silent intergenic regions in the genome of S. cerevisiae are actually transcribed by RNA polymerase II, suggesting that the expressed fraction of the genome is higher than anticipated. Surprisingly, however, RNAs originating from these regions are rap ...[more]

PMID: 15935759

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rrp6 delta and rrp6 delta, trf4 delta vs WT

Project description:BMA64 rrp6 delta::HIS3 vs BMA64 WT (Mat a), grown at 30°C to OD 0.6 in YPD. BMA64 rrp6 delta::URA3, trf4 delta::KAN vs BMA64 WT, grown at 30°C to OD<0.6 in YPD. Keywords: other

2005-04-28 | GSE2579 | GEO

Saccharomyces cerevisiae

Project description:rrp6 delta and rrp6 delta, trf4 delta vs WT

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Project description:Red channel: 3 independent polysome preparations from BY4741 cells, grown in YPD to mid-log phase (OD 0.6-0.9). In each experiment 14 fractions were collected. In-vitro transcribed B.subtilis controls were added to each fraction and used for normalization. Green channel: Total RNA prepared from S288c cells. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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ChIP-chip analyses of H3K9 methylation in rrp6 deletion and rrp6 alp13 double mutant S.pombe cells.

Project description:ChIP-chip analyses of H3K9 methylation in rrp6 deletion (exosome mutant) and in rrp6 alp13 double mutant S.pombe cells. Keywords: ChIP-chip

2007-04-23 | GSE7136 | GEO

RNA processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.

Project description:Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by HR, suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability. Strand-specific transcriptome analysis of biological replicates of WT cells (JKM139 strain) at T0, or 60 and 240 minutes after HO induction, and of xrn1∆, rrp6∆ and trf4∆ cells at T0.

2014-11-20 | E-GEOD-63444 | biostudies-arrayexpress

Perturbation of mRNP biogenesis reveals a dynamic landscape of the Rrp6-dependent surveillance machinery trafficking along the yeast genome (RNA-seq dataset)

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2019-12-04 | E-MTAB-7538 | biostudies-arrayexpress

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2019-12-04 | E-MTAB-7539 | biostudies-arrayexpress

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Transcription profiling of yeast treated with rapamycin

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.

2003-11-09 | E-MANP-2 | biostudies-arrayexpress

An Interaction between RRP6 and SU(VAR)3-9 Targets RRP6 to Heterochromatin and Contributes to Heterochromatin Maintenance in Drosophila melanogaster [RNA-seq]

Project description:We have investigated the effect of RRP6 depletion on the transcriptome of S2 cells using Illumina deep RNA sequencing. We have also carried out Illumina ChIP-seq analysis of RRP6 genome occupancy in control S2 cells (GFP-KD) and in cells depleted of SU(VAR)3-9.

2015-08-20 | GSE70625 | GEO

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