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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression dynamics in yeast BY4741 and a strain lacking MSN2 and MSN4 responding to 0.4mM H2O2 over time (0-60min)

ABSTRACT: Numerous factors have been implicated in regulating gene expression changes, including changes to nucleosome occupancy. Here we followed dynamic changes to nucleosome occupancy, gene expression and DNA binding of the transcription factor Msn2p genome-wide in yeast cells responding to hydrogen peroxide and reveal new relationships between regulators of stress-dependent gene expression in yeast. Gene expression was measured in response to 0.4mM H2O2 in the S288c derivative BY4741 in wild-type cells and cells lacking MSN2 and MSN4. A single replicate of a time course spanning from 4 to 60 minutes after treatment in each cell type. An additional 3 repliactes were collected from cells 30 minutes after treatment.

ORGANISM(S): Saccharomyces cerevisiae S288c

SUBMITTER: Dana Huebert

PROVIDER: E-GEOD-30899 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators.

Huebert Dana J DJ Kuan Pei-Fen PF Keleş Sündüz S Gasch Audrey P AP

Molecular and cellular biology 20120221 9

The response to stressful stimuli requires rapid, precise, and dynamic gene expression changes that must be coordinated across the genome. To gain insight into the temporal ordering of genome reorganization, we investigated dynamic relationships between changing nucleosome occupancy, transcription factor binding, and gene expression in Saccharomyces cerevisiae yeast responding to oxidative stress. We applied deep sequencing to nucleosomal DNA at six time points before and after hydrogen peroxide ...[more]

PMID: 22354995

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Dynamic changes to nucleosome occupancy and genomic expression in yeast responding to oxidative stress

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Cells pretreated with NaCl have an altered gene expression in response to H2O2.

Project description:BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.

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Nucleosome occupancy in yeast BY4741and a strain lacking MSN2 and MSN4 responding to 20 min treatment with 0.4mM H2O2

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2012-06-17 | E-GEOD-30897 | biostudies-arrayexpress

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2010-12-17 | E-GEOD-22904 | biostudies-arrayexpress

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