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Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities.

Castells-Roca L, García-Martínez J, Moreno J, Herrero E, Bellí G, Pérez-Ortín JE - PLoS ONE (2011)

Bottom Line: This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response.In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found.The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.

View Article: PubMed Central - PubMed

Affiliation: Departament de Ciències Mèdiques Bàsiques and IRBLleida, Universitat de Lleida, Lleida, Catalunya, Spain.

ABSTRACT
We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25 °C to 37 °C. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO promoter. This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response. In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found. The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.

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Related in: MedlinePlus

Clustering of TR and RA data.Time course profiles for both parameters were considered for clustering. Both dataset series are normalized to time 0 value to allow a comparison between the TR and RA data. The discontinuation between the last TR point and the time 0 RA value has no real meaning and is represented as a vertical black bar. For each cluster in the tree, the number of genes and data profiles are indicated. Ordinates are on a log scale, and the horizontal line in each graph marks the time 0 level. The most significant GO categories (p value ≤10−5) are shown. The individual data for each gene and the list of genes in each cluster can be seen in Tables S1 and S2, respectively. The scale bar on the lower left side reflects the distances between the cluster profiles.
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pone-0017272-g002: Clustering of TR and RA data.Time course profiles for both parameters were considered for clustering. Both dataset series are normalized to time 0 value to allow a comparison between the TR and RA data. The discontinuation between the last TR point and the time 0 RA value has no real meaning and is represented as a vertical black bar. For each cluster in the tree, the number of genes and data profiles are indicated. Ordinates are on a log scale, and the horizontal line in each graph marks the time 0 level. The most significant GO categories (p value ≤10−5) are shown. The individual data for each gene and the list of genes in each cluster can be seen in Tables S1 and S2, respectively. The scale bar on the lower left side reflects the distances between the cluster profiles.

Mentions: By following the GRO experimental procedures [16], we have determined the TR and RA values for 5532 yeast genes during the S. cerevisiae cell response to moderate heat shock. The signals obtained for both parameters were normalized by genomic DNA hybridization to fully compare the values obtained for individual genes. These values are listed in Table S1. Both the TR and RA data were used to perform the clustering analyses. Values relative to t0 were used to avoid differences in scale for these two datasets. Therefore, TR and RA at t0 take a value of 0 in the log scale. The ten-point profiles obtained reflect the variation of TR (first 5 points) and its effect on RA (last 5 points, Fig. 2). As in a previous work [4], most of the mRNAs in our experiment are not under steady-state conditions (RA is not constant) and, therefore, RA profiles depend on both TR and mRNA stability according to kinetic laws [3].


Heat shock response in yeast involves changes in both transcription rates and mRNA stabilities.

Castells-Roca L, García-Martínez J, Moreno J, Herrero E, Bellí G, Pérez-Ortín JE - PLoS ONE (2011)

Clustering of TR and RA data.Time course profiles for both parameters were considered for clustering. Both dataset series are normalized to time 0 value to allow a comparison between the TR and RA data. The discontinuation between the last TR point and the time 0 RA value has no real meaning and is represented as a vertical black bar. For each cluster in the tree, the number of genes and data profiles are indicated. Ordinates are on a log scale, and the horizontal line in each graph marks the time 0 level. The most significant GO categories (p value ≤10−5) are shown. The individual data for each gene and the list of genes in each cluster can be seen in Tables S1 and S2, respectively. The scale bar on the lower left side reflects the distances between the cluster profiles.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045430&req=5

pone-0017272-g002: Clustering of TR and RA data.Time course profiles for both parameters were considered for clustering. Both dataset series are normalized to time 0 value to allow a comparison between the TR and RA data. The discontinuation between the last TR point and the time 0 RA value has no real meaning and is represented as a vertical black bar. For each cluster in the tree, the number of genes and data profiles are indicated. Ordinates are on a log scale, and the horizontal line in each graph marks the time 0 level. The most significant GO categories (p value ≤10−5) are shown. The individual data for each gene and the list of genes in each cluster can be seen in Tables S1 and S2, respectively. The scale bar on the lower left side reflects the distances between the cluster profiles.
Mentions: By following the GRO experimental procedures [16], we have determined the TR and RA values for 5532 yeast genes during the S. cerevisiae cell response to moderate heat shock. The signals obtained for both parameters were normalized by genomic DNA hybridization to fully compare the values obtained for individual genes. These values are listed in Table S1. Both the TR and RA data were used to perform the clustering analyses. Values relative to t0 were used to avoid differences in scale for these two datasets. Therefore, TR and RA at t0 take a value of 0 in the log scale. The ten-point profiles obtained reflect the variation of TR (first 5 points) and its effect on RA (last 5 points, Fig. 2). As in a previous work [4], most of the mRNAs in our experiment are not under steady-state conditions (RA is not constant) and, therefore, RA profiles depend on both TR and mRNA stability according to kinetic laws [3].

Bottom Line: This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response.In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found.The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.

View Article: PubMed Central - PubMed

Affiliation: Departament de Ciències Mèdiques Bàsiques and IRBLleida, Universitat de Lleida, Lleida, Catalunya, Spain.

ABSTRACT
We have analyzed the heat stress response in the yeast Saccharomyces cerevisiae by determining mRNA levels and transcription rates for the whole transcriptome after a shift from 25 °C to 37 °C. Using an established mathematical algorithm, theoretical mRNA decay rates have also been calculated from the experimental data. We have verified the mathematical predictions for selected genes by determining their mRNA decay rates at different times during heat stress response using the regulatable tetO promoter. This study indicates that the yeast response to heat shock is not only due to changes in transcription rates, but also to changes in the mRNA stabilities. mRNA stability is affected in 62% of the yeast genes and it is particularly important in shaping the mRNA profile of the genes belonging to the environmental stress response. In most cases, changes in transcription rates and mRNA stabilities are homodirectional for both parameters, although some interesting cases of antagonist behavior are found. The statistical analysis of gene targets and sequence motifs within the clusters of genes with similar behaviors shows that both transcriptional and post-transcriptional regulons apparently contribute to the general heat stress response by means of transcriptional factors and RNA binding proteins.

Show MeSH
Related in: MedlinePlus