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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

Sub-partition of genes in clusters 11 and 12 and Transcription Factor enrichment analysis.The genes in clusters 11 and 12 of Figure 2 (listed in Table S2) were partitioned into subclusters using the same criteria as for the general clustering analysis. See the legend of Figure 2 for details of the representation. The most significant GO categories in each resulting subcluster (p value≤10−5) are shown on the right. Transcription factor targets enrichment in each cluster (left) or subcluster (right) is shown with its p-value. nf: not significant categories found.
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pone-0017272-g003: Sub-partition of genes in clusters 11 and 12 and Transcription Factor enrichment analysis.The genes in clusters 11 and 12 of Figure 2 (listed in Table S2) were partitioned into subclusters using the same criteria as for the general clustering analysis. See the legend of Figure 2 for details of the representation. The most significant GO categories in each resulting subcluster (p value≤10−5) are shown on the right. Transcription factor targets enrichment in each cluster (left) or subcluster (right) is shown with its p-value. nf: not significant categories found.

Mentions: The lower part of the tree (clusters 11–16) may be considered as a whole because of the short branches connecting the clusters. In all cases, RA is upregulated upon heat shock which, in most cases, is paralleled by a more or less sustained increase of TR. The exceptions are clusters 15 and 16, where TR remains constant (cluster 15) or decreases (cluster 16), while RA increases in a sustained manner, suggesting mRNA stabilization effects. Remarkably, clusters 11 and 12 together represent 80% of the upregulated genes analyzed in this study, which indicates a rather homogeneous behavior among the yeast genes in this positive response to heat shock. In both clusters, TR displays a strong upregulation upon stress; yet while there is a delayed but sustained increase of RA in cluster 11 (enriched in the ‘Proteasome complex’ and ‘Endoplasmic reticulum’ GO categories, see below), the RA increase in cluster 12 is faster and stronger. Although these differences may appear as minor ones, they suggest a marked divergence in mRNA stability upon heat shock between genes of clusters 11 and 12 (see below). A more stringent clustering analysis of the genes of clusters 11 and 12 resulted in four and three subgroups respectively (Fig. 3). Proteasome complex genes mostly fall grouped in the subcluster 11D in this Fig. 3, which denotes a homogeneous behavior of these GO category genes.


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)

Sub-partition of genes in clusters 11 and 12 and Transcription Factor enrichment analysis.The genes in clusters 11 and 12 of Figure 2 (listed in Table S2) were partitioned into subclusters using the same criteria as for the general clustering analysis. See the legend of Figure 2 for details of the representation. The most significant GO categories in each resulting subcluster (p value≤10−5) are shown on the right. Transcription factor targets enrichment in each cluster (left) or subcluster (right) is shown with its p-value. nf: not significant categories found.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017272-g003: Sub-partition of genes in clusters 11 and 12 and Transcription Factor enrichment analysis.The genes in clusters 11 and 12 of Figure 2 (listed in Table S2) were partitioned into subclusters using the same criteria as for the general clustering analysis. See the legend of Figure 2 for details of the representation. The most significant GO categories in each resulting subcluster (p value≤10−5) are shown on the right. Transcription factor targets enrichment in each cluster (left) or subcluster (right) is shown with its p-value. nf: not significant categories found.
Mentions: The lower part of the tree (clusters 11–16) may be considered as a whole because of the short branches connecting the clusters. In all cases, RA is upregulated upon heat shock which, in most cases, is paralleled by a more or less sustained increase of TR. The exceptions are clusters 15 and 16, where TR remains constant (cluster 15) or decreases (cluster 16), while RA increases in a sustained manner, suggesting mRNA stabilization effects. Remarkably, clusters 11 and 12 together represent 80% of the upregulated genes analyzed in this study, which indicates a rather homogeneous behavior among the yeast genes in this positive response to heat shock. In both clusters, TR displays a strong upregulation upon stress; yet while there is a delayed but sustained increase of RA in cluster 11 (enriched in the ‘Proteasome complex’ and ‘Endoplasmic reticulum’ GO categories, see below), the RA increase in cluster 12 is faster and stronger. Although these differences may appear as minor ones, they suggest a marked divergence in mRNA stability upon heat shock between genes of clusters 11 and 12 (see below). A more stringent clustering analysis of the genes of clusters 11 and 12 resulted in four and three subgroups respectively (Fig. 3). Proteasome complex genes mostly fall grouped in the subcluster 11D in this Fig. 3, which denotes a homogeneous behavior of these GO category genes.

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