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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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RNA binding protein (RBP) and mRNA 3′UTR motif enrichment analyses.Supervised and unsupervised analyses for RBP and mRNA 3′UTR motif enrichment, were carried out. In the left part of the panel, the p-values associated with the presence of the well established RBP binding motifs in the clusters are displayed. On the right, the consensus sequence motifs found in the 3′UTR of the genes belonging to the clusters are shown, as obtained by the FIRE algorithm [24]. Only those clusters with over-representation of RBPs or significant 3′UTR motifs are shown.
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pone-0017272-g005: RNA binding protein (RBP) and mRNA 3′UTR motif enrichment analyses.Supervised and unsupervised analyses for RBP and mRNA 3′UTR motif enrichment, were carried out. In the left part of the panel, the p-values associated with the presence of the well established RBP binding motifs in the clusters are displayed. On the right, the consensus sequence motifs found in the 3′UTR of the genes belonging to the clusters are shown, as obtained by the FIRE algorithm [24]. Only those clusters with over-representation of RBPs or significant 3′UTR motifs are shown.

Mentions: Since we have found groups of genes that behave co-coordinately with regard to mRNA stability, we investigated also the possible existence of RBPs, which may be responsible for this coordination. There are several known RBPs with established or predicted mRNA targets. Some of the targets have been detected experimentally by immunoprecipitation of RBP [21]–[23]. Others have been predicted by algorithms that use information from gene expression data and features of the putative motif sequence [24]. Using published data [21]–[24], we found that some of the clusters from Fig. 2 are enriched in targets or putative targets for several RBPs (Fig. 5). Using the FIRE algorithm as described by Elemento et al. [24], we also found enrichment in an unsupervised fashion for some known and unknown motifs. The most significant enrichments found are shown in Fig. 5. Pub1 targets are enriched in clusters 2 and 3. This protein has been shown to have a quite large (368 according to [23], >1000 according to [22]) number of mRNAs enriched in GOs related to translation [33], which are also enriched in cluster 3. Npl3 targets are also significantly enriched in cluster 3, coinciding with its known preference for ribosomal protein mRNAs [22]. Other significantly enriched RBP targets are those of Puf3 (cluster 8) and Puf4 (clusters 4, 5, 10). In this last case, there is again a good correspondence with the known selectivity of Puf4 for ribosome biogenesis mRNAs [22].


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)

RNA binding protein (RBP) and mRNA 3′UTR motif enrichment analyses.Supervised and unsupervised analyses for RBP and mRNA 3′UTR motif enrichment, were carried out. In the left part of the panel, the p-values associated with the presence of the well established RBP binding motifs in the clusters are displayed. On the right, the consensus sequence motifs found in the 3′UTR of the genes belonging to the clusters are shown, as obtained by the FIRE algorithm [24]. Only those clusters with over-representation of RBPs or significant 3′UTR motifs are shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0017272-g005: RNA binding protein (RBP) and mRNA 3′UTR motif enrichment analyses.Supervised and unsupervised analyses for RBP and mRNA 3′UTR motif enrichment, were carried out. In the left part of the panel, the p-values associated with the presence of the well established RBP binding motifs in the clusters are displayed. On the right, the consensus sequence motifs found in the 3′UTR of the genes belonging to the clusters are shown, as obtained by the FIRE algorithm [24]. Only those clusters with over-representation of RBPs or significant 3′UTR motifs are shown.
Mentions: Since we have found groups of genes that behave co-coordinately with regard to mRNA stability, we investigated also the possible existence of RBPs, which may be responsible for this coordination. There are several known RBPs with established or predicted mRNA targets. Some of the targets have been detected experimentally by immunoprecipitation of RBP [21]–[23]. Others have been predicted by algorithms that use information from gene expression data and features of the putative motif sequence [24]. Using published data [21]–[24], we found that some of the clusters from Fig. 2 are enriched in targets or putative targets for several RBPs (Fig. 5). Using the FIRE algorithm as described by Elemento et al. [24], we also found enrichment in an unsupervised fashion for some known and unknown motifs. The most significant enrichments found are shown in Fig. 5. Pub1 targets are enriched in clusters 2 and 3. This protein has been shown to have a quite large (368 according to [23], >1000 according to [22]) number of mRNAs enriched in GOs related to translation [33], which are also enriched in cluster 3. Npl3 targets are also significantly enriched in cluster 3, coinciding with its known preference for ribosomal protein mRNAs [22]. Other significantly enriched RBP targets are those of Puf3 (cluster 8) and Puf4 (clusters 4, 5, 10). In this last case, there is again a good correspondence with the known selectivity of Puf4 for ribosome biogenesis mRNAs [22].

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