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The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin.

Machné R, Murray DB - PLoS ONE (2012)

Bottom Line: We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling.We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries.Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria. raim@tbi.univie.ac.at

ABSTRACT
When grown in continuous culture, budding yeast cells tend to synchronize their respiratory activity to form a stable oscillation that percolates throughout cellular physiology and involves the majority of the protein-coding transcriptome. Oscillations in batch culture and at single cell level support the idea that these dynamics constitute a general growth principle. The precise molecular mechanisms and biological functions of the oscillation remain elusive. Fourier analysis of transcriptome time series datasets from two different oscillation periods (0.7 h and 5 h) reveals seven distinct co-expression clusters common to both systems (34% of all yeast ORF), which consolidate into two superclusters when correlated with a compilation of 1,327 unrelated transcriptome datasets. These superclusters encode for cell growth and anabolism during the phase of high, and mitochondrial growth, catabolism and stress response during the phase of low oxygen uptake. The promoters of each cluster are characterized by different nucleotide contents, promoter nucleosome configurations, and dependence on ATP-dependent nucleosome remodeling complexes. We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling. We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries. Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions.

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Related in: MedlinePlus

Changes in nucleosome occupancy and transcription in mcm1-1 and rsc3-1 strains.SDP plots were constructed as described for Figure 4. Figure 1C provides a color legend. All data are from [41] and were provided (by the original authors) as shown, i.e.,  where I are the processed signal intensities from the individual experiments in mutant and isogenic control strains. In all figures, the top panel shows change of nucleosome occupancy from tiling arrays in 4 bp resolution, the middle and bottom panels show the change in transcriptome tiling array signal in 8 bp resolution from the sense and the antisense strands, respectively. 6A: mcm1-1; 6B: rsc3-1. Results for background clusters are shown in Figures S13 & S18.
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pone-0037906-g006: Changes in nucleosome occupancy and transcription in mcm1-1 and rsc3-1 strains.SDP plots were constructed as described for Figure 4. Figure 1C provides a color legend. All data are from [41] and were provided (by the original authors) as shown, i.e., where I are the processed signal intensities from the individual experiments in mutant and isogenic control strains. In all figures, the top panel shows change of nucleosome occupancy from tiling arrays in 4 bp resolution, the middle and bottom panels show the change in transcriptome tiling array signal in 8 bp resolution from the sense and the antisense strands, respectively. 6A: mcm1-1; 6B: rsc3-1. Results for background clusters are shown in Figures S13 & S18.

Mentions: The mcm1-1 (Figures 6A & S13) and tbf1 (Figure S14) strains showed a typical ESR transcriptional response, i.e., cluster A, AB & B are downregulated and clusters B.D & D upregulated. Both strains show a higher average nucleosome occupancy at the promoters of all clusters (all just before TSS), but this increase is significantly lower in the upregulated cluster B.D & D genes and significantly higher in the downregulated clusters A & AB. The change of occupancy in clusters B.C & C is similar between mcm1-1 and tbf1 strains, yet, the transcriptome shows a differential response, i.e., B.C & C are downregulated in tbf1 but upregulated in mcm1-1, perhaps reflecting the differences between the 0.7 h and the 5 h period cycles (Figure 1). Mcm1p binding sites are slightly enriched in clusters B.C (4% of cluster genes, ), and D (3%, ), and the binding motif of Tbf1p is enriched in cluster D promoters (21%, ). The cep3, abf1-101 and rap1-1 strains (Figures S15, S16, S17) also show a ESR-like response, but with more subtle features. In cep3, the total nucleosome occupancy seems increased over the control strain, indicated by in all clusters over the complete analyzed range, but the occupancy increase is significantly higher in promoters of clusters A, AB & C. Clusters B.C & C are uncoupled from the ESR and downregulated. Cep3p binds to centromers and we find no enrichment of it’s binding motif in any cluster. In contrast, Abf1p binding sites are highly enriched in cluster A (11%, ) and Rap1p in clusters AB (50%, , Figure 5F). Thus, the strong downregulation of cluster A in abf1-101, and of AB in rap1-1 may in part be related to specific and local effects of these proteins. In both mutants, nucleosome occupancy of cluster AB promoters is strongly increased, and we observe an increase of transcription upstream of the TSS, a moderate downregulation at the 5′ end, most likely stemming from the introns that are enriched in 5′ regions of these ribosomal protein genes, and strong downregulation 3′ of this intronic region. And lastly, nucleosome occupancy at the promoters of clusters A & AB is significantly decreased in the rsc3-1 (Figure 6B) and reb1-212 (Figure S19) strains, but without concurrent increase in transcript levels, suggesting that these growth clusters are highly expressed in the control strains. Clusters B, B.C, B.D & D have increased nucleosome occupancy in rsc3-1. While in the reb1-212 mutant all clusters show a slight global decrease in nucleosome occupancy just before the TSS (all ), the decrease is less in clusters B, B.C, B.D & D. Only the mitochondrial clusters B.C & C are significantly downregulated in both mutants. In the rsc3-1 strain, clusters B.C, B.D & D all show increased transcription upstream of the TSS (Figure 6B, middle panel). The signal from the antisense strand of this mutant is generally lower than in the control strain (all , right of TSS), but the decrease is significantly less in clusters B.D & D compared to other clusters (Figure 6B, bottom panel). A unique uncoupling of clusters B.D and D was observed in the reb1-212 strain where only B.D is significantly upregulated, coinciding with an unusual signal peak of the intronic region of cluster AB genes. This may result from premature transcription termination, indicated also by small peaks around the TSS of all clusters. In summary, the observed effects reach well beyond specific promoter binding sites of the tested set of GRF mutants, implying a stress-response or change of growth rates in these cell lines, accompanied by genome-wide remodeling of chromatin structure. The mutant cell lines tested by Badis et al.[41] thus clearly show, that distinct nucleosome occupancy states are indeed associated with transcriptional states akin to the transcriptional phases observed during synchronized respiratory cycling of budding yeast cell cultures.


The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin.

Machné R, Murray DB - PLoS ONE (2012)

Changes in nucleosome occupancy and transcription in mcm1-1 and rsc3-1 strains.SDP plots were constructed as described for Figure 4. Figure 1C provides a color legend. All data are from [41] and were provided (by the original authors) as shown, i.e.,  where I are the processed signal intensities from the individual experiments in mutant and isogenic control strains. In all figures, the top panel shows change of nucleosome occupancy from tiling arrays in 4 bp resolution, the middle and bottom panels show the change in transcriptome tiling array signal in 8 bp resolution from the sense and the antisense strands, respectively. 6A: mcm1-1; 6B: rsc3-1. Results for background clusters are shown in Figures S13 & S18.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3369881&req=5

pone-0037906-g006: Changes in nucleosome occupancy and transcription in mcm1-1 and rsc3-1 strains.SDP plots were constructed as described for Figure 4. Figure 1C provides a color legend. All data are from [41] and were provided (by the original authors) as shown, i.e., where I are the processed signal intensities from the individual experiments in mutant and isogenic control strains. In all figures, the top panel shows change of nucleosome occupancy from tiling arrays in 4 bp resolution, the middle and bottom panels show the change in transcriptome tiling array signal in 8 bp resolution from the sense and the antisense strands, respectively. 6A: mcm1-1; 6B: rsc3-1. Results for background clusters are shown in Figures S13 & S18.
Mentions: The mcm1-1 (Figures 6A & S13) and tbf1 (Figure S14) strains showed a typical ESR transcriptional response, i.e., cluster A, AB & B are downregulated and clusters B.D & D upregulated. Both strains show a higher average nucleosome occupancy at the promoters of all clusters (all just before TSS), but this increase is significantly lower in the upregulated cluster B.D & D genes and significantly higher in the downregulated clusters A & AB. The change of occupancy in clusters B.C & C is similar between mcm1-1 and tbf1 strains, yet, the transcriptome shows a differential response, i.e., B.C & C are downregulated in tbf1 but upregulated in mcm1-1, perhaps reflecting the differences between the 0.7 h and the 5 h period cycles (Figure 1). Mcm1p binding sites are slightly enriched in clusters B.C (4% of cluster genes, ), and D (3%, ), and the binding motif of Tbf1p is enriched in cluster D promoters (21%, ). The cep3, abf1-101 and rap1-1 strains (Figures S15, S16, S17) also show a ESR-like response, but with more subtle features. In cep3, the total nucleosome occupancy seems increased over the control strain, indicated by in all clusters over the complete analyzed range, but the occupancy increase is significantly higher in promoters of clusters A, AB & C. Clusters B.C & C are uncoupled from the ESR and downregulated. Cep3p binds to centromers and we find no enrichment of it’s binding motif in any cluster. In contrast, Abf1p binding sites are highly enriched in cluster A (11%, ) and Rap1p in clusters AB (50%, , Figure 5F). Thus, the strong downregulation of cluster A in abf1-101, and of AB in rap1-1 may in part be related to specific and local effects of these proteins. In both mutants, nucleosome occupancy of cluster AB promoters is strongly increased, and we observe an increase of transcription upstream of the TSS, a moderate downregulation at the 5′ end, most likely stemming from the introns that are enriched in 5′ regions of these ribosomal protein genes, and strong downregulation 3′ of this intronic region. And lastly, nucleosome occupancy at the promoters of clusters A & AB is significantly decreased in the rsc3-1 (Figure 6B) and reb1-212 (Figure S19) strains, but without concurrent increase in transcript levels, suggesting that these growth clusters are highly expressed in the control strains. Clusters B, B.C, B.D & D have increased nucleosome occupancy in rsc3-1. While in the reb1-212 mutant all clusters show a slight global decrease in nucleosome occupancy just before the TSS (all ), the decrease is less in clusters B, B.C, B.D & D. Only the mitochondrial clusters B.C & C are significantly downregulated in both mutants. In the rsc3-1 strain, clusters B.C, B.D & D all show increased transcription upstream of the TSS (Figure 6B, middle panel). The signal from the antisense strand of this mutant is generally lower than in the control strain (all , right of TSS), but the decrease is significantly less in clusters B.D & D compared to other clusters (Figure 6B, bottom panel). A unique uncoupling of clusters B.D and D was observed in the reb1-212 strain where only B.D is significantly upregulated, coinciding with an unusual signal peak of the intronic region of cluster AB genes. This may result from premature transcription termination, indicated also by small peaks around the TSS of all clusters. In summary, the observed effects reach well beyond specific promoter binding sites of the tested set of GRF mutants, implying a stress-response or change of growth rates in these cell lines, accompanied by genome-wide remodeling of chromatin structure. The mutant cell lines tested by Badis et al.[41] thus clearly show, that distinct nucleosome occupancy states are indeed associated with transcriptional states akin to the transcriptional phases observed during synchronized respiratory cycling of budding yeast cell cultures.

Bottom Line: We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling.We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries.Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria. raim@tbi.univie.ac.at

ABSTRACT
When grown in continuous culture, budding yeast cells tend to synchronize their respiratory activity to form a stable oscillation that percolates throughout cellular physiology and involves the majority of the protein-coding transcriptome. Oscillations in batch culture and at single cell level support the idea that these dynamics constitute a general growth principle. The precise molecular mechanisms and biological functions of the oscillation remain elusive. Fourier analysis of transcriptome time series datasets from two different oscillation periods (0.7 h and 5 h) reveals seven distinct co-expression clusters common to both systems (34% of all yeast ORF), which consolidate into two superclusters when correlated with a compilation of 1,327 unrelated transcriptome datasets. These superclusters encode for cell growth and anabolism during the phase of high, and mitochondrial growth, catabolism and stress response during the phase of low oxygen uptake. The promoters of each cluster are characterized by different nucleotide contents, promoter nucleosome configurations, and dependence on ATP-dependent nucleosome remodeling complexes. We show that the ATP:ADP ratio oscillates, compatible with alternating metabolic activity of the two superclusters and differential feedback on their transcription via activating (RSC) and repressive (Isw2) types of promoter structure remodeling. We propose a novel feedback mechanism, where the energetic state of the cell, reflected in the ATP:ADP ratio, gates the transcription of large, but functionally coherent groups of genes via differential effects of ATP-dependent nucleosome remodeling machineries. Besides providing a mechanistic hypothesis for the delayed negative feedback that results in the oscillatory phenotype, this mechanism may underpin the continuous adaptation of growth to environmental conditions.

Show MeSH
Related in: MedlinePlus