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A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions

View Article: PubMed Central - PubMed

ABSTRACT

The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodelling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation requires, at least partially, RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits do not define alternate versions of the complex.

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Comparison of the fission yeast rsc1 deletion mutant and the snf21 switch-off strains. a The profile of nucleosome occupancy ratios between fission yeast rsc1 deletion mutant (rsc1Δ) and control strains on the left panel (note that this panel is identical to Fig. 2b and repeated here for clarity), and between the fission yeast snf21 switch-off mutant [tetO-snf21, 3 h of inhibition, (Materne et al. 2015)] and control strains on the right panel are presented as a heatmap, where blue represents a gain in nucleosome occupancy and red represents a loss within a region ranging from −750 bp to +750 bp around the TSS at single nucleotide resolution. Rows represent genes and are organized into five groups by k-means clustering. bBox plot representing the difference in NDR length between the rsc1Δ and tetO-snf21 strains and the corresponding wt strains. Statistical significance was calculated by a one-sample Wilcoxon test (pval <0.01). c Frequency of genes downregulated (log2 fold change < −0.5, based on (Monahan et al. 2008) in rsc1Δ strain sorted by cluster. Cluster 3 includes the ste11 gene and is enriched (Fisher’s exact test P value <0.05) for genes whose expression is downregulated in the rsc1Δ strain
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Fig3: Comparison of the fission yeast rsc1 deletion mutant and the snf21 switch-off strains. a The profile of nucleosome occupancy ratios between fission yeast rsc1 deletion mutant (rsc1Δ) and control strains on the left panel (note that this panel is identical to Fig. 2b and repeated here for clarity), and between the fission yeast snf21 switch-off mutant [tetO-snf21, 3 h of inhibition, (Materne et al. 2015)] and control strains on the right panel are presented as a heatmap, where blue represents a gain in nucleosome occupancy and red represents a loss within a region ranging from −750 bp to +750 bp around the TSS at single nucleotide resolution. Rows represent genes and are organized into five groups by k-means clustering. bBox plot representing the difference in NDR length between the rsc1Δ and tetO-snf21 strains and the corresponding wt strains. Statistical significance was calculated by a one-sample Wilcoxon test (pval <0.01). c Frequency of genes downregulated (log2 fold change < −0.5, based on (Monahan et al. 2008) in rsc1Δ strain sorted by cluster. Cluster 3 includes the ste11 gene and is enriched (Fisher’s exact test P value <0.05) for genes whose expression is downregulated in the rsc1Δ strain

Mentions: We next applied identical analyses to the data obtained in a fission yeast rsc1 mutant. It should be noted straight away that Rsc1 is a non-essential subunit of RSC while the work done in budding yeast targeted the gene encoding the catalytic subunit. Nonetheless, the general picture obtained when rsc1 is absent (Fig. 2b) is reminiscent of the budding yeast data (Fig. 2a). Compared to budding yeast, the shortening of NDR is observed with a slight shift towards the TSS that recalls the shift of the position of the +1 nucleosome between budding and fission yeast (Fig. 1b). In addition, the leftward shift in nucleosome positions over the transcribed region is also obvious in most clusters. These data suggest that similarly to budding yeast, RSC also play an important conserved role in the establishment of NDRs in fission yeast in contrast to previous conclusions (Pointner et al. 2012). However, it is important to keep in mind that the previous study relies on a ts allele of snf21. As rightly pointed by the authors in their manuscript, it is possible that the inactivation of the snf21-ts was not complete despite the fact that the strain has obvious phenotypes (see below), somehow masking an effect of most NDR. Supporting this possibility, we report here that while switching-off snf21 expression using a Tet-off system eventually results in cell death on plates (Materne et al. 2015), it has a weak genome-wide effect on NDR formation when a short time point is used (Fig. 3a). This suggests that lowering RSC activity by switching-off the transcription of the snf21 gene (with about 35 % of the snf21 mRNA left) may only affect the most sensitive RSC-dependent processes. These data claim for the generation of a much more efficient switch-off system that could quickly deplete the vast majority of the Snf21 protein pool in the cell.Fig. 3


A conserved role of the RSC chromatin remodeler in the establishment of nucleosome-depleted regions
Comparison of the fission yeast rsc1 deletion mutant and the snf21 switch-off strains. a The profile of nucleosome occupancy ratios between fission yeast rsc1 deletion mutant (rsc1Δ) and control strains on the left panel (note that this panel is identical to Fig. 2b and repeated here for clarity), and between the fission yeast snf21 switch-off mutant [tetO-snf21, 3 h of inhibition, (Materne et al. 2015)] and control strains on the right panel are presented as a heatmap, where blue represents a gain in nucleosome occupancy and red represents a loss within a region ranging from −750 bp to +750 bp around the TSS at single nucleotide resolution. Rows represent genes and are organized into five groups by k-means clustering. bBox plot representing the difference in NDR length between the rsc1Δ and tetO-snf21 strains and the corresponding wt strains. Statistical significance was calculated by a one-sample Wilcoxon test (pval <0.01). c Frequency of genes downregulated (log2 fold change < −0.5, based on (Monahan et al. 2008) in rsc1Δ strain sorted by cluster. Cluster 3 includes the ste11 gene and is enriched (Fisher’s exact test P value <0.05) for genes whose expression is downregulated in the rsc1Δ strain
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Fig3: Comparison of the fission yeast rsc1 deletion mutant and the snf21 switch-off strains. a The profile of nucleosome occupancy ratios between fission yeast rsc1 deletion mutant (rsc1Δ) and control strains on the left panel (note that this panel is identical to Fig. 2b and repeated here for clarity), and between the fission yeast snf21 switch-off mutant [tetO-snf21, 3 h of inhibition, (Materne et al. 2015)] and control strains on the right panel are presented as a heatmap, where blue represents a gain in nucleosome occupancy and red represents a loss within a region ranging from −750 bp to +750 bp around the TSS at single nucleotide resolution. Rows represent genes and are organized into five groups by k-means clustering. bBox plot representing the difference in NDR length between the rsc1Δ and tetO-snf21 strains and the corresponding wt strains. Statistical significance was calculated by a one-sample Wilcoxon test (pval <0.01). c Frequency of genes downregulated (log2 fold change < −0.5, based on (Monahan et al. 2008) in rsc1Δ strain sorted by cluster. Cluster 3 includes the ste11 gene and is enriched (Fisher’s exact test P value <0.05) for genes whose expression is downregulated in the rsc1Δ strain
Mentions: We next applied identical analyses to the data obtained in a fission yeast rsc1 mutant. It should be noted straight away that Rsc1 is a non-essential subunit of RSC while the work done in budding yeast targeted the gene encoding the catalytic subunit. Nonetheless, the general picture obtained when rsc1 is absent (Fig. 2b) is reminiscent of the budding yeast data (Fig. 2a). Compared to budding yeast, the shortening of NDR is observed with a slight shift towards the TSS that recalls the shift of the position of the +1 nucleosome between budding and fission yeast (Fig. 1b). In addition, the leftward shift in nucleosome positions over the transcribed region is also obvious in most clusters. These data suggest that similarly to budding yeast, RSC also play an important conserved role in the establishment of NDRs in fission yeast in contrast to previous conclusions (Pointner et al. 2012). However, it is important to keep in mind that the previous study relies on a ts allele of snf21. As rightly pointed by the authors in their manuscript, it is possible that the inactivation of the snf21-ts was not complete despite the fact that the strain has obvious phenotypes (see below), somehow masking an effect of most NDR. Supporting this possibility, we report here that while switching-off snf21 expression using a Tet-off system eventually results in cell death on plates (Materne et al. 2015), it has a weak genome-wide effect on NDR formation when a short time point is used (Fig. 3a). This suggests that lowering RSC activity by switching-off the transcription of the snf21 gene (with about 35 % of the snf21 mRNA left) may only affect the most sensitive RSC-dependent processes. These data claim for the generation of a much more efficient switch-off system that could quickly deplete the vast majority of the Snf21 protein pool in the cell.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

The occupancy of nucleosomes governs access to the eukaryotic genomes and results from a combination of biophysical features and the effect of ATP-dependent remodelling complexes. Most promoter regions show a conserved pattern characterized by a nucleosome-depleted region (NDR) flanked by nucleosomal arrays. The conserved RSC remodeler was reported to be critical to establish NDR in vivo in budding yeast but other evidences suggested that this activity may not be conserved in fission yeast. By reanalysing and expanding previously published data, we propose that NDR formation requires, at least partially, RSC in both yeast species. We also discuss the most prominent biological role of RSC and the possibility that non-essential subunits do not define alternate versions of the complex.

No MeSH data available.


Related in: MedlinePlus