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Topoisomerase II regulates yeast genes with singular chromatin architectures.

Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J - Nucleic Acids Res. (2013)

Bottom Line: To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II.We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II.These genes present distinctive functional and structural traits in comparison with the genome average.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain.

ABSTRACT
Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes, whereas topo IIβ regulates developmental genes in conjunction with chromatin remodeling and heterochromatin transitions. Here we show that in budding yeast, topo II regulates the expression of specific gene subsets. To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II. We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II. These genes present distinctive functional and structural traits in comparison with the genome average. Yeast topo II is a positive regulator of genes with well-defined promoter architecture that associates to chromatin remodeling complexes; it is a negative regulator of genes extremely hypo-acetylated with complex promoters and undefined nucleosome positioning, many of which are involved in polyamine transport. These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability.

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Nucleosome stability and chromatin remodelers at the promoter region of deregulated genes. (A) Relative occupancy of regions around the TSS of deregulated and total yeast genes by ‘appearing’ nucleosomes (54), (B) ‘evicted’ nucleosomes (Shivaswamy et al., 2008) and (C) ‘fragile’ nucleosomes (55). Relative occupancies were defined as the percentage of overlap of the underlying region by a nucleosome at 10 bp resolution. (D) Relative enrichments/depletions of down- and upregulated genes among genes whose TSS are occupied by eight chromatin remodellers (57). Values are calculated as deviations from the expected values for the genome average (corresponding to 1). Bootstrap P-values were calculated on the basis of 1000 randomized gene sets. Stars denote P < 0.001.
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gkt707-F5: Nucleosome stability and chromatin remodelers at the promoter region of deregulated genes. (A) Relative occupancy of regions around the TSS of deregulated and total yeast genes by ‘appearing’ nucleosomes (54), (B) ‘evicted’ nucleosomes (Shivaswamy et al., 2008) and (C) ‘fragile’ nucleosomes (55). Relative occupancies were defined as the percentage of overlap of the underlying region by a nucleosome at 10 bp resolution. (D) Relative enrichments/depletions of down- and upregulated genes among genes whose TSS are occupied by eight chromatin remodellers (57). Values are calculated as deviations from the expected values for the genome average (corresponding to 1). Bootstrap P-values were calculated on the basis of 1000 randomized gene sets. Stars denote P < 0.001.

Mentions: In addition to nucleosome positioning, other studies have described yeast nucleosomes as ‘appearing’ or ‘evicted’ according to their presence or absence after a heat shock (54) and as ‘fragile’ based on their susceptibility to MNase digestion (55). We obtained such nucleosomes and examined their relative enrichment near the TSS in genes deregulated by topo II. Compared with the yeast average, genes deregulated by topo II presented a more dynamic nucleosomal pattern. In particular, downregulated genes showed a prominent peak for an appearing nucleosome at position +1 (Figure 5A); both up and downregulated genes presented a higher occurrence of evicted and fragile nucleosomes in positions upstream the TSS (Figure 5B and C). Recent studies have reported also the genome-wide localization of different chromatin remodelers in S. cerevisiae (57). Thus, we examined the association of these remodeling complexes (Arp5, Ino80, Loc3, Loc4, Isw1, Isw2, Rsc8, Snf2) with the promoter regions of the genes deregulated after topo II deactivation. The results were revealing. Relative to the yeast gene average, the downregulated genes were highly enriched in chromatin remodeler activities, whereas the contrary occurred in the upregulated group (Figure 5D). These opposite trends occurred in the eight remodelers examined and markedly contrasted with the relative enrichments observed in genes up- and downregulated during general stress and in TATA-containing genes (Figure 5E).Figure 5.


Topoisomerase II regulates yeast genes with singular chromatin architectures.

Nikolaou C, Bermúdez I, Manichanh C, García-Martinez J, Guigó R, Pérez-Ortín JE, Roca J - Nucleic Acids Res. (2013)

Nucleosome stability and chromatin remodelers at the promoter region of deregulated genes. (A) Relative occupancy of regions around the TSS of deregulated and total yeast genes by ‘appearing’ nucleosomes (54), (B) ‘evicted’ nucleosomes (Shivaswamy et al., 2008) and (C) ‘fragile’ nucleosomes (55). Relative occupancies were defined as the percentage of overlap of the underlying region by a nucleosome at 10 bp resolution. (D) Relative enrichments/depletions of down- and upregulated genes among genes whose TSS are occupied by eight chromatin remodellers (57). Values are calculated as deviations from the expected values for the genome average (corresponding to 1). Bootstrap P-values were calculated on the basis of 1000 randomized gene sets. Stars denote P < 0.001.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3814376&req=5

gkt707-F5: Nucleosome stability and chromatin remodelers at the promoter region of deregulated genes. (A) Relative occupancy of regions around the TSS of deregulated and total yeast genes by ‘appearing’ nucleosomes (54), (B) ‘evicted’ nucleosomes (Shivaswamy et al., 2008) and (C) ‘fragile’ nucleosomes (55). Relative occupancies were defined as the percentage of overlap of the underlying region by a nucleosome at 10 bp resolution. (D) Relative enrichments/depletions of down- and upregulated genes among genes whose TSS are occupied by eight chromatin remodellers (57). Values are calculated as deviations from the expected values for the genome average (corresponding to 1). Bootstrap P-values were calculated on the basis of 1000 randomized gene sets. Stars denote P < 0.001.
Mentions: In addition to nucleosome positioning, other studies have described yeast nucleosomes as ‘appearing’ or ‘evicted’ according to their presence or absence after a heat shock (54) and as ‘fragile’ based on their susceptibility to MNase digestion (55). We obtained such nucleosomes and examined their relative enrichment near the TSS in genes deregulated by topo II. Compared with the yeast average, genes deregulated by topo II presented a more dynamic nucleosomal pattern. In particular, downregulated genes showed a prominent peak for an appearing nucleosome at position +1 (Figure 5A); both up and downregulated genes presented a higher occurrence of evicted and fragile nucleosomes in positions upstream the TSS (Figure 5B and C). Recent studies have reported also the genome-wide localization of different chromatin remodelers in S. cerevisiae (57). Thus, we examined the association of these remodeling complexes (Arp5, Ino80, Loc3, Loc4, Isw1, Isw2, Rsc8, Snf2) with the promoter regions of the genes deregulated after topo II deactivation. The results were revealing. Relative to the yeast gene average, the downregulated genes were highly enriched in chromatin remodeler activities, whereas the contrary occurred in the upregulated group (Figure 5D). These opposite trends occurred in the eight remodelers examined and markedly contrasted with the relative enrichments observed in genes up- and downregulated during general stress and in TATA-containing genes (Figure 5E).Figure 5.

Bottom Line: To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II.We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II.These genes present distinctive functional and structural traits in comparison with the genome average.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain.

ABSTRACT
Eukaryotic topoisomerase II (topo II) is the essential decatenase of newly replicated chromosomes and the main relaxase of nucleosomal DNA. Apart from these general tasks, topo II participates in more specialized functions. In mammals, topo IIα interacts with specific RNA polymerases and chromatin-remodeling complexes, whereas topo IIβ regulates developmental genes in conjunction with chromatin remodeling and heterochromatin transitions. Here we show that in budding yeast, topo II regulates the expression of specific gene subsets. To uncover this, we carried out a genomic transcription run-on shortly after the thermal inactivation of topo II. We identified a modest number of genes not involved in the general stress response but strictly dependent on topo II. These genes present distinctive functional and structural traits in comparison with the genome average. Yeast topo II is a positive regulator of genes with well-defined promoter architecture that associates to chromatin remodeling complexes; it is a negative regulator of genes extremely hypo-acetylated with complex promoters and undefined nucleosome positioning, many of which are involved in polyamine transport. These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability.

Show MeSH
Related in: MedlinePlus