Histone deacetylase inhibition redistributes topoisomerase IIb from heterochromatin to euchromatin

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
Nucleus (Austin, Texas) (Impact Factor: 3.03). 01/2011; 2(1):61-71. DOI: 10.4161/nucl.2.1.14194
Source: PubMed


The genome is organized into large scale structures in the interphase nucleus. Pericentromeric heterochromatin represents one such compartment characterized by histones H3 and H4 tri-methylated at K9 and K20 respectively and with a correspondingly low level of histone acetylation. HP1 proteins are concentrated in pericentric heterochromatin and histone deacetylase inhibitors such as trichostatin A (TSA) promote hyperacetylation of heterochromatic nucleosomes and the dispersal of HP1 proteins. We observed that in mouse cells, which contain prominent heterochromatin, DNA topoisomerase IIβ (topoIIβ) is also concentrated in heterochromatic regions. Similarly, a detergent-resistant fraction of topoIIβ is associated with heterochromatin in human cell lines. Treatment with TSA displaced topoIIβ from the heterochromatin with similar kinetics to the displacement of HP1β. Topoisomerase II is the cellular target for a number of clinically important cytotoxic anti-cancer agents known collectively as topoisomerase poisons, and it has been previously reported that histone deacetylase inhibitors can sensitize cells to these drugs. While topoIIα appears to be the major target for most topoisomerase poisons, histone deacetylase-mediated potentiation of these drugs is dependent on topoIIβ. We find that while prior treatment with TSA did not increase the quantity of etoposide-mediated topoIIβ-DNA covalent complexes, it did result in a shift in their distribution from a largely heterochromatin-associated to a pannuclear pattern. We suggest that this redistribution of topoIIβ converts this isoform of topoII to a effective relevant target for topoisomerase poisons.

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    • "Topo II has been long involved in high-order organization of chromatin (9), centromere configuration (82) and genome compaction in sperm cells (83–85). In mammalian cells, topo IIβ is implicated in heterochromatin transitions that depend on histone deacetylase (81). Therefore, yeast topo II and mammalian topo IIβ may use similar mechanisms to repress transcription by inducing or stabilizing condensed chromatin states. "
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    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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    • "The same immunoprecipitates and in vitro incubation conditions did not decrease the topoisomerase IIb complexes, in fact the immunofluorescent signal increased. This may be due to increased accessibility to the anti-topoisomerase IIb antisera following detergent and salt treatment of heterochromatin (Cowell et al., 2011b). Etoposide stabilised topoisomerase II adducts were also removed from genomic DNA in vitro by recombinant MRE11, 49% of the topoisomerase IIa adducts were removed (P.0.0001), but only 7% of the topoisomerase IIb complexes (p50.0302). "
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    ABSTRACT: The bromodomain is a highly conserved motif of 110 amino acids that is bundled into four anti-parallel α-helices and found in proteins that interact with chromatin, such as transcription factors, histone acetylases and nucleosome remodelling complexes. Bromodomain proteins are chromatin 'readers'; they recruit chromatin-regulating enzymes, including 'writers' and 'erasers' of histone modification, to target promoters and to regulate gene expression. Conventional wisdom held that complexes involved in chromatin dynamics are not 'druggable' targets. However, small molecules that inhibit bromodomain and extraterminal (BET) proteins have been described. We examine these developments and discuss the implications for small molecule epigenetic targeting of chromatin networks in cancer.
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