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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    • "Human TOP2B protein directly interacts with a number of proteins including CD3ε UBC9, TOPBP1, p53, pRB, SNF2H, HDAC1 and HDAC2 (Cowell et al., 2000;Johnson et al., 2001;LeRoy et al., 2000;Mao et al., 2000;Nakano et al., 1996;Tsai et al., 2000;Xiao and Goodrich, 2005;Yamane et al., 1997;Yuwen et al., 1997) several of which are involved in transcriptional regulation. Inhibition of HDACs by TSA redistributes TOP2B from heterochromatin to euchromatin in mouse epithelial cells (Cowell et al., 2011). TOP2B is also found associated with several complexes involved in the regulation of transcriptional initiation. "
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    ABSTRACT: We report the whole genome ChIP seq for human TOP2B from MCF7 cells. Using three different peak calling methods, regions of binding were identified in the presence or absence of the nuclear hormone estradiol, as TOP2B has been reported to play a role in ligand-induced transcription. TOP2B peaks were found across the whole genome, 50% of the peaks fell either within a gene or within 5 kb of a transcription start site. TOP2B peaks coincident with gene promoters were less frequently associated with epigenetic features marking active promoters in estradiol treated than in untreated cells. Significantly enriched transcription factor motifs within the DNA sequences underlying the peaks were identified. These included SP1, KLF4, TFAP2A, MYF, REST, CTCF, ESR1 and ESR2. Gene ontology analysis of genes associated with TOP2B peaks found neuronal development terms including axonogenesis and axon guidance were significantly enriched. In the absence of functional TOP2B there are errors in axon guidance in the zebrafish eye. Specific heparin sulphate structures are involved in retinal axon targeting. The glycosaminoglycan biosynthesis-heparin sulphate/heparin pathway is significantly enriched in the TOP2B gene ontology analysis, suggesting changes in this pathway in the absence of TOP2B may cause the axon guidance faults.
    Full-text · Article · Oct 2015 · Biology Open
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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.
    Full-text · Article · Aug 2013 · Nucleic Acids Research
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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: Topoisomerase II creates a double-strand break intermediate with topoisomerase covalently coupled to the DNA via a 5'-phosphotyrosyl bond. These intermediate complexes can become cytotoxic protein-DNA adducts and DSB repair at these lesions requires removal of topoisomerase II. To analyse removal of topoisomerase II from genomic DNA we adapted the trapped in agarose DNA immunostaining assay. Recombinant MRE11 from 2 sources removed topoisomerase IIα from genomic DNA in vitro, as did MRE11 immunoprecipitates isolated from A-TLD or K562 cells. Basal topoisomerase II complex levels were very high in A-TLD cells lacking full-length wild type MRE11, suggesting that MRE11 facilitates the processing of topoisomerase complexes that arise as part of normal cellular metabolism. In K562 cells inhibition of MRE11, PARP or replication increased topoisomerase IIα and β complex levels formed in the absence of an anti-topoisomerase II drug.
    Full-text · Article · Sep 2012 · Biology Open
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