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. 1998 May 1;26(9):2042–2049. doi: 10.1093/nar/26.9.2042

DNA topoisomerase II sites in the histone H4 gene during the highly synchronous cell cycle of Physarum polycephalum.

V Borde 1, M Duguet 1
PMCID: PMC147523  PMID: 9547257

Abstract

The nearly perfect synchrony of nuclear division in a plasmodium of Physarum polycephalum provides a powerful system to analyze topoisomerase II cleavage sites in the course of the cell cycle. The histone H4 locus, whose schedule of replication and transcription is precisely known, was chosen for this analysis. Drug-induced topoisomerase II sites are clustered downstream of the histone H4 gene and appear highly dependent on cell cycle stage. They were only detected in mitosis and at the very beginning of S phase, precisely at the time of replication of the histone H4 region. The sites, which were absent in G2 phase, reappeared at the next mitosis. Remarkably, DNase I hypersensitive sites occurred in nearly the same location, but their schedule was totally different: they were absent in mitosis and present in G2. This schedule follows H4 transcription, which peaks in mid-S phase and in the second part of G2 phase and is off during mitosis. These results suggest that topoisomerase II may not be involved in transcription, but plays a role in remodeling chromatin structure, both during chromosome condensation in prophase/metaphase to allow their decatenation and during chromosome decondensation after metaphase to allow replication fork passage throughout the region.

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Selected References

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  1. Adachi Y., Luke M., Laemmli U. K. Chromosome assembly in vitro: topoisomerase II is required for condensation. Cell. 1991 Jan 11;64(1):137–148. doi: 10.1016/0092-8674(91)90215-k. [DOI] [PubMed] [Google Scholar]
  2. Berrios M., Osheroff N., Fisher P. A. In situ localization of DNA topoisomerase II, a major polypeptide component of the Drosophila nuclear matrix fraction. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4142–4146. doi: 10.1073/pnas.82.12.4142. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Borde V., Duguet M. In vivo topoisomerase II cleavage sites in the ribosomal DNA of Physarum polycephalum. Biochemistry. 1996 May 7;35(18):5787–5795. doi: 10.1021/bi952676q. [DOI] [PubMed] [Google Scholar]
  4. Capranico G., Jaxel C., Roberge M., Kohn K. W., Pommier Y. Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin. Nucleic Acids Res. 1990 Aug 11;18(15):4553–4559. doi: 10.1093/nar/18.15.4553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Carrino J. J., Kueng V., Braun R., Laffler T. G. Distinct replication-independent and -dependent phases of histone gene expression during the Physarum cell cycle. Mol Cell Biol. 1987 May;7(5):1933–1937. doi: 10.1128/mcb.7.5.1933. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chow K. C., Ross W. E. Topoisomerase-specific drug sensitivity in relation to cell cycle progression. Mol Cell Biol. 1987 Sep;7(9):3119–3123. doi: 10.1128/mcb.7.9.3119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cockerill P. N., Garrard W. T. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell. 1986 Jan 31;44(2):273–282. doi: 10.1016/0092-8674(86)90761-0. [DOI] [PubMed] [Google Scholar]
  8. DiNardo S., Voelkel K., Sternglanz R. DNA topoisomerase II mutant of Saccharomyces cerevisiae: topoisomerase II is required for segregation of daughter molecules at the termination of DNA replication. Proc Natl Acad Sci U S A. 1984 May;81(9):2616–2620. doi: 10.1073/pnas.81.9.2616. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ebert S. N., Shtrom S. S., Muller M. T. Topoisomerase II cleavage of herpes simplex virus type 1 DNA in vivo is replication dependent. J Virol. 1990 Sep;64(9):4059–4066. doi: 10.1128/jvi.64.9.4059-4066.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Elsea S. H., Osheroff N., Nitiss J. L. Cytotoxicity of quinolones toward eukaryotic cells. Identification of topoisomerase II as the primary cellular target for the quinolone CP-115,953 in yeast. J Biol Chem. 1992 Jul 5;267(19):13150–13153. [PubMed] [Google Scholar]
  11. Estey E., Adlakha R. C., Hittelman W. N., Zwelling L. A. Cell cycle stage dependent variations in drug-induced topoisomerase II mediated DNA cleavage and cytotoxicity. Biochemistry. 1987 Jul 14;26(14):4338–4344. doi: 10.1021/bi00388a023. [DOI] [PubMed] [Google Scholar]
  12. Holm C., Stearns T., Botstein D. DNA topoisomerase II must act at mitosis to prevent nondisjunction and chromosome breakage. Mol Cell Biol. 1989 Jan;9(1):159–168. doi: 10.1128/mcb.9.1.159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Iarovaia O., Hancock R., Lagarkova M., Miassod R., Razin S. V. Mapping of genomic DNA loop organization in a 500-kilobase region of the Drosophila X chromosome by the topoisomerase II-mediated DNA loop excision protocol. Mol Cell Biol. 1996 Jan;16(1):302–308. doi: 10.1128/mcb.16.1.302. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jalouzot R., Toublan B., Wilhelm M. L., Wilhelm F. X. Replication timing of the H4 histone genes in Physarum polycephalum. Proc Natl Acad Sci U S A. 1985 Oct;82(19):6475–6479. doi: 10.1073/pnas.82.19.6475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kubbies M., Pierron G. Mitotic cell cycle control in Physarum. Unprecedented insights via flow-cytometry. Exp Cell Res. 1983 Nov;149(1):57–67. doi: 10.1016/0014-4827(83)90380-4. [DOI] [PubMed] [Google Scholar]
  16. Käs E., Laemmli U. K. In vivo topoisomerase II cleavage of the Drosophila histone and satellite III repeats: DNA sequence and structural characteristics. EMBO J. 1992 Feb;11(2):705–716. doi: 10.1002/j.1460-2075.1992.tb05103.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Liu L. F. DNA topoisomerase poisons as antitumor drugs. Annu Rev Biochem. 1989;58:351–375. doi: 10.1146/annurev.bi.58.070189.002031. [DOI] [PubMed] [Google Scholar]
  18. Miassod R., Razin S. V., Hancock R. Distribution of topoisomerase II-mediated cleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA. Nucleic Acids Res. 1997 Jun 1;25(11):2041–2046. doi: 10.1093/nar/25.11.2041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Newport J., Spann T. Disassembly of the nucleus in mitotic extracts: membrane vesicularization, lamin disassembly, and chromosome condensation are independent processes. Cell. 1987 Jan 30;48(2):219–230. doi: 10.1016/0092-8674(87)90425-9. [DOI] [PubMed] [Google Scholar]
  20. Pierron G., Durica D. S., Sauer H. W. Invariant temporal order of replication of the four actin gene loci during the naturally synchronous mitotic cycles of Physarum polycephalum. Proc Natl Acad Sci U S A. 1984 Oct;81(20):6393–6397. doi: 10.1073/pnas.81.20.6393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Pierron G., Sauer H. W. More evidence for replication-transcription-coupling in Physarum polycephalum. J Cell Sci. 1980 Feb;41:105–113. doi: 10.1242/jcs.41.1.105. [DOI] [PubMed] [Google Scholar]
  22. Pommier Y., Capranico G., Orr A., Kohn K. W. Distribution of topoisomerase II cleavage sites in simian virus 40 DNA and the effects of drugs. J Mol Biol. 1991 Dec 20;222(4):909–924. doi: 10.1016/0022-2836(91)90585-t. [DOI] [PubMed] [Google Scholar]
  23. Pruss G. J., Manes S. H., Drlica K. Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell. 1982 Nov;31(1):35–42. doi: 10.1016/0092-8674(82)90402-0. [DOI] [PubMed] [Google Scholar]
  24. Razin S. V., Petrov P., Hancock R. Precise localization of the alpha-globin gene cluster within one of the 20- to 300-kilobase DNA fragments released by cleavage of chicken chromosomal DNA at topoisomerase II sites in vivo: evidence that the fragments are DNA loops or domains. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8515–8519. doi: 10.1073/pnas.88.19.8515. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Reitman M., Felsenfeld G. Developmental regulation of topoisomerase II sites and DNase I-hypersensitive sites in the chicken beta-globin locus. Mol Cell Biol. 1990 Jun;10(6):2774–2786. doi: 10.1128/mcb.10.6.2774. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Riou J. F., Gabillot M., Riou G. Analysis of topoisomerase II-mediated DNA cleavage of the c-myc gene during HL60 differentiation. FEBS Lett. 1993 Nov 22;334(3):369–372. doi: 10.1016/0014-5793(93)80714-6. [DOI] [PubMed] [Google Scholar]
  27. Riou J. F., Lefevre D., Riou G. Stimulation of the topoisomerase II induced DNA cleavage sites in the c-myc protooncogene by antitumor drugs is associated with gene expression. Biochemistry. 1989 Nov 14;28(23):9104–9110. doi: 10.1021/bi00449a022. [DOI] [PubMed] [Google Scholar]
  28. Riou J. F., Multon E., Vilarem M. J., Larsen C. J., Riou G. In vivo stimulation by antitumor drugs of the topoisomerase II induced cleavage sites in c-myc protooncogene. Biochem Biophys Res Commun. 1986 May 29;137(1):154–160. doi: 10.1016/0006-291x(86)91189-7. [DOI] [PubMed] [Google Scholar]
  29. Schaack J., Schedl P., Shenk T. Topoisomerase I and II cleavage of adenovirus DNA in vivo: both topoisomerase activities appear to be required for adenovirus DNA replication. J Virol. 1990 Jan;64(1):78–85. doi: 10.1128/jvi.64.1.78-85.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Udvardy A., Schedl P. Chromatin structure, not DNA sequence specificity, is the primary determinant of topoisomerase II sites of action in vivo. Mol Cell Biol. 1991 Oct;11(10):4973–4984. doi: 10.1128/mcb.11.10.4973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Udvardy A., Schedl P. The dynamics of chromatin condensation: redistribution of topoisomerase II in the 87A7 heat shock locus during induction and recovery. Mol Cell Biol. 1993 Dec;13(12):7522–7530. doi: 10.1128/mcb.13.12.7522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Varga-Weisz P. D., Wilm M., Bonte E., Dumas K., Mann M., Becker P. B. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature. 1997 Aug 7;388(6642):598–602. doi: 10.1038/41587. [DOI] [PubMed] [Google Scholar]
  33. Wang J. C. DNA topoisomerases. Annu Rev Biochem. 1996;65:635–692. doi: 10.1146/annurev.bi.65.070196.003223. [DOI] [PubMed] [Google Scholar]
  34. Warburton P. E., Earnshaw W. C. Untangling the role of DNA topoisomerase II in mitotic chromosome structure and function. Bioessays. 1997 Feb;19(2):97–99. doi: 10.1002/bies.950190203. [DOI] [PubMed] [Google Scholar]
  35. Wilhelm M. L., Wilhelm F. X. A transposon-like DNA fragment interrupts a Physarum polycephalum histone H4 gene. FEBS Lett. 1984 Mar 26;168(2):249–254. doi: 10.1016/0014-5793(84)80256-2. [DOI] [PubMed] [Google Scholar]
  36. Wilhelm M. L., Wilhelm F. X. Histone genes in Physarum polycephalum: transcription and analysis of the flanking regions of the two H4 genes. J Mol Evol. 1989 Apr;28(4):322–326. doi: 10.1007/BF02103428. [DOI] [PubMed] [Google Scholar]
  37. Worland S. T., Wang J. C. Inducible overexpression, purification, and active site mapping of DNA topoisomerase II from the yeast Saccharomyces cerevisiae. J Biol Chem. 1989 Mar 15;264(8):4412–4416. [PubMed] [Google Scholar]
  38. Yang L., Rowe T. C., Nelson E. M., Liu L. F. In vivo mapping of DNA topoisomerase II-specific cleavage sites on SV40 chromatin. Cell. 1985 May;41(1):127–132. doi: 10.1016/0092-8674(85)90067-4. [DOI] [PubMed] [Google Scholar]

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