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. 1996 Oct;16(10):5754–5763. doi: 10.1128/mcb.16.10.5754

Induction of DNA replication by transcription in the region upstream of the human c-myc gene in a model replication system.

R Ohba 1, K Matsumoto 1, Y Ishimi 1
PMCID: PMC231576  PMID: 8816489

Abstract

An important relationship between transcription and initiation of DNA replication in both eukaryotes and prokaryotes has been suggested. In an attempt to understand the molecular mechanism of this interaction, we examined whether transcription can induce DNA replication in vitro by constructing a system in which both replication and transcription were combined. Relaxed circular DNA possessing a replication initiation zone located upstream of the human c-myc gene and a T7 promoter near the P1 promoter of the gene was replicated in the presence of T7 RNA polymerase. In our model system, replication was carried out with the proteins required for simian virus 40 DNA replication. DNA synthesis, which was dependent on both T7 RNA polymerase and the replication proteins, was detected mainly in the promoter and upstream regions of the c-myc gene. Blocking RNA synthesis at the initial stage of the reaction severely reduced DNA synthesis, suggesting that RNA chain elongation is required to induce DNA synthesis. The results indicated that transcription can induce DNA replication in the upstream region of the transcribed gene, most likely by introducing negative supercoiling into the region, which results in unwinding of the DNA duplex.

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Selected References

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  1. Asai T., Takanami M., Imai M. The AT richness and gid transcription determine the left border of the replication origin of the E. coli chromosome. EMBO J. 1990 Dec;9(12):4065–4072. doi: 10.1002/j.1460-2075.1990.tb07628.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Baker T. A., Kornberg A. Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell. 1988 Oct 7;55(1):113–123. doi: 10.1016/0092-8674(88)90014-1. [DOI] [PubMed] [Google Scholar]
  3. Bell S. P., Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. doi: 10.1038/357128a0. [DOI] [PubMed] [Google Scholar]
  4. Benbow R. M., Zhao J., Larson D. D. On the nature of origins of DNA replication in eukaryotes. Bioessays. 1992 Oct;14(10):661–670. doi: 10.1002/bies.950141004. [DOI] [PubMed] [Google Scholar]
  5. Berberich S., Trivedi A., Daniel D. C., Johnson E. M., Leffak M. In vitro replication of plasmids containing human c-myc DNA. J Mol Biol. 1995 Jan 13;245(2):92–109. doi: 10.1006/jmbi.1994.0010. [DOI] [PubMed] [Google Scholar]
  6. Biamonti G., Perini G., Weighardt F., Riva S., Giacca M., Norio P., Zentilin L., Diviacco S., Dimitrova D., Falaschi A. A human DNA replication origin: localization and transcriptional characterization. Chromosoma. 1992;102(1 Suppl):S24–S31. doi: 10.1007/BF02451782. [DOI] [PubMed] [Google Scholar]
  7. Borowiec J. A., Dean F. B., Bullock P. A., Hurwitz J. Binding and unwinding--how T antigen engages the SV40 origin of DNA replication. Cell. 1990 Jan 26;60(2):181–184. doi: 10.1016/0092-8674(90)90730-3. [DOI] [PubMed] [Google Scholar]
  8. Bramhill D., Kornberg A. A model for initiation at origins of DNA replication. Cell. 1988 Sep 23;54(7):915–918. doi: 10.1016/0092-8674(88)90102-x. [DOI] [PubMed] [Google Scholar]
  9. Bénard M., Pierron G. Mapping of a Physarum chromosomal origin of replication tightly linked to a developmentally-regulated profilin gene. Nucleic Acids Res. 1992 Jul 11;20(13):3309–3315. doi: 10.1093/nar/20.13.3309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. DePamphilis M. L. Eukaryotic DNA replication: anatomy of an origin. Annu Rev Biochem. 1993;62:29–63. doi: 10.1146/annurev.bi.62.070193.000333. [DOI] [PubMed] [Google Scholar]
  11. Diffley J. F., Stillman B. Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2120–2124. doi: 10.1073/pnas.85.7.2120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Dröge P. Transcription-driven site-specific DNA recombination in vitro. Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2759–2763. doi: 10.1073/pnas.90.7.2759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gazin C., Dupont de Dinechin S., Hampe A., Masson J. M., Martin P., Stehelin D., Galibert F. Nucleotide sequence of the human c-myc locus: provocative open reading frame within the first exon. EMBO J. 1984 Feb;3(2):383–387. doi: 10.1002/j.1460-2075.1984.tb01816.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Giacca M., Zentilin L., Norio P., Diviacco S., Dimitrova D., Contreas G., Biamonti G., Perini G., Weighardt F., Riva S. Fine mapping of a replication origin of human DNA. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7119–7123. doi: 10.1073/pnas.91.15.7119. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gilbert D. M., Miyazawa H., DePamphilis M. L. Site-specific initiation of DNA replication in Xenopus egg extract requires nuclear structure. Mol Cell Biol. 1995 Jun;15(6):2942–2954. doi: 10.1128/mcb.15.6.2942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Goldman M. A., Holmquist G. P., Gray M. C., Caston L. A., Nag A. Replication timing of genes and middle repetitive sequences. Science. 1984 May 18;224(4650):686–692. doi: 10.1126/science.6719109. [DOI] [PubMed] [Google Scholar]
  17. Gromova I. I., Thomsen B., Razin S. V. Different topoisomerase II antitumor drugs direct similar specific long-range fragmentation of an amplified c-MYC gene locus in living cells and in high-salt-extracted nuclei. Proc Natl Acad Sci U S A. 1995 Jan 3;92(1):102–106. doi: 10.1073/pnas.92.1.102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Guo Z. S., DePamphilis M. L. Specific transcription factors stimulate simian virus 40 and polyomavirus origins of DNA replication. Mol Cell Biol. 1992 Jun;12(6):2514–2524. doi: 10.1128/mcb.12.6.2514. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hamlin J. L. Mammalian origins of replication. Bioessays. 1992 Oct;14(10):651–659. doi: 10.1002/bies.950141002. [DOI] [PubMed] [Google Scholar]
  20. Hann S. R., Thompson C. B., Eisenman R. N. c-myc oncogene protein synthesis is independent of the cell cycle in human and avian cells. 1985 Mar 28-Apr 3Nature. 314(6009):366–369. doi: 10.1038/314366a0. [DOI] [PubMed] [Google Scholar]
  21. Hassan A. B., Errington R. J., White N. S., Jackson D. A., Cook P. R. Replication and transcription sites are colocalized in human cells. J Cell Sci. 1994 Feb;107(Pt 2):425–434. doi: 10.1242/jcs.107.2.425. [DOI] [PubMed] [Google Scholar]
  22. Hatton K. S., Dhar V., Brown E. H., Iqbal M. A., Stuart S., Didamo V. T., Schildkraut C. L. Replication program of active and inactive multigene families in mammalian cells. Mol Cell Biol. 1988 May;8(5):2149–2158. doi: 10.1128/mcb.8.5.2149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Held P. G., Heintz N. H. Eukaryotic replication origins. Biochim Biophys Acta. 1992 Apr 6;1130(3):235–246. doi: 10.1016/0167-4781(92)90435-3. [DOI] [PubMed] [Google Scholar]
  24. Iguchi-Ariga S. M., Okazaki T., Itani T., Ogata M., Sato Y., Ariga H. An initiation site of DNA replication with transcriptional enhancer activity present upstream of the c-myc gene. EMBO J. 1988 Oct;7(10):3135–3142. doi: 10.1002/j.1460-2075.1988.tb03180.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ishimi Y., Claude A., Bullock P., Hurwitz J. Complete enzymatic synthesis of DNA containing the SV40 origin of replication. J Biol Chem. 1988 Dec 25;263(36):19723–19733. [PubMed] [Google Scholar]
  26. Ishimi Y., Matsumoto K. Loading of a DNA helicase on the DNA unwinding element in the yeast replication origin: mechanism of DNA replication in a model system. Biochemistry. 1994 Mar 8;33(9):2733–2740. doi: 10.1021/bi00175a049. [DOI] [PubMed] [Google Scholar]
  27. Ishimi Y., Matsumoto K. Model system for DNA replication of a plasmid DNA containing the autonomously replicating sequence from Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5399–5403. doi: 10.1073/pnas.90.12.5399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ishimi Y., Matsumoto K., Ohba R. DNA replication from initiation zones of mammalian cells in a model system. Mol Cell Biol. 1994 Oct;14(10):6489–6496. doi: 10.1128/mcb.14.10.6489. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ishimi Y., Sugasawa K., Hanaoka F., Kikuchi A. Replication of the simian virus 40 chromosome with purified proteins. J Biol Chem. 1991 Aug 25;266(24):16141–16148. [PubMed] [Google Scholar]
  30. Kitsberg D., Selig S., Keshet I., Cedar H. Replication structure of the human beta-globin gene domain. Nature. 1993 Dec 9;366(6455):588–590. doi: 10.1038/366588a0. [DOI] [PubMed] [Google Scholar]
  31. Kowalski D., Eddy M. J. The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 1989 Dec 20;8(13):4335–4344. doi: 10.1002/j.1460-2075.1989.tb08620.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kumar S., Leffak M. DNA topology of the ordered chromatin domain 5' to the human c-myc gene. Nucleic Acids Res. 1989 Apr 11;17(7):2819–2833. doi: 10.1093/nar/17.7.2819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Leffak M., James C. D. Opposite replication polarity of the germ line c-myc gene in HeLa cells compared with that of two Burkitt lymphoma cell lines. Mol Cell Biol. 1989 Feb;9(2):586–593. doi: 10.1128/mcb.9.2.586. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027. doi: 10.1073/pnas.84.20.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Marahrens Y., Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science. 1992 Feb 14;255(5046):817–823. doi: 10.1126/science.1536007. [DOI] [PubMed] [Google Scholar]
  36. Marians K. J. Prokaryotic DNA replication. Annu Rev Biochem. 1992;61:673–719. doi: 10.1146/annurev.bi.61.070192.003325. [DOI] [PubMed] [Google Scholar]
  37. Matsumoto K., Ishimi Y. Single-stranded-DNA-binding protein-dependent DNA unwinding of the yeast ARS1 region. Mol Cell Biol. 1994 Jul;14(7):4624–4632. doi: 10.1128/mcb.14.7.4624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Matsumoto K., Seki M., Masutani C., Tada S., Enomoto T., Ishimi Y. Stimulation of DNA synthesis by mouse DNA helicase B in a DNA replication system containing eukaryotic replication origins. Biochemistry. 1995 Jun 20;34(24):7913–7922. doi: 10.1021/bi00024a016. [DOI] [PubMed] [Google Scholar]
  39. McWhinney C., Leffak M. Autonomous replication of a DNA fragment containing the chromosomal replication origin of the human c-myc gene. Nucleic Acids Res. 1990 Mar 11;18(5):1233–1242. doi: 10.1093/nar/18.5.1233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Murakami Y., Satake M., Yamaguchi-Iwai Y., Sakai M., Muramatsu M., Ito Y. The nuclear protooncogenes c-jun and c-fos as regulators of DNA replication. Proc Natl Acad Sci U S A. 1991 May 1;88(9):3947–3951. doi: 10.1073/pnas.88.9.3947. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nagata K., Guggenheimer R. A., Enomoto T., Lichy J. H., Hurwitz J. Adenovirus DNA replication in vitro: identification of a host factor that stimulates synthesis of the preterminal protein-dCMP complex. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6438–6442. doi: 10.1073/pnas.79.21.6438. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Natale D. A., Schubert A. E., Kowalski D. DNA helical stability accounts for mutational defects in a yeast replication origin. Proc Natl Acad Sci U S A. 1992 Apr 1;89(7):2654–2658. doi: 10.1073/pnas.89.7.2654. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. O'Neill E. A., Fletcher C., Burrow C. R., Heintz N., Roeder R. G., Kelly T. J. Transcription factor OTF-1 is functionally identical to the DNA replication factor NF-III. Science. 1988 Sep 2;241(4870):1210–1213. doi: 10.1126/science.3413485. [DOI] [PubMed] [Google Scholar]
  44. Pruijn G. J., van Driel W., van der Vliet P. C. Nuclear factor III, a novel sequence-specific DNA-binding protein from HeLa cells stimulating adenovirus DNA replication. Nature. 1986 Aug 14;322(6080):656–659. doi: 10.1038/322656a0. [DOI] [PubMed] [Google Scholar]
  45. Santoro C., Mermod N., Andrews P. C., Tjian R. A family of human CCAAT-box-binding proteins active in transcription and DNA replication: cloning and expression of multiple cDNAs. Nature. 1988 Jul 21;334(6179):218–224. doi: 10.1038/334218a0. [DOI] [PubMed] [Google Scholar]
  46. Seki M., Kohda T., Yano T., Tada S., Yanagisawa J., Eki T., Ui M., Enomoto T. Characterization of DNA synthesis and DNA-dependent ATPase activity at a restrictive temperature in temperature-sensitive tsFT848 cells with thermolabile DNA helicase B. Mol Cell Biol. 1995 Jan;15(1):165–172. doi: 10.1128/mcb.15.1.165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Taira T., Iguchi-Ariga S. M., Ariga H. A novel DNA replication origin identified in the human heat shock protein 70 gene promoter. Mol Cell Biol. 1994 Sep;14(9):6386–6397. doi: 10.1128/mcb.14.9.6386. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Thompson C. B., Challoner P. B., Neiman P. E., Groudine M. Levels of c-myc oncogene mRNA are invariant throughout the cell cycle. 1985 Mar 28-Apr 3Nature. 314(6009):363–366. doi: 10.1038/314363a0. [DOI] [PubMed] [Google Scholar]
  49. Trempe J. P., Lindstrom Y. I., Leffak M. Opposite replication polarities of transcribed and nontranscribed histone H5 genes. Mol Cell Biol. 1988 Apr;8(4):1657–1663. doi: 10.1128/mcb.8.4.1657. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Umek R. M., Kowalski D. The ease of DNA unwinding as a determinant of initiation at yeast replication origins. Cell. 1988 Feb 26;52(4):559–567. doi: 10.1016/0092-8674(88)90469-2. [DOI] [PubMed] [Google Scholar]
  51. Umek R. M., Kowalski D. Thermal energy suppresses mutational defects in DNA unwinding at a yeast replication origin. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2486–2490. doi: 10.1073/pnas.87.7.2486. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Vassilev L., Johnson E. M. An initiation zone of chromosomal DNA replication located upstream of the c-myc gene in proliferating HeLa cells. Mol Cell Biol. 1990 Sep;10(9):4899–4904. doi: 10.1128/mcb.10.9.4899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Zhao Y., Tsutsumi R., Yamaki M., Nagatsuka Y., Ejiri S., Tsutsumi K. Initiation zone of DNA replication at the aldolase B locus encompasses transcription promoter region. Nucleic Acids Res. 1994 Dec 11;22(24):5385–5390. doi: 10.1093/nar/22.24.5385. [DOI] [PMC free article] [PubMed] [Google Scholar]

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