DNA tetraplex formation in the control region of c-myc (original) (raw)

Abstract

The c-myc oncogene is one of the most commonly malfunctioning genes in human cancers, and is an attractive target for anti-gene therapy. Although synthetic oligonucleotides designed to silence c-myc expression via one of its major control elements function well in vitro, their mode of action has been indefinite. Here we show that the targeted control element adopts an intrastrand fold-back DNA tetraplex, which requires potassium ions for stability in vitro. We believe formation of the tetraplex is important for c-myc activation in vivo, and propose a transcription initiation mechanism that explains how anti-gene therapy silence c-myc at the molecular level.

Full Text

The Full Text of this article is available as a PDF (341.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alitalo K., Schwab M., Lin C. C., Varmus H. E., Bishop J. M. Homogeneously staining chromosomal regions contain amplified copies of an abundantly expressed cellular oncogene (c-myc) in malignant neuroendocrine cells from a human colon carcinoma. Proc Natl Acad Sci U S A. 1983 Mar;80(6):1707–1711. doi: 10.1073/pnas.80.6.1707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Angel P., Hattori K., Smeal T., Karin M. The jun proto-oncogene is positively autoregulated by its product, Jun/AP-1. Cell. 1988 Dec 2;55(5):875–885. doi: 10.1016/0092-8674(88)90143-2. [DOI] [PubMed] [Google Scholar]
  3. Bell G. I., Selby M. J., Rutter W. J. The highly polymorphic region near the human insulin gene is composed of simple tandemly repeating sequences. Nature. 1982 Jan 7;295(5844):31–35. doi: 10.1038/295031a0. [DOI] [PubMed] [Google Scholar]
  4. Berberich S. J., Postel E. H. PuF/NM23-H2/NDPK-B transactivates a human c-myc promoter-CAT gene via a functional nuclease hypersensitive element. Oncogene. 1995 Jun 15;10(12):2343–2347. [PubMed] [Google Scholar]
  5. Blackburn E. H. Structure and function of telomeres. Nature. 1991 Apr 18;350(6319):569–573. doi: 10.1038/350569a0. [DOI] [PubMed] [Google Scholar]
  6. Boles T. C., Hogan M. E. DNA structure equilibria in the human c-myc gene. Biochemistry. 1987 Jan 27;26(2):367–376. doi: 10.1021/bi00376a006. [DOI] [PubMed] [Google Scholar]
  7. Bonham K., Fujita D. J. Organization and analysis of the promoter region and 5' non-coding exons of the human c-src proto-oncogene. Oncogene. 1993 Jul;8(7):1973–1981. [PubMed] [Google Scholar]
  8. Brownell E., Mittereder N., Rice N. R. A human rel proto-oncogene cDNA containing an Alu fragment as a potential coding exon. Oncogene. 1989 Jul;4(7):935–942. [PubMed] [Google Scholar]
  9. Collins S. J., Robertson K. A., Mueller L. Retinoic acid-induced granulocytic differentiation of HL-60 myeloid leukemia cells is mediated directly through the retinoic acid receptor (RAR-alpha). Mol Cell Biol. 1990 May;10(5):2154–2163. doi: 10.1128/mcb.10.5.2154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Cooney M., Czernuszewicz G., Postel E. H., Flint S. J., Hogan M. E. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science. 1988 Jul 22;241(4864):456–459. doi: 10.1126/science.3293213. [DOI] [PubMed] [Google Scholar]
  11. Davis T. L., Firulli A. B., Kinniburgh A. J. Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9682–9686. doi: 10.1073/pnas.86.24.9682. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Erlitzki R., Fry M. Sequence-specific binding protein of single-stranded and unimolecular quadruplex telomeric DNA from rat hepatocytes. J Biol Chem. 1997 Jun 20;272(25):15881–15890. doi: 10.1074/jbc.272.25.15881. [DOI] [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. Giraldo R., Rhodes D. The yeast telomere-binding protein RAP1 binds to and promotes the formation of DNA quadruplexes in telomeric DNA. EMBO J. 1994 May 15;13(10):2411–2420. doi: 10.1002/j.1460-2075.1994.tb06526.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Graham M., Adams J. M., Cory S. Murine T lymphomas with retroviral inserts in the chromosomal 15 locus for plasmacytoma variant translocations. 1985 Apr 25-May 1Nature. 314(6013):740–743. doi: 10.1038/314740a0. [DOI] [PubMed] [Google Scholar]
  16. Harrington C., Lan Y., Akman S. A. The identification and characterization of a G4-DNA resolvase activity. J Biol Chem. 1997 Sep 26;272(39):24631–24636. doi: 10.1074/jbc.272.39.24631. [DOI] [PubMed] [Google Scholar]
  17. Helm C. W., Shrestha K., Thomas S., Shingleton H. M., Miller D. M. A unique c-myc-targeted triplex-forming oligonucleotide inhibits the growth of ovarian and cervical carcinomas in vitro. Gynecol Oncol. 1993 Jun;49(3):339–343. doi: 10.1006/gyno.1993.1136. [DOI] [PubMed] [Google Scholar]
  18. Henderson E., Hardin C. C., Walk S. K., Tinoco I., Jr, Blackburn E. H. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 1987 Dec 24;51(6):899–908. doi: 10.1016/0092-8674(87)90577-0. [DOI] [PubMed] [Google Scholar]
  19. Hildebrandt M., Lacombe M. L., Mesnildrey S., Véron M. A human NDP-kinase B specifically binds single-stranded poly-pyrimidine sequences. Nucleic Acids Res. 1995 Oct 11;23(19):3858–3864. doi: 10.1093/nar/23.19.3858. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Katzav S., Cleveland J. L., Heslop H. E., Pulido D. Loss of the amino-terminal helix-loop-helix domain of the vav proto-oncogene activates its transforming potential. Mol Cell Biol. 1991 Apr;11(4):1912–1920. doi: 10.1128/mcb.11.4.1912. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kettani A., Bouaziz S., Wang W., Jones R. A., Patel D. J. Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads. Nat Struct Biol. 1997 May;4(5):382–389. doi: 10.1038/nsb0597-382. [DOI] [PubMed] [Google Scholar]
  22. Kinniburgh A. J., Firulli A. B., Kolluri R. DNA triplexes and regulation of the c-myc gene. Gene. 1994 Nov 4;149(1):93–100. doi: 10.1016/0378-1119(94)90416-2. [DOI] [PubMed] [Google Scholar]
  23. Majello B., Kenyon L. C., Dalla-Favera R. Human c-myb protooncogene: nucleotide sequence of cDNA and organization of the genomic locus. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9636–9640. doi: 10.1073/pnas.83.24.9636. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Marcu K. B., Bossone S. A., Patel A. J. myc function and regulation. Annu Rev Biochem. 1992;61:809–860. doi: 10.1146/annurev.bi.61.070192.004113. [DOI] [PubMed] [Google Scholar]
  25. Matsuzawa Y., Semba K., Kawamura-Tsuzuku J., Sudo T., Ishii S., Toyoshima K., Yamamoto T. Characterization of the promoter region of the c-yes proto-oncogene: the importance of the GC boxes on its promoter activity. Oncogene. 1991 Sep;6(9):1561–1567. [PubMed] [Google Scholar]
  26. Mavrothalassitis G. J., Watson D. K., Papas T. S. Molecular and functional characterization of the promoter of ETS2, the human c-ets-2 gene. Proc Natl Acad Sci U S A. 1990 Feb;87(3):1047–1051. doi: 10.1073/pnas.87.3.1047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Michelotti E. F., Michelotti G. A., Aronsohn A. I., Levens D. Heterogeneous nuclear ribonucleoprotein K is a transcription factor. Mol Cell Biol. 1996 May;16(5):2350–2360. doi: 10.1128/mcb.16.5.2350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Michelotti E. F., Sanford S., Freije J. M., MacDonald N. J., Steeg P. S., Levens D. Nm23/PuF does not directly stimulate transcription through the CT element in vivo. J Biol Chem. 1997 Sep 5;272(36):22526–22530. doi: 10.1074/jbc.272.36.22526. [DOI] [PubMed] [Google Scholar]
  29. Michelotti E. F., Tomonaga T., Krutzsch H., Levens D. Cellular nucleic acid binding protein regulates the CT element of the human c-myc protooncogene. J Biol Chem. 1995 Apr 21;270(16):9494–9499. doi: 10.1074/jbc.270.16.9494. [DOI] [PubMed] [Google Scholar]
  30. Michelotti G. A., Michelotti E. F., Pullner A., Duncan R. C., Eick D., Levens D. Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo. Mol Cell Biol. 1996 Jun;16(6):2656–2669. doi: 10.1128/mcb.16.6.2656. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Mirkin S. M., Lyamichev V. I., Drushlyak K. N., Dobrynin V. N., Filippov S. A., Frank-Kamenetskii M. D. DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature. 1987 Dec 3;330(6147):495–497. doi: 10.1038/330495a0. [DOI] [PubMed] [Google Scholar]
  32. Murchie A. I., Lilley D. M. Retinoblastoma susceptibility genes contain 5' sequences with a high propensity to form guanine-tetrad structures. Nucleic Acids Res. 1992 Jan 11;20(1):49–53. doi: 10.1093/nar/20.1.49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Olivas W. M., Maher L. J., 3rd Competitive triplex/quadruplex equilibria involving guanine-rich oligonucleotides. Biochemistry. 1995 Jan 10;34(1):278–284. doi: 10.1021/bi00001a034. [DOI] [PubMed] [Google Scholar]
  34. Patel M., Leevers S. J., Brickell P. M. Structure of the complete human c-fgr proto-oncogene and identification of multiple transcriptional start sites. Oncogene. 1990 Feb;5(2):201–206. [PubMed] [Google Scholar]
  35. Postel E. H., Berberich S. J., Flint S. J., Ferrone C. A. Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis. Science. 1993 Jul 23;261(5120):478–480. doi: 10.1126/science.8392752. [DOI] [PubMed] [Google Scholar]
  36. Postel E. H., Flint S. J., Kessler D. J., Hogan M. E. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8227–8231. doi: 10.1073/pnas.88.18.8227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Ratner L., Thielan B., Collins T. Sequences of the 5' portion of the human c-sis gene: characterization of the transcriptional promoter and regulation of expression of the protein product by 5' untranslated mRNA sequences. Nucleic Acids Res. 1987 Aug 11;15(15):6017–6036. doi: 10.1093/nar/15.15.6017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Reddy E. S., Rao V. N. Structure, expression and alternative splicing of the human c-ets-1 proto-oncogene. Oncogene Res. 1988;3(3):239–246. [PubMed] [Google Scholar]
  39. Roebroek A. J., Schalken J. A., Verbeek J. S., Van den Ouweland A. M., Onnekink C., Bloemers H. P., Van de Ven W. J. The structure of the human c-fes/fps proto-oncogene. EMBO J. 1985 Nov;4(11):2897–2903. doi: 10.1002/j.1460-2075.1985.tb04020.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Sen D., Gilbert W. A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature. 1990 Mar 29;344(6265):410–414. doi: 10.1038/344410a0. [DOI] [PubMed] [Google Scholar]
  41. Sen D., Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 1988 Jul 28;334(6180):364–366. doi: 10.1038/334364a0. [DOI] [PubMed] [Google Scholar]
  42. Shtivelman E., Lifshitz B., Gale R. P., Roe B. A., Canaani E. Alternative splicing of RNAs transcribed from the human abl gene and from the bcr-abl fused gene. Cell. 1986 Oct 24;47(2):277–284. doi: 10.1016/0092-8674(86)90450-2. [DOI] [PubMed] [Google Scholar]
  43. Siebenlist U., Hennighausen L., Battey J., Leder P. Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma. Cell. 1984 Jun;37(2):381–391. doi: 10.1016/0092-8674(84)90368-4. [DOI] [PubMed] [Google Scholar]
  44. Slamon D. J., deKernion J. B., Verma I. M., Cline M. J. Expression of cellular oncogenes in human malignancies. Science. 1984 Apr 20;224(4646):256–262. doi: 10.1126/science.6538699. [DOI] [PubMed] [Google Scholar]
  45. Takimoto M., Tomonaga T., Matunis M., Avigan M., Krutzsch H., Dreyfuss G., Levens D. Specific binding of heterogeneous ribonucleoprotein particle protein K to the human c-myc promoter, in vitro. J Biol Chem. 1993 Aug 25;268(24):18249–18258. [PubMed] [Google Scholar]
  46. Tomonaga T., Levens D. Activating transcription from single stranded DNA. Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5830–5835. doi: 10.1073/pnas.93.12.5830. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Vandenbark G. R., deCastro C. M., Taylor H., Dew-Knight S., Kaufman R. E. Cloning and structural analysis of the human c-kit gene. Oncogene. 1992 Jul;7(7):1259–1266. [PubMed] [Google Scholar]
  48. Watson R., Oskarsson M., Vande Woude G. F. Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus. Proc Natl Acad Sci U S A. 1982 Jul;79(13):4078–4082. doi: 10.1073/pnas.79.13.4078. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Woodford K. J., Howell R. M., Usdin K. A novel K(+)-dependent DNA synthesis arrest site in a commonly occurring sequence motif in eukaryotes. J Biol Chem. 1994 Oct 28;269(43):27029–27035. [PubMed] [Google Scholar]
  50. van Straaten F., Müller R., Curran T., Van Beveren C., Verma I. M. Complete nucleotide sequence of a human c-onc gene: deduced amino acid sequence of the human c-fos protein. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3183–3187. doi: 10.1073/pnas.80.11.3183. [DOI] [PMC free article] [PubMed] [Google Scholar]