G-quadruplexes are four-stranded nucleic acid structures that are implicated in the regulation of transcription, translation and replication. Genome regions enriched in putative G-quadruplex motifs include telomeres and gene promoters. Tumour suppressor p53 plays a critical role in regulatory pathways leading to cell cycle arrest, DNA repair and apoptosis. In addition to transcriptional regulation mediated via sequence-specific DNA binding, p53 can selectively bind various non-B DNA structures. In the present study, wild-type p53 (wtp53) binding to G-quadruplex formed by MYC promoter nuclease hypersensitive element (NHE) III1 region was investigated. Wtp53 binding to MYC G-quadruplex is comparable to interaction with specific p53 consensus sequence (p53CON). Apart from the full-length wtp53, its isolated C-terminal region (aa 320-393) as well, is capable of high-affinity MYC G-quadruplex binding, suggesting its critical role in this type of interaction. Moreover, wtp53 binds to MYC promoter region containing putative G-quadruplex motif in two wtp53-expressing cell lines. The results suggest that wtp53 binding to G-quadruplexes can take part in transcriptional regulation of its target genes.

Department of Biophysical Chemistry and Molecular Oncology Institute of Biophysics The Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

Department of CD Spectroscopy of Nucleic Acids Institute of Biophysics The Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

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Burge S., Parkinson G.N., Hazel P., Todd A.K., Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34:5402–5415. doi: 10.1093/nar/gkl655. PubMed DOI PMC

Lane A.N., Chaires J.B., Gray R.D., Trent J.O. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 2008;36:5482–5515. doi: 10.1093/nar/gkn517. PubMed DOI PMC

Huppert J.L., Balasubramanian S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 2007;35:406–413. doi: 10.1093/nar/gkl1057. PubMed DOI PMC

Eddy J., Maizels N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 2006;34:3887–3896. doi: 10.1093/nar/gkl529. PubMed DOI PMC

Grand C.L., Han H., Munoz R.M., Weitman S., Von Hoff D.D., Hurley L.H., Bearss D.J. The cationic porphyrin TMPyP4 down-regulates c-MYC and human telomerase reverse transcriptase expression and inhibits tumor growth in vivo. Mol. Cancer Ther. 2002;1:565–573. PubMed

Siddiqui-Jain A., Grand C.L., Bearss D.J., Hurley L.H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl. Acad. Sci. U.S.A. 2002;99:11593–11598. doi: 10.1073/pnas.182256799. PubMed DOI PMC

Borgognone M., Armas P., Calcaterra N.B. Cellular nucleic-acid-binding protein, a transcriptional enhancer of c-Myc, promotes the formation of parallel G-quadruplexes. Biochem. J. 2010;428:491–498. doi: 10.1042/BJ20100038. PubMed DOI

Brooks T.A., Kendrick S., Hurley L. Making sense of G-quadruplex and i-motif functions in oncogene promoters. FEBS J. 2010;277:3459–3469. doi: 10.1111/j.1742-4658.2010.07759.x. PubMed DOI PMC

Gonzalez V., Hurley L.H. The C-terminus of nucleolin promotes the formation of the c-MYC G-quadruplex and inhibits c-MYC promoter activity. Biochemistry. 2010;49:9706–9714. doi: 10.1021/bi100509s. PubMed DOI PMC

Gu H.P., Lin S., Xu M., Yu H.Y., Du X.J., Zhang Y.Y., Yuan G., Gao W. Up-regulating relaxin expression by G-quadruplex interactive ligand to achieve antifibrotic action. Endocrinology. 2012;153:3692–3700. doi: 10.1210/en.2012-1114. PubMed DOI

Rhodes D., Lipps H.J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 2015;43:8627–8637. doi: 10.1093/nar/gkv862. PubMed DOI PMC

Qin Y., Hurley L.H. Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie. 2008;90:1149–1171. doi: 10.1016/j.biochi.2008.02.020. PubMed DOI PMC

Slamon D.J., deKernion J.B., Verma I.M., Cline M.J. Expression of cellular oncogenes in human malignancies. Science. 1984;224:256–262. doi: 10.1126/science.6538699. PubMed DOI

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;10:2343–2347. PubMed

Postel E.H., Mango S.E., Flint S.J. A nuclease-hypersensitive element of the human c-myc promoter interacts with a transcription initiation factor. Mol. Cell Biol. 1989;9:5123–5133. doi: 10.1128/MCB.9.11.5123. PubMed DOI PMC

Meyer N., Penn L.Z. Reflecting on 25 years with MYC. Nat. Rev. Cancer. 2008;8:976–990. doi: 10.1038/nrc2231. PubMed DOI

Beckett J., Burns J., Broxson C., Tornaletti S. Spontaneous DNA lesions modulate DNA structural transitions occurring at nuclease hypersensitive element III(1) of the human c-myc proto-oncogene. Biochemistry. 2012;51:5257–5268. doi: 10.1021/bi300304k. PubMed DOI

Phan A.T., Modi Y.S., Patel D.J. Propeller-type parallel-stranded G-quadruplexes in the human c-myc promoter. J. Am. Chem. Soc. 2004;126:8710–8716. doi: 10.1021/ja048805k. PubMed DOI PMC

Ambrus A., Chen D., Dai J., Jones R.A., Yang D. Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for G-quadruplex stabilization. Biochemistry. 2005;44:2048–2058. doi: 10.1021/bi048242p. PubMed DOI

Mathad R.I., Hatzakis E., Dai J., Yang D. c-MYC promoter G-quadruplex formed at the 5′-end of NHE III1 element: insights into biological relevance and parallel-stranded G-quadruplex stability. Nucleic Acids Res. 2011;39:9023–9033. doi: 10.1093/nar/gkr612. PubMed DOI PMC

Seenisamy J., Rezler E.M., Powell T.J., Tye D., Gokhale V., Joshi C.S., Siddiqui-Jain A., Hurley L.H. The dynamic character of the G-quadruplex element in the c-MYC promoter and modification by TMPyP4. J. Am. Chem. Soc. 2004;126:8702–8709. doi: 10.1021/ja040022b. PubMed DOI

Sun D., Hurley L.H. The importance of negative superhelicity in inducing the formation of G-quadruplex and i-motif structures in the c-Myc promoter: implications for drug targeting and control of gene expression. J. Med. Chem. 2009;52:2863–2874. doi: 10.1021/jm900055s. PubMed DOI PMC

Gonzalez V., Guo K., Hurley L., Sun D. Identification and characterization of nucleolin as a c-myc G-quadruplex-binding protein. J. Biol. Chem. 2009;284:23622–23635. doi: 10.1074/jbc.M109.018028. PubMed DOI PMC

Dexheimer T.S., Carey S.S., Zuohe S., Gokhale V.M., Hu X., Murata L.B., Maes E.M., Weichsel A., Sun D., Meuillet E.J., et al. NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1) Mol. Cancer Ther. 2009;8:1363–1377. doi: 10.1158/1535-7163.MCT-08-1093. PubMed DOI PMC

Thakur R.K., Kumar P., Halder K., Verma A., Kar A., Parent J.L., Basundra R., Kumar A., Chowdhury S. Metastases suppressor NM23-H2 interaction with G-quadruplex DNA within c-MYC promoter nuclease hypersensitive element induces c-MYC expression. Nucleic Acids Res. 2009;37:172–183. doi: 10.1093/nar/gkn919. PubMed DOI PMC

Fekete A., Kenesi E., Hunyadi-Gulyas E., Durgo H., Berko B., Dunai Z.A., Bauer P.I. The guanine-quadruplex structure in the human c-myc gene's promoter is converted into B-DNA form by the human poly(ADP-ribose)polymerase-1. PLoS One. 2012;7:e42690. doi: 10.1371/journal.pone.0042690. PubMed DOI PMC

Chen S., Su L., Qiu J., Xiao N., Lin J., Tan J.H., Ou T.M., Gu L.Q., Huang Z.S., Li D. Mechanistic studies for the role of cellular nucleic-acid-binding protein (CNBP) in regulation of c-myc transcription. Biochim. Biophys. Acta. 2013;1830:4769–4777. doi: 10.1016/j.bbagen.2013.06.007. PubMed DOI

Byrd A.K., Raney K.D. A parallel quadruplex DNA is bound tightly but unfolded slowly by pif1 helicase. J. Biol. Chem. 2015;290:6482–6494. doi: 10.1074/jbc.M114.630749. PubMed DOI PMC

Federici L., Arcovito A., Scaglione G.L., Scaloni F., Lo Sterzo C., Di Matteo A., Falini B., Giardina B., Brunori M. Nucleophosmin C-terminal leukemia-associated domain interacts with G-rich quadruplex forming DNA. J. Biol. Chem. 2010;285:37138–37149. doi: 10.1074/jbc.M110.166736. PubMed DOI PMC

Vousden K.H., Prives C. Blinded by the light: the growing complexity of p53. Cell. 2009;137:413–431. doi: 10.1016/j.cell.2009.04.037. PubMed DOI

Selivanova G., Iotsova V., Kiseleva E., Strom M., Bakalkin G., Grafstrom R.C., Wiman K.G. The single-stranded DNA end binding site of p53 coincides with the C-terminal regulatory region. Nucleic Acids Res. 1996;24:3560–3567. doi: 10.1093/nar/24.18.3560. PubMed DOI PMC

el-Deiry W.S., Kern S.E., Pietenpol J.A., Kinzler K.W., Vogelstein B. Definition of a consensus binding site for p53. Nat. Genet. 1992;1:45–49. doi: 10.1038/ng0492-45. PubMed DOI

Bargonetti J., Manfredi J.J., Chen X., Marshak D.R., Prives C. A proteolytic fragment from the central region of p53 has marked sequence-specific DNA-binding activity when generated from wild-type but not from oncogenic mutant p53 protein. Genes Dev. 1993;7:2565–2574. doi: 10.1101/gad.7.12b.2565. PubMed DOI

Dudenhoffer C., Rohaly G., Will K., Deppert W., Wiesmuller L. Specific mismatch recognition in heteroduplex intermediates by p53 suggests a role in fidelity control of homologous recombination. Mol. Cell Biol. 1998;18:5332–5342. doi: 10.1128/MCB.18.9.5332. PubMed DOI PMC

Lee S., Cavallo L., Griffith J. Human p53 binds Holliday junctions strongly and facilitates their cleavage. J. Biol. Chem. 1997;272:7532–7539. doi: 10.1074/jbc.272.11.7532. PubMed DOI

Palecek E., Brazda V., Jagelska E., Pecinka P., Karlovska L., Brazdova M. Enhancement of p53 sequence-specific binding by DNA supercoiling. Oncogene. 2004;23:2119–2127. doi: 10.1038/sj.onc.1207324. PubMed DOI

Stansel R.M., Subramanian D., Griffith J.D. p53 binds telomeric single strand overhangs and t-loop junctions in vitro. J. Biol. Chem. 2002;277:11625–11628. doi: 10.1074/jbc.C100764200. PubMed DOI

Gohler T., Reimann M., Cherny D., Walter K., Warnecke G., Kim E., Deppert W. Specific interaction of p53 with target binding sites is determined by DNA conformation and is regulated by the C-terminal domain. J. Biol. Chem. 2002;277:41192–41203. doi: 10.1074/jbc.M202344200. PubMed DOI

Cobb A.M., Jackson B.R., Kim E., Bond P.L., Bowater R.P. Sequence-specific and DNA structure-dependent interactions of Escherichia coli MutS and human p53 with DNA. Anal. Biochem. 2013;442:51–61. doi: 10.1016/j.ab.2013.07.033. PubMed DOI

Walter K., Warnecke G., Bowater R., Deppert W., Kim E. tumor suppressor p53 binds with high affinity to CTG.CAG trinucleotide repeats and induces topological alterations in mismatched duplexes. J. Biol. Chem. 2005;280:42497–42507. doi: 10.1074/jbc.M507038200. PubMed DOI

Brazdova M., Palecek J., Cherny D.I., Billova S., Fojta M., Pecinka P., Vojtesek B., Jovin T.M., Palecek E. Role of tumor suppressor p53 domains in selective binding to supercoiled DNA. Nucleic Acids Res. 2002;30:4966–4974. doi: 10.1093/nar/gkf616. PubMed DOI PMC

Palecek E., Vlk D., Stankova V., Brazda V., Vojtesek B., Hupp T.R., Schaper A., Jovin T.M. Tumor suppressor protein p53 binds preferentially to supercoiled DNA. Oncogene. 1997;15:2201–2209. doi: 10.1038/sj.onc.1201398. PubMed DOI

Simonsson T., Pecinka P., Kubista M. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 1998;26:1167–1172. doi: 10.1093/nar/26.5.1167. PubMed DOI PMC

Brazdova M., Navratilova L., Tichy V., Nemcova K., Lexa M., Hrstka R., Pecinka P., Adamik M., Vojtesek B., Palecek E., et al. Preferential binding of hot spot mutant p53 proteins to supercoiled DNA in vitro and in cells. PLoS One. 2013;8:e59567. doi: 10.1371/journal.pone.0059567. PubMed DOI PMC

Bunz F., Dutriaux A., Lengauer C., Waldman T., Zhou S., Brown J.P., Sedivy J.M., Kinzler K.W., Vogelstein B. Requirement for p53 and p21 to sustain G2 arrest after DNA damage. Science. 1998;282:1497–1501. doi: 10.1126/science.282.5393.1497. PubMed DOI

Rohaly G., Chemnitz J., Dehde S., Nunez A.M., Heukeshoven J., Deppert W., Dornreiter I. A novel human p53 isoform is an essential element of the ATR-intra-S phase checkpoint. Cell. 2005;122:21–32. doi: 10.1016/j.cell.2005.04.032. PubMed DOI

Ho J.S., Ma W., Mao D.Y., Benchimol S. p53-dependent transcriptional repression of c-myc is required for G1 cell cycle arrest. Mol. Cell Biol. 2005;25:7423–7431. doi: 10.1128/MCB.25.17.7423-7431.2005. PubMed DOI PMC

Levy N., Yonish-Rouach E., Oren M., Kimchi A. Complementation by wild-type p53 of interleukin-6 effects on M1 cells: induction of cell cycle exit and cooperativity with c-myc suppression. Mol. Cell Biol. 1993;13:7942–7952. doi: 10.1128/MCB.13.12.7942. PubMed DOI PMC

Moberg K.H., Tyndall W.A., Hall D.J. Wild-type murine p53 represses transcription from the murine c-myc promoter in a human glial cell line. J. Cell. Biochem. 1992;49:208–215. doi: 10.1002/jcb.240490213. PubMed DOI

Ragimov N., Krauskopf A., Navot N., Rotter V., Oren M., Aloni Y. Wild-type but not mutant p53 can repress transcription initiation in vitro by interfering with the binding of basal transcription factors to the TATA motif. Oncogene. 1993;8:1183–1193. PubMed

Menendez D., Inga A., Resnick M.A. The expanding universe of p53 targets. Nat. Rev. Cancer. 2009;9:724–737. doi: 10.1038/nrc2730. PubMed DOI

Anderson M.E., Woelker B., Reed M., Wang P., Tegtmeyer P. Reciprocal interference between the sequence-specific core and nonspecific C-terminal DNA binding domains of p53: implications for regulation. Mol. Cell Biol. 1997;17:6255–6264. doi: 10.1128/MCB.17.11.6255. PubMed DOI PMC

Hamard P.J., Barthelery N., Hogstad B., Mungamuri S.K., Tonnessen C.A., Carvajal L.A., Senturk E., Gillespie V., Aaronson S.A., Merad M., et al. The C terminus of p53 regulates gene expression by multiple mechanisms in a target- and tissue-specific manner in vivo. Genes Dev. 2013;27:1868–1885. doi: 10.1101/gad.224386.113. PubMed DOI PMC

Laptenko O., Shiff I., Freed-Pastor W., Zupnick A., Mattia M., Freulich E., Shamir I., Kadouri N., Kahan T., Manfredi J., et al. The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Mol. Cell. 2015;57:1034–1046. doi: 10.1016/j.molcel.2015.02.015. PubMed DOI PMC

Quante T., Otto B., Brazdova M., Kejnovska I., Deppert W., Tolstonog G.V. Mutant p53 is a transcriptional co-factor that binds to G-rich regulatory regions of active genes and generates transcriptional plasticity. Cell cycle. 2012;11:3290–3303. doi: 10.4161/cc.21646. PubMed DOI PMC

Frazier M.W., He X., Wang J., Gu Z., Cleveland J.L., Zambetti G.P. Activation of c-myc gene expression by tumor-derived p53 mutants requires a discrete C-terminal domain. Mol. Cell Biol. 1998;18:3735–3743. doi: 10.1128/MCB.18.7.3735. PubMed DOI PMC

Scian M.J., Carchman E.H., Mohanraj L., Stagliano K.E., Anderson M.A., Deb D., Crane B.M., Kiyono T., Windle B., Deb S.P., et al. Wild-type p53 and p73 negatively regulate expression of proliferation related genes. Oncogene. 2008;27:2583–2593. doi: 10.1038/sj.onc.1210898. PubMed DOI

Rinn J.L., Huarte M. To repress or not to repress: this is the guardian's question. Trends Cell Biol. 2011;21:344–353. doi: 10.1016/j.tcb.2011.04.002. PubMed DOI

Sachdeva M., Zhu S., Wu F., Wu H., Walia V., Kumar S., Elble R., Watabe K., Mo Y.Y. p53 represses c-Myc through induction of the tumor suppressor miR-145. Proc. Natl. Acad. Sci. U.S.A. 2009;106:3207–3212. doi: 10.1073/pnas.0808042106. PubMed DOI PMC

Yan H., Solozobova V., Zhang P., Armant O., Kuehl B., Brenner-Weiss G., Blattner C. p53 is active in murine stem cells and alters the transcriptome in a manner that is reminiscent of mutant p53. Cell Death Dis. 2015;6:e1662. doi: 10.1038/cddis.2015.33. PubMed DOI PMC

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