Abstract
In this study, we have identified 20 human sequences containing Myc network binding sites in a library from the whole human chromosome 19. We demonstrated binding of the Max protein to these sequences both in vitro and in vivo. The majority of the identified sequences contained one or several CACGTG or CATGTG E-boxes. Several of these sites were located within introns or in their vicinity and the corresponding genes were found to be up-or down-regulated in differentiating HL-60 cells. Our data show the proof of principle for using this strategy in identification of Max target genes, and this method can also be applied for other transcription factors.
Similar content being viewed by others
Abbreviations
- BSA:
-
bovine serum albumin
- ChIP:
-
chromatin immunoprecipitation assay
- DMSO:
-
dimethylsulfoxide
- DTT:
-
dithiothreitol
- EMSA:
-
electrophoretic mobility shift assay
- MPC:
-
magnetic particle concentrator
- PBS:
-
phosphate buffered saline
References
Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., Doyle, M., FitzHugh, W., et al. (2001) Nature, 409, 860–921.
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science, 291, 1304–1351.
Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., et al. (2002) Nature, 420, 520–562.
Carninci, P. (2006) Trends Genet., 22, 501–510.
Nikolaev, L. G., Akopov, S. B., Chernov, I. P., and Sverdlov, E. D. (2007) Curr. Genom., 8, 137–149.
Henriksson, M., and Luscher, B. (1996) Adv. Cancer Res., 68, 109–182.
Luscher, B. (2001) Gene, 277, 1–14.
Grandori, C., Cowley, S. M., James, L. P., and Eisenman, R. N. (2000) Annu. Rev. Cell. Dev. Biol., 16, 653–699.
Hurlin, P. J., and Huang, J. (2006) Semin. Cancer Biol., 16, 265–274.
Wahlstrom, T., and Henriksson, M. (2007) Adv. Cancer Res., 97, 61–80.
Luscher, B., and Larsson, L. G. (1999) Oncogene, 18, 2955–2966.
O’Hagan, R. C., Schreiber-Agus, N., Chen, K., David, G., Engelman, J. A., Schwab, R., Alland, L., Thomson, C., Ronning, D. R., Sacchettini, J. C., et al. (2000) Nat. Genet., 24, 113–119.
Hurlin, P. J., Zhou, Z. Q., Toyo-oka, K., Ota, S., Walker, W. L., Hirotsune, S., and Wynshaw-Boris, A. (2003) Embo J., 22, 4584–4596.
Nilsson, J. A., and Cleveland, J. L. (2004) Cell Cycle, 3, 588–590.
Popov, N., Wahlstrom, T., Hurlin, P. J., and Henriksson, M. (2005) Oncogene, 24, 8326–8337.
Walker, W., Zhou, Z. Q., Ota, S., Wynshaw-Boris, A., and Hurlin, P. J. (2005) J. Cell Biol., 169, 405–413.
Zeller, K. I., Zhao, X., Lee, C. W., Chiu, K. P., Yao, F., Yustein, J. T., Ooi, H. S., Orlov, Y. L., Shahab, A., Yong, H. C., et al. (2006) Proc. Natl. Acad. Sci. USA, 103, 17834–17839.
Nikolaev, L. G., Tsevegiyn, T., Akopov, S. B., Ashworth, L. K., and Sverdlov, E. D. (1996) Nucleic Acids Res., 24, 1330–1336.
Xu, D., Popov, N., Hou, M., Wang, Q., Bjorkholm, M., Gruber, A., Menkel, A. R., and Henriksson, M. (2001) Proc. Natl. Acad. Sci. USA, 98, 3826–3831.
Sambrook, J., and Russell, D. W. (eds.) (2001) Molecular Cloning. A Laboratory Manual, 3rd Edn., CSHL Press, Cold Spring Harbor.
Bousset, K., Henriksson, M., Luscher-Firzlaff, J. M., Litchfield, D. W., and Luscher, B. (1993) Oncogene, 8, 3211–3220.
Chernov, I. P., Akopov, S. B., Nikolaev, L. G., and Sverdlov, E. D. (2002) J. Cell. Biochem., 84, 590–600.
Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Nucleic Acids Res., 25, 3389–3402.
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002) Genome Res., 12, 996–1006.
Walhout, A. J., Gubbels, J. M., Bernards, R., van der Vliet, P. C., and Timmers, H. T. (1997) Nucleic Acids Res., 25, 1493–501.
Tsuneoka, M., Nakano, F., Ohgusu, H., and Mekada, E. (1997) Oncogene, 14, 2301–2311.
Gaubatz, S., Meichle, A., and Eilers, M. (1994) Mol. Cell. Biol., 14, 3853–3862.
Greasley, P. J., Bonnard, C., and Amati, B. (2000) Nucleic Acids Res., 28, 446–453.
Horikawa, I., Cable, P. L., Afshari, C., and Barrett, J. C. (1999) Cancer Res., 59, 826–830.
Shannon, M., Ashworth, L. K., Mucenski, M. L., Lamerdin, J. E., Branscomb, E., and Stubbs, L. (1996) Genomics, 33, 112–120.
Orlando, V. (2000) Trends Biochem. Sci., 25, 99–104.
Larsson, L. G., Pettersson, M., Oberg, F., Nilsson, K., and Luscher, B. (1994) Oncogene, 9, 1247–1252.
Sommer, A., Bousset, K., Kremmer, E., Austen, M., and Luscher, B. (1998) J. Biol. Chem., 273, 6632–6642.
Bouchard, C., Dittrich, O., Kiermaier, A., Dohmann, K., Menkel, A., Eilers, M., and Luscher, B. (2001) Genes Dev., 15, 2042–2047.
Femino, A. M., Fay, F. S., Fogarty, K., and Singer, R. H. (1998) Science, 280, 585–590.
Konat, G. W. (1996) Acta. Neurobiol. Exp., 56, 281–285.
Sawzdargo, M., George, S. R., Nguyen, T., Xu, S., Kolakowski, L. F., and O’Dowd, B. F. (1997) Biochem. Biophys. Res. Commun., 239, 543–547.
Brown, A. J., Goldsworthy, S. M., Barnes, A. A., Eilert, M. M., Tcheang, L., Daniels, D., Muir, A. I., Wigglesworth, M. J., Kinghorn, I., Fraser, N. J., et al. (2003) J. Biol. Chem., 278, 11312–11319.
Schreiber-Agus, N., and DePinho, R. A. (1998) Bioessays, 20, 808–818.
Dang, C. V., O’Donnell, K. A., Zeller, K. I., Nguyen, T., Osthus, R. C., and Li, F. (2006) Semin. Cancer. Biol., 16, 253–264.
Mac, S. M., D’Cunha, C. A., and Farnham, P. J. (2000) Mol. Carcinog., 29, 76–86.
Ben-Porath, I., Yanuka, O., and Benvenisty, N. (1999) Mol. Cell. Biol., 19, 3529–3539.
Kyo, S., Takakura, M., Taira, T., Kanaya, T., Itoh, H., Yutsudo, M., Ariga, H., and Inoue, M. (2000) Nucleic Acids Res., 28, 669–677.
Grandori, C., Mac, J., Siebelt, F., Ayer, D. E., and Eisenman, R. N. (1996) Embo J., 15, 4344–4357.
Lee, L. A., and Dang, C. V. (2006) Curr. Top. Microbiol. Immunol., 302, 145–167.
Prendergast, G. C., and Ziff, E. B. (1991) Science, 251, 186–189.
Hurlin, P. J., Queva, C., and Eisenman, R. N. (1997) Genes Dev., 11, 44–58.
Meroni, G., Reymond, A., Alcalay, M., Borsani, G., Tanigami, A., Tonlorenzi, R., Nigro, C. L., Messali, S., Zollo, M., Ledbetter, D. H., et al. (1997) Embo J., 16, 2892–2906.
Iarovaia, O. V., Akopov, S. B., Nikolaev, L. G., Sverdlov, E. D., and Razin, S. V. (2005) Nucleic Acids Res., 33, 4157–4163.
Senga, T., Iwamoto, S., Yoshida, T., Yokota, T., Adachi, K., Azuma, E., Hamaguchi, M., and Iwamoto, T. (2003) Blood, 101, 1185–1187.
Yang, H., Yuan, W., Wang, Y., Zhu, C., Liu, B., Yang, D., Li, Y., Wang, C., Wu, X., and Liu, M. (2005) Biochem. Biophys. Res. Commun., 333, 206–215.
Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., Sugnet, C. W., Stanke, M., Smith, K. E., Siepel, A., et al. (2007) Nucleic Acids Res., 35, D668–D673.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published in Russian in Biokhimiya, 2008, Vol. 73, No. 11, pp. 1569–1579.
Originally published in Biochemistry (Moscow) On-Line Papers in Press, as Manuscript BM08-074, October 12, 2008.
Rights and permissions
About this article
Cite this article
Akopov, S.B., Chernov, I.P., Wahlström, T. et al. Identification of recognition sites for Myc/Max/Mxd network proteins by a whole human chromosome 19 selection strategy. Biochemistry Moscow 73, 1260–1268 (2008). https://doi.org/10.1134/S0006297908110138
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297908110138