22
Views
49
CrossRef citations to date
0
Altmetric
Gene Expression

Whole-Genome Analysis Reveals a Strong Positional Bias of Conserved dMyc-Dependent E-Boxes

, , , , , & show all
Pages 3401-3410 | Received 03 Jan 2005, Accepted 19 Jan 2005, Published online: 27 Mar 2023

REFERENCES

  • Amati, B., S. R. Frank, D. Donjerkovic, and S. Taubert. 2001. Function of the c-Myc oncoprotein in chromatin remodeling and transcription. Biochim. Biophys. Acta 1471:M135–M145.
  • Bailey, T. L., and C. Elkan. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2:28–36.
  • Baldi, P., and A. D. Long. 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17:509–519.
  • Baudino, T. A., and J. L. Cleveland. 2001. The Max network gone mad. Mol. Cell. Biol. 21:691–702.
  • Bergman, C. M., B. D. Pfeiffer, D. E. Rincon-Limas, R. A. Hoskins, A. Gnirke, C. J. Mungall, A. M. Wang, B. Kronmiller, J. Pacleb, S. Park, M. Stapleton, K. Wan, R. A. George, P. J. de Jong, J. Botas, G. M. Rubin, and S. E. Celniker. 2002. Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome. Genome Biol. 3:RESEARCH0086.
  • Bourbon, H. M., G. Gonzy-Treboul, F. Peronnet, M. F. Alin, C. Ardourel, C. Benassayag, D. Cribbs, J. Deutsch, P. Ferrer, M. Haenlin, J. A. Lepesant, S. Noselli, and A. Vincent. 2002. A P-insertion screen identifying novel X-linked essential genes in Drosophila. Mech. Dev. 110:71–83.
  • Cawley, S., S. Bekiranov, H. H. Ng, P. Kapranov, E. A. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, J. Cheng, A. J. Williams, R. Wheeler, B. Wong, J. Drenkow, M. Yamanaka, S. Patel, S. Brubaker, H. Tammana, G. Helt, K. Struhl, and T. R. Gingeras. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499–509.
  • Celniker, S. E., and G. M. Rubin. 2003. The Drosophila melanogaster genome. Annu. Rev. Genomics Hum. Genet. 4:89–117.
  • Celniker, S. E., D. A. Wheeler, B. Kronmiller, J. W. Carlson, A. Halpern, S. Patel, M. Adams, M. Champe, S. P. Dugan, E. Frise, A. Hodgson, R. A. George, R. A. Hoskins, T. Laverty, D. M. Muzny, C. R. Nelson, J. M. Pacleb, S. Park, B. D. Pfeiffer, S. Richards, E. J. Sodergren, R. Svirskas, P. E. Tabor, K. Wan, M. Stapleton, G. G. Sutton, C. Venter, G. Weinstock, S. E. Scherer, E. W. Myers, R. A. Gibbs, and G. M. Rubin. 2002. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3:RESEARCH0079.
  • Clemens, J. C., C. A. Worby, N. Simonson-Leff, M. Muda, T. Maehama, B. A. Hemmings, and J. E. Dixon. 2000. Use of double-stranded RNA interference in Drosophila cell lines to dissect signal transduction pathways. Proc. Natl. Acad. Sci. USA 97:6499–6503.
  • Dang, C. V. 1999. c-Myc target genes involved in cell growth, apoptosis, and metabolism. Mol. Cell. Biol. 19:1–11.
  • De La Cova, C., M. Abril, P. Bellosta, P. Gallant, and L. A. Johnston. 2004. Drosophila myc regulates organ size by inducing cell competition. Cell 117:107–116.
  • Eberhardy, S. R., C. A. D'Cunha, and P. J. Farnham. 2000. Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation. J. Biol. Chem. 275:33798–33805.
  • Eberhardy, S. R., and P. J. Farnham. 2001. c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism. J. Biol. Chem. 276:48562–48571.
  • Eberhardy, S. R., and P. J. Farnham. 2002. Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter. J. Biol. Chem. 277:40156–40162.
  • Eisenman, R. N. 2001. Deconstructing myc. Genes Dev. 15:2023–2030.
  • Fernandez, P. C., S. R. Frank, L. Wang, M. Schroeder, S. Liu, J. Greene, A. Cocito, and B. Amati. 2003. Genomic targets of the human c-Myc protein. Genes Dev. 17:1115–1129.
  • FlyBase Consortium. 2003. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 31:172–175.
  • Frank, S. R., T. Parisi, S. Taubert, P. Fernandez, M. Fuchs, H. M. Chan, D. M. Livingston, and B. Amati. 2003. MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep. 4:575–580.
  • Frank, S. R., M. Schroeder, P. Fernandez, S. Taubert, and B. Amati. 2001. Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation. Genes Dev. 15:2069–2082.
  • Gallant, P., Y. Shiio, P. F. Cheng, S. M. Parkhurst, and R. N. Eisenman. 1996. Myc and Max homologs in Drosophila. Science 274:1523–1527.
  • Haggerty, T. J., K. I. Zeller, R. C. Osthus, D. R. Wonsey, and C. V. Dang. 2003. A strategy for identifying transcription factor binding sites reveals two classes of genomic c-Myc target sites. Proc. Natl. Acad. Sci. USA 100:5313–5318.
  • Hateboer, G., H. T. Timmers, A. K. Rustgi, M. Billaud, L. J. van't Veer, and R. Bernards. 1993. TATA-binding protein and the retinoblastoma gene product bind to overlapping epitopes on c-Myc and adenovirus E1A protein. Proc. Natl. Acad. Sci. USA 90:8489–8493.
  • Jin, W., R. M. Riley, R. D. Wolfinger, K. P. White, G. Passador-Gurgel, and G. Gibson. 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 29:389–395.
  • Johnston, L. A., D. A. Prober, B. A. Edgar, R. N. Eisenman, and P. Gallant. 1999. Drosophila myc regulates cellular growth during development. Cell 98:779–790.
  • Kanazawa, S., L. Soucek, G. Evan, T. Okamoto, and B. M. Peterlin. 2003. c-Myc recruits P-TEFb for transcription, cellular proliferation and apoptosis. Oncogene 22:5707–5711.
  • Maheswaran, S., H. Lee, and G. E. Sonenshein. 1994. Intracellular association of the protein product of the c-myc oncogene with the TATA-binding protein. Mol. Cell. Biol. 14:1147–1152.
  • Maldonado-Codina, G., S. Llamazares, and D. M. Glover. 1993. Heat shock results in cell cycle delay and synchronisation of mitotic domains in cellularised Drosophila melanogaster embryos. J. Cell Sci. 105:711–720.
  • Nair, S. K., and S. K. Burley. 2003. X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112:193–205.
  • Nilsson, J. A., and J. L. Cleveland. 2003. Myc pathways provoking cell suicide and cancer. Oncogene 22:9007–9021.
  • O'Connell, B. C., A. F. Cheung, C. P. Simkevich, W. Tam, X. Ren, M. K. Mateyak, and J. M. Sedivy. 2003. A large scale genetic analysis of c-Myc-regulated gene expression patterns. J. Biol. Chem. 278:12563–12573.
  • Ohler, U., G. C. Liao, H. Niemann, and G. M. Rubin. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3:RESEARCH0087.
  • Orian, A., B. Van Steensel, J. Delrow, H. J. Bussemaker, L. Li, T. Sawado, E. Williams, L. W. Loo, S. M. Cowley, C. Yost, S. Pierce, B. A. Edgar, S. M. Parkhurst, and R. N. Eisenman. 2003. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev. 17:1101–1114.
  • Oster, S. K., C. S. Ho, E. L. Soucie, and L. Z. Penn. 2002. The myc oncogene: MarvelouslY Complex. Adv. Cancer Res. 84:81–154.
  • Pal, S., R. Yun, A. Datta, L. Lacomis, H. Erdjument-Bromage, J. Kumar, P. Tempst, and S. Sif. 2003. mSin3A/histone deacetylase 2- and PRMT5-containing Brg1 complex is involved in transcriptional repression of the Myc target gene cad. Mol. Cell. Biol. 23:7475–7487.
  • Pease, A. C., D. Solas, E. J. Sullivan, M. T. Cronin, C. P. Holmes, and S. P. Fodor. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91:5022–5026.
  • Schneider, I. 1972. Cell lines derived from late embryonic stages of Drosophila melanogaster. J. Embryol. Exp. Morphol. 27:353–365.
  • Schreiber-Agus, N., D. Stein, K. Chen, J. S. Goltz, L. Stevens, and R. A. DePinho. 1997. Drosophila Myc is oncogenic in mammalian cells and plays a role in the diminutive phenotype. Proc. Natl. Acad. Sci. USA 94:1235–1240.
  • Schuldiner, O., S. Shor, and N. Benvenisty. 2002. A computerized database-scan to identify c-MYC targets. Gene 292:91–99.
  • Trumpp, A., Y. Refaeli, T. Oskarsson, S. Gasser, M. Murphy, G. R. Martin, and J. M. Bishop. 2001. c-Myc regulates mammalian body size by controlling cell number but not cell size. Nature 414:768–773.
  • Vervoorts, J., J. M. Luscher-Firzlaff, S. Rottmann, R. Lilischkis, G. Walsemann, K. Dohmann, M. Austen, and B. Luscher. 2003. Stimulation of c-MYC transcriptional activity and acetylation by recruitment of the cofactor CBP. EMBO Rep. 4:1–7.
  • Wanzel, M., S. Herold, and M. Eilers. 2003. Transcriptional repression by Myc. Trends Cell Biol. 13:146–150.
  • Zeller, K. I., A. G. Jegga, B. J. Aronow, K. A. O'Donnell, and C. V. Dang. 2003. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets. Genome Biol. 4:R69.
  • Zhou, Z. Q., and P. J. Hurlin. 2001. The interplay between Mad and Myc in proliferation and differentiation. Trends Cell Biol. 11:S10–S14.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.