Predicting expression patterns from regulatory sequence in Drosophila segmentation (original) (raw)
Jackle, H. et al. Transcriptional control by Drosophila gap genes. J. Cell Sci. (suppl.) 16, 39–51 (1992) ArticleCAS Google Scholar
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science290, 2306–2309 (2000) ArticleADSCAS Google Scholar
Berman, B. P. et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophilapseudoobscura. Genome Biol.5, R61 (2004) Article Google Scholar
Ochoa-Espinosa, A. et al. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc. Natl Acad. Sci. USA102, 4960–4965 (2005) ArticleADSCAS Google Scholar
Schroeder, M. D. et al. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol.2, E271 (2004) Article Google Scholar
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature434, 338–345 (2005) ArticleADSCAS Google Scholar
Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. & Church, G. M. Systematic determination of genetic network architecture. Nature Genet.22, 281–285 (1999) ArticleCAS Google Scholar
Albert, R. & Othmer, H. G. The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol.223, 1–18 (2003) ArticleMathSciNetCAS Google Scholar
Segal, E. et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genet.34, 166–176 (2003) ArticleCAS Google Scholar
Granek, J. A. & Clarke, N. D. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol.6, R87 (2005) Article Google Scholar
Bintu, L. et al. Transcriptional regulation by the numbers: models. Curr. Opin. Genet. Dev.15, 116–124 (2005) ArticleCAS Google Scholar
Zinzen, R. P., Senger, K., Levine, M. & Papatsenko, D. Computational models for neurogenic gene expression in the Drosophila embryo. Curr. Biol.16, 1358–1365 (2006) ArticleCAS Google Scholar
von Dassow, G., Meir, E., Munro, E. M. & Odell, G. M. The segment polarity network is a robust developmental module. Nature406, 188–192 (2000) ArticleADSCAS Google Scholar
Eldar, A. et al. Robustness of the BMP morphogen gradient in Drosophila embryonic patterning. Nature419, 304–308 (2002) ArticleADSCAS Google Scholar
Jaeger, J. et al. Dynamic control of positional information in the early Drosophila embryo. Nature430, 368–371 (2004) ArticleADSCAS Google Scholar
Janssens, H. et al. Quantitative and predictive model of transcriptional control of the Drosophila melanogastereven skipped gene. Nature Genet.38, 1159–1165 (2006) ArticleCAS Google Scholar
Nasiadka, A., Dietrich, B. H. & Krause, H. M. in Advances in Developmental Biology and Biochemistry: Regulation of Gene Expression at the Beginning of Development (ed. DePamphilis, M.). 155–204 (2002) Google Scholar
Rivera-Pomar, R. & Jackle, H. From gradients to stripes in Drosophila embryogenesis: filling in the gaps. Trends Genet.12, 478–483 (1996) ArticleCAS Google Scholar
Furriols, M. & Casanova, J. In and out of Torso RTK signalling. EMBO J.22, 1947–1952 (2003) ArticleCAS Google Scholar
St Johnston, D. & Nusslein-Volhard, C. The origin of pattern and polarity in the Drosophila embryo. Cell68, 201–219 (1992) ArticleCAS Google Scholar
Stormo, G. D. & Hartzell, G. W. Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA86, 1183–1187 (1989) ArticleADSCAS Google Scholar
Myasnikova, E., Samsonova, A., Kozlov, K., Samsonova, M. & Reinitz, J. Registration of the expression patterns of Drosophila segmentation genes by two independent methods. Bioinformatics17, 3–12 (2001) ArticleCAS Google Scholar
Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E. D. Computational detection of genomic _cis_-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics3, 30 (2002) Article Google Scholar
Simpson-Brose, M., Treisman, J. & Desplan, C. Synergy between the hunchback and bicoid morphogens is required for anterior patterning in Drosophila. Cell78, 855–865 (1994) ArticleCAS Google Scholar
Tanay, A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res.16, 962–972 (2006) ArticleCAS Google Scholar
Carr, A. & Biggin, M. D. A comparison of in vivo and in vitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos. EMBO J.18, 1598–1608 (1999) ArticleCAS Google Scholar
Biggin, M. D. & Tjian, R. Transcriptional regulation in Drosophila: the post-genome challenge. Funct. Integr. Genomics1, 223–234 (2001) ArticleCAS Google Scholar
Raser, J. M. & O'Shea, E. K. Control of stochasticity in eukaryotic gene expression. Science304, 1811–1814 (2004) ArticleADSCAS Google Scholar
Ptashne, M. & Gann, A. Genes and Signals 26–37 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2002) Google Scholar
Crauk, O. & Dostatni, N. Bicoid determines sharp and precise target gene expression in the Drosophila embryo. Curr. Biol.15, 1888–1898 (2005) ArticleCAS Google Scholar
Lebrecht, D. et al. Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila. Proc. Natl Acad. Sci. USA102, 13176–13181 (2005) ArticleADSCAS Google Scholar
Segal, E. et al. A genomic code for nucleosome positioning. Nature442, 772–778 (2006) ArticleADSCAS Google Scholar
Vashee, S., Melcher, K., Ding, W. V., Johnston, S. A. & Kodadek, T. Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein–protein interactions. Curr. Biol.8, 452–458 (1998) ArticleCAS Google Scholar
Hoch, M., Seifert, E. & Jackle, H. Gene expression mediated by _cis_-acting sequences of the Krüppel gene in response to the Drosophila morphogens bicoid and hunchback. EMBO J.10, 2267–2278 (1991) ArticleCAS Google Scholar
Small, S., Kraut, R., Hoey, T., Warrior, R. & Levine, M. Transcriptional regulation of a pair-rule stripe in Drosophila. Genes Dev.5, 827–839 (1991) ArticleCAS Google Scholar
Rivera-Pomar, R., Lu, X., Perrimon, N., Taubert, H. & Jackle, H. Activation of posterior gap gene expression in the Drosophila blastoderm. Nature376, 253–256 (1995) ArticleADSCAS Google Scholar
Arnosti, D. N., Barolo, S., Levine, M. & Small, S. The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development122, 205–214 (1996) CASPubMed Google Scholar
Sauer, F. & Jackle, H. Heterodimeric Drosophila gap gene protein complexes acting as transcriptional repressors. EMBO J.14, 4773–4780 (1995) ArticleCAS Google Scholar
La Rosee, A., Hader, T., Taubert, H., Rivera-Pomar, R. & Jackle, H. Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo. EMBO J.16, 4403–4411 (1997) ArticleCAS Google Scholar
Langeland, J. A., Attai, S. F., Vorwerk, K. & Carroll, S. B. Positioning adjacent pair-rule stripes in the posterior Drosophila embryo. Development120, 2945–2955 (1994) CASPubMed Google Scholar
Meinhardt, H. Hierarchical inductions of cell states: a model for segmentation in Drosophila. J. Cell Sci. (Suppl.) 4, 357–381 (1986) ArticleCAS Google Scholar
Driever, W. & Nusslein-Volhard, C. The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner. Cell54, 95–104 (1988) ArticleCAS Google Scholar
Ephrussi, A. & St Johnston, D. Seeing is believing: the bicoid morphogen gradient matures. Cell116, 143–152 (2004) ArticleCAS Google Scholar
Hoch, M., Gerwin, N., Taubert, H. & Jackle, H. Competition for overlapping sites in the regulatory region of the Drosophila gene Kruppel. Science256, 94–97 (1992) ArticleADSCAS Google Scholar
Stanojevic, D., Small, S. & Levine, M. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science254, 1385–1387 (1991) ArticleADSCAS Google Scholar
Sutrias-Grau, M. & Arnosti, D. N. CtBP contributes quantitatively to Knirps repression activity in an NAD binding-dependent manner. Mol. Cell. Biol.24, 5953–5966 (2004) ArticleCAS Google Scholar
Gray, S. & Levine, M. Short-range transcriptional repressors mediate both quenching and direct repression within complex loci in Drosophila. Genes Dev.10, 700–710 (1996) ArticleCAS Google Scholar
Arnosti, D. N., Gray, S., Barolo, S., Zhou, J. & Levine, M. The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. EMBO J.15, 3659–3666 (1996) ArticleCAS Google Scholar