Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 14, 2005, Pages 4966-4971

  Papatsenko, Dmitri ^a   Levine, Michael ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Development; Expression patterns; Fitting expression; Site quality

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DORSAL; TRANSCRIPTION FACTOR TWIST; UNCLASSIFIED DRUG;

ANOPHELES GAMBIAE; ARTICLE; BINDING SITE; CONCENTRATION RESPONSE; DROSOPHILA MELANOGASTER; ECTODERM; EMBRYO; EMBRYO PATTERN FORMATION; ENHANCER REGION; GASTRULATION; GENE ACTIVATION; GENE EXPRESSION; GENE LOCUS; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CONSERVATION; GENOME; IN VIVO STUDY; MATHEMATICAL COMPUTING; MOSQUITO; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REGULATORY MECHANISM;

ANIMALS; BASE SEQUENCE; BINDING SITES; BODY PATTERNING; CONSERVED SEQUENCE; DNA; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENES, INSECT; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PHOSPHOPROTEINS; PHYLOGENY; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION FACTORS; TWIST TRANSCRIPTION FACTOR;

EID: 17044380888     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0409414102     Document Type: Article

References (51)

1. Fortini, M. E. & Rubin, G. M. (1990) Genes Dev. 4, 444-463.
2. Ludwig, M. Z., Patel, N. H. & Kreitman, M. (1998) Development (Cambridge, U.K.) 125, 949-958.
3. Lukowitz, W., Schroder, C., Glaser, G., Hulskamp, M. & Tautz, D. (1994) Mech. Dev. 45, 105-115.
4. Emberly, E., Rajewsky, N. & Siggia, E. D. (November 20, 2003) BMC Bioinformatics, 10.1186/1471-2105-4-57.
5. Berman, B. P., Pfeiffer, B. D., Laverty, T. R., Salzberg, S. L., Rubin, G. M., Eisen, M. B. & Celniker, S. E. (August 20, 2004) Genome Biol., 10.1186/gb-2004-5-9-r61.
6. Ludwig, M. Z. & Kreitman, M. (1995) Mol. Biol. Evol. 12, 1002-1011.
7. Costas, J., Casares, F. & Vieira, J. (2003) Gene 310, 215-220.
8. Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M. & Levine, M. (2004) Cell 111, 687-701.
9. Markstein, M., Zinzen, R., Markstein, P., Yee, K. P., Erives, A., Stathopoulos, A. & Levine, M. (2004) Development (Cambridge, U.K.) 131, 2387-2394.
10. Rushlow, C. A., Han, K., Manley, J. L. & Levine, M. (1989) Cell 59, 1165-1177.
11. Roth, S., Stein, D. & Nusslein-Volhard, C. (1989) Cell 59, 1189-1202.
12. Stathopoulos, A. & Levine, M. (2002) Development (Cambridge, U.K.) 129, 3411-3419.
13. Roth, S. (2003) Philos. Trans. R. Soc. London B 358, 1317-1329, and discussion (2003) 358, 1329.
14. Jiang, J., Kosman, D., Ip, Y. T. & Levine, M. (1991) Genes Dev. 5, 1881-1891.
15. Szymanski, P. & Levine, M. (1995) EMBO J. 14, 2229-2238.
16. Stathopoulos, A. & Levine, M. (2002) Dev. Cell 3, 464-465.
17. Casal, J. & Leptin, M. (1996) Proc. Natl. Acad. Sci. USA 93, 10327-10332.
18. Stathopoulos, A., Tam, B., Ronshaugen, M., Frasch, M. & Levine, M. (2004) Genes Dev. 18, 687-699.
19. Podos, S. D. & Ferguson, E. L. (1999) Trends Genet. 15, 396-402.
20. Jiang, J. & Levine, M. (1993) Cell 72, 741-753.
21. Ip, Y. T., Levine, M. & Small, S. J. (1592) J. Cell. Sci. Suppl. 16, 33-38.
22. Zhao, C., Dave, V., Yang, F., Scarborough, T. & Ma, J. (2000) Mol. Cell. Biol. 20, 8112-8123.
23. Papatsenko, D. A., Makeev, V. J., Lifanov, A. P., Regnier, M., Nazina, A. G. & Desplan, C. (2002) Genome Res. 12, 470-481.
24. Makeev, V. J., Lifanov, A. P., Nazina, A. G. & Papatsenko, D. A. (2003) Nucleic Acids Res. 31, 6016-6026.
25. Lifanov, A. P., Makeev, V. J., Nazina, A. G. & Papatsenko, D. A. (2003) Genome Res. 13, 579-588.
26. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
27. Hammond, M. P. & Birney, E. (2004) Trends Genet. 20, 268-272.
28. Burland, T. G. (2000) Methods Mol. Biol. 132, 71-91.
29. Bailey, T. L. & Gribskov, M. (1998) J. Comput. Biol. 5, 211-221.
30. Stormo, G. D. (1990) Methods Enzymol. 183, 211-221.
31. Wagner, A. (1997) Nucleic Acids Res. 25, 3594-3604.
32. van Helden, J., Andre, B. & Collado-Vides, J. (1998) J. Mol. Biol. 281, 827-842.
33. Bussemaker, H. J., Li, H. & Siggia, E. D. (2001) Nat. Genet 27, 167-171.
34. Middendorf, M., Kundaje, A., Wiggins, C., Freund, Y. & Leslie, C. (2004) Bioinformatics 20, 1232-1240.
35. Keles, S., van der Laan, M. J. & Vulpe, C. (2004) Bioinformatics 20, 2799-2811.
36. Driever, W. & Nusslein-Volhard, C. (1988) Cell 54, 95-104.
37. Arnosti, D. N. (2003) Annu. Rev. Entomol. 48, 579-602.
38. Berman, B. P., Nihu, Y., Pfeiffer, B. D., Tomancak, P., Celniker, S. E., Levine, M., Rubin, G. M. & Eisen, M. B. (2002) Proc. Natl. Acad. Sci. USA 99, 757-762.
39. Markstein, M., Markstein, P., Markstein, V. & Levine, M. S. (2002) Proc. Natl. Acad. Sci. USA 99, 763-768.
40. Kosman, D., Ip, Y.T., Levine, M. & Arora, K. (1991) Science 254, 118-122.
41. Erives, A. & Levine, M. (2004) Proc. Natl. Acad. Sci. USA 101, 3851-3856.
42. Sanchez, L., van Helden, J. & Thieffry, D. (1997)7. Theor. Biol. 189, 377-389.
43. Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E. D. (October 24, 2002) BMC Bioinformatics, 10.1186/1471-2105-3-30.
44. Valentine, S. A., Chen, G., Shandala, T., Fernandez, J., Mische, S., Saint, R. & Courey, A. J. (1998) Mol. Cell. Biol. 18, 6584-6594.
45. Jimenez, G., Guichet, A., Ephrussi, A. & Casanova, J. (2000) Genes Dev. 14, 224-231.
46. Jiang, J., Cai, H., Zhou, Q. & Levine, M. (1993) EMBO J. 12, 3201-3209.
47. Kirov, N., Zhelnin, L., Shah, J. & Rushlow, C. (1993) EMBO J. 12, 3193-3199.
48. Leptin, M. (1991) Genes Dev. 5, 1568-1576.
49. Ip, Y. T., Park, R. E., Kosman, D., Yazdanbakhsh, K. & Levine, M. (1992) Genes Dev. 6, 1518-1530.
50. Ruban, S., Brown. G. & Freeman, M. (2004) Development (Cambridge, U.K.) 131, 1835-1845.
51. Ochoa-Espinosa, A., Yucel, G., Kaplan, L., Parc, A., Pura, N., Oberstein, A., Papatsenko, D. & Small, S. (2005) Proc. Natl. Acad. Sci. USA 102, 4960-4965.