Functional conservation of Rel binding sites in drosophilid genomes

Genome Research

Volumn 17, Issue 9, 2007, Pages 1327-1335

  Copley, Richard R ^a   Totrov, Maxim ^b   Linnell, Jane ^a   Field, Simon ^a   Ragoussis, Jiannis ^a   Udalova, Irina A ^a,c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b Molsoft LLC   (United States)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DIF; PROTEIN DORSAL; PROTEIN RELISH; TRANSCRIPTION FACTOR REL; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; DEVELOPMENTAL GENE; DIMERIZATION; DNA BINDING; DNA MICROARRAY; DNA SEQUENCE; DROSOPHILA; GENE CONTROL; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC STABILITY; GENETIC VARIABILITY; GENOME; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN TERTIARY STRUCTURE; QUANTITATIVE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; DATABASES, FACTUAL; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENOME; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHOSPHOPROTEINS; PHYLOGENY; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-REL; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS;

DROSOPHILIDAE;

EID: 34548441990     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.6490707     Document Type: Article

References (42)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. doi: 10.1093/nar/25.17.3389.
2. Benos, P.V., Lapedes, A.S., and Stormo, G.D. 2002. Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays 24: 466-475.
3. Bergman, C.M., Carlson, J.W., and Celniker, S.E. 2005. Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21: 1747-1749.
4. Biemar, F., Nix, D.A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., Manak, J.R., and Levine, M.S. 2006. Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc. Natl. Acad. Sci. 103: 12763-12768.
5. Birney, E., Clamp, M., and Durbin, R. 2004. GeneWise and Genomewise. Genome Res. 14: 988-995.
6. Bulyk, M.L., Huang, X., Choo, Y., and Church, G.M. 2001. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. 98: 7158-7163.
7. Bulyk, M.L., Johnson, P.L., and Church, G.M. 2002. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30: 1255-1261. doi: 10.1093/nar/30.5.1255.
8. Cramer, P., Varrot, A., Barillas-Mury, C., Kafatos, F.C., and Muller, C.W. 1999. Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA. Structure 7: 841-852.
9. Crooks, G.E., Hon, G., Chandonia, J.M., and Brenner, S.E. 2004. WebLogo: A sequence logo generator. Genome Res. 14: 1188-1190.
10. De Gregorio, E., Spellman, P.T., Rubin, G.M., and Lemaitre, B. 2001. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc. Natl. Acad. Sci. 98: 12590-12595.
11. De Gregorio, E., Spellman, P.T., Tzou, P., Rubin, G.M., and Lemaitre, B. 2002. The Toll and Imd pathways are the major regulators of the immune response in Drosophila. EMBO J. 21: 2568-2579.
12. Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., et al. 2006. Pfam: Clans, web tools and services. Nucleic Acids Res. 34: D247-D251. doi: 10.1093/nar/gkj149.
13. Ganguly, A., Jiang, J., and Ip, Y.T. 2005. Drosophila WntD is a target and an inhibitor of the Dorsal/Twist/Snail network in the gastrulating embryo. Development 132: 3419-3429.
14. Gerland, U. and Hwa, T. 2002. On the selection and evolution of regulatory DNA motifs. J. Mol. Evol. 55: 386-400.
15. Gompel, N., Prud'homme, B., Wittkopp, P.J., Kassner, V.A., and Carroll, S.B. 2005. Chance caught on the wing: Cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433: 481-487.
16. Gordon, M.D., Dionne, M.S., Schneider, D.S., and Nusse, R. 2005. WntD is a feedback inhibitor of Dorsal/NF-κB in Drosophila development and immunity. Nature 437: 746-749.
17. Guindon, S., Lethiec, F., Duroux, P., and Gascuel, O. 2005. PHYML Online - A web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33: W557-W559. doi: 10.1093/nar/gki352.
18. Hoffmann, J.A. 2003. The immune response of Drosophila. Nature 426: 33-38.
19. Hoffmann, J.A., Kafatos, F.C., Janeway, C.A., and Ezekowitz, R.A. 1999. Phylogenetic perspectives in innate immunity. Science 284: 1313-1318.
20. Huang, D.B., Chen, Y.Q., Ruetsche, M., Phelps, C.B., and Ghosh, G. 2001. X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2. Structure 9: 669-678.
21. Juarez, K., Flores, H., Davila, S., Olvera, L., Gonzalez, V., and Morett, E. 2000. Reciprocal domain evolution within a transactivator in a restricted sequence space. Proc. Natl. Acad. Sci. 97: 3314-3318.
22. Jukes, T.H. and Kimura, M. 1984. Evolutionary constraints and the neutral theory. J. Mol. Evol. 21: 90-92.
23. Landry, C.R., Wittkopp, P.J., Taubes, C.H., Ranz, J.M., Clark, A.G., and Hartl, D.L. 2005. Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics 171: 1813-1822.
24. Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J., and Bork, P. 2006. SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res. 34: D257-D260. doi: 10.1093/nar/gkj079.
25. Linnell, J., Mott, R., Field, S., Kwiatkowski, D.P., Ragoussis, J., and Udalova, I.A. 2004. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 32: e44. doi: 10.1093/nar/gnh042.
26. Ludwig, M.Z. 2002. Functional evolution of noncoding DNA. Curr. Opin. Genet. Dev. 12: 634-639.
27. Ludwig, M.Z., Patel, N.H., and Kreitman, M. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change. Development 125: 949-958.
28. Ludwig, M.Z., Bergman, C., Patel, N.H., and Kreitman, M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
29. Ludwig, M.Z., Palsson, A., Alekseeva, E., Bergman, C.M., Nathan, J., and Kreitman, M. 2005. Functional evolution of a cis-regulatory module. PLoS Biol. 3: e93. doi: 10.1371/journal.pbio.0030093.
30. Mukherjee, S., Berger, M.F., Jona, G., Wang, X.S., Muzzey, D., Snyder, M., Young, R.A., and Bulyk, M.L. 2004. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36: 1331-1339.
31. Nobrega, M.A. and Pennacchio, L.A. 2004. Comparative genomic analysis as a tool for biological discovery. J. Physiol. 554: 31-39.
32. Papatsenko, D. and Levine, M. 2005. Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc. Natl. Acad. Sci. 102: 4966-4971.
33. Prud'homme, B., Gompel, N., Rokas, A., Kassner, V.A., Williams, T.M., Yeh, S.D., True, J.R., and Carroll, S.B. 2006. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440: 1050-1053.
34. Senger, K., Armstrong, G.W., Rowell, W.J., Kwan, J.M., Markstein, M., and Levine, M. 2004. Immunity regulatory DNAs share common organizational features in Drosophila. Mol. Cell 13: 19-32.
35. Silverman, N. and Maniatis, T. 2001. NF-κB signaling pathways in mammalian and insect innate immunity. Genes & Dev. 15: 2321-2342.
36. Stanojevic, D., Small, S., and Levine, M. 1991. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254: 1385-1387.
37. Stathopoulos, A. and Levine, M. 2002. Dorsal gradient networks in the Drosophila embryo. Dev. Biol. 246: 57-67.
38. Stathopoulos, A. and Levine, M. 2005. Localized repressors delineate the neurogenic ectoderm in the early Drosophila embryo. Dev. Biol. 280: 482-493.
39. Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M., and Levine, M. 2002. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 111: 687-701.
40. Udalova, I.A., Knight, J.C., Vidal, V., Nedospasov, S.A., and Kwiatkowski, D. 1998. Complex NF-κB interactions at the distal tumor necrosis factor promoter region in human monocytes. J. Biol. Chem. 273: 21178-21186.
41. Udalova, I.A., Mott, R., Field, D., and Kwiatkowski, D. 2002. Quantitative prediction of NF-κB DNA-protein interactions. Proc. Natl. Acad. Sci. 99: 8167-8172.
42. Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., and Kellis, M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.