Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless

Genome Research

Volumn 16, Issue 4, 2006, Pages 466-476

  Ostrin, Edwin J ^a   Li, Yumei ^a   Hoffman, Kristi ^a   Liu, Jing ^a   Wang, Keqing ^a   Zhang, Li ^b   Mardon, Graeme ^a   Chen, Rui ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA PROTEIN; PROTEIN EYELESS; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER MODEL; CONSENSUS SEQUENCE; CONTROLLED STUDY; DROSOPHILA; EYE DEVELOPMENT; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE INDUCTION; GENE SEQUENCE; GENE TARGETING; GENETIC EPISTASIS; GENOME; GENOMIC IN SITU HYBRIDIZATION; MICROARRAY ANALYSIS; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN EXPRESSION; RETINA CELL; TRANSCRIPTION REGULATION;

ANIMALS; CHROMOSOME MAPPING; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, INSECT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

DROSOPHILA MELANOGASTER;

EID: 33645515900     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4673006     Document Type: Article

References (54)

1. Akimaru, H., Chen, Y., Dai, P., Hou, D.X., Nonaka, M., Smolik, S.M., Armstrong, S., Goodman, R.H., and Ishii, S. 1997. Drosophila Cbp is a co-activator of cubitus interruptus in hedgehog signalling. Nature 386: 735-738.
2. Barolo, S., Carver, L.A., and Posakony, J.W. 2000. GFP and β-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques 29: 726-732.
3. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., Rubin, G.M., and Eisen, M.B. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. 99: 757-762.
4. Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, E.M. 2003. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299: 1391-1394.
5. Bonini, N.M., Leiserson, W.M., and Benzer, S. 1993. The eyes absent gene: Genetic control of cell survival and differentiation in the developing Drosophila eye. Cell 72: 379-395.
6. Chen, R., Amoui, M., Zhang, Z.H., and Mardon, G. 1997. Dachshund and Eyes Absent proteins form a complex and function synergistically to induce ectopic eye development in Drosophila. Cell 91: 893-903.
7. Cheyette, B.N., Green, P.J., Martin, K., Garren, H., Hartenstein, V., and Zipursky, S.L. 1994. The Drosophila sine oculis locus encodes a homeodomain-containing protein required for the development of the entire visual system. Neuron 12: 977-996.
8. Czerny, T., Halder, G., Kloter, U., Souabni, A., Gehring, W.J., and Busslinger, M. 1999. Twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development. Mol. Cell 3: 297-307.
9. Dahl, E., Koseki, H., and Balling, R. 1997. PAX genes and organogenesis [Review]. Bioessays 19: 755-765.
10. Dalton, S. and Treisman, R. 1992. Characterization of SAP-1, a protein recruited by serum response factor to the c-fos serum response element. Cell 68: 597-612.
11. Dow, J.A. 1999. The multifunctional Drosophila melanogaster V-ATPase is encoded by a multigene family. J. Bioenerg. Biomembr. 31: 75-83.
12. Elnitski, L., Hardison, R.C., Li, J., Yang, S., Kolbe, D., Eswara, P., O'Connor, M.J., Schwartz, S., Miller, W., and Chiaromonte, F. 2003. Distinguishing regulatory DNA from neutral sites. Genome Res. 13: 64-72.
13. Epstein, J., Cai, J., Glaser, T., Jepeal, L., and Maas, R. 1994. Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. J. Biol. Chem. 269: 8355-8361.
14. Frankfort, B.J., Nolo, R., Zhang, Z., Bellen, H., and Mardon, G. 2001. Senseless repression of rough is required for R8 photoreceptor differentiation in the developing Drosophila eye. Neuron 32: 403-414.
15. Garcia-Bellido, A. and Merriam, J.R. 1969. Cell lineage of the imaginal discs in Drosophila gynandromorphs. J. Exp. Zool. 170: 61-75.
16. Glise, B., Miller, C.A., Crozatier, M., Halbisen, M.A., Wise, S., Olson, D.J., Vincent, A., and Blair, S.S. 2005. Shifted, the Drosophila ortholog of Wnt inhibitory factor-1, controls the distribution and movement of Hedgehog. Dev. Cell 8: 255-266.
17. Gorfinkiel, N., Sierra, J., Callejo, A., Ibanez, C., and Guerrero, I. 2005. The Drosophila ortholog of the human Wnt inhibitor factor Shifted controls the diffusion of lipid-modified Hedgehog. Dev. Cell 8: 241-253.
18. Halder, G., Callaerts, P., and Gehring, W.J. 1995. Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila [see comments]. Science 267: 1788-1792.
19. Halder, G., Callaerts, P., Flister, S., Walldorf, U., Kloter, U., and Gehring, W.J. 1998. Eyeless initiates the expression of both sine oculis and eyes absent during Drosophila compound eye development. Development 125: 2181-2191.
20. Halfon, M.S., Grad, Y., Church, G.M., and Michelson, A.M. 2002. Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res. 12: 1019-1028.
21. Hauck, B., Gehring, W.J., and Walldorf, U. 1999. Functional analysis of an eye specific enhancer of the eyeless gene in Drosophila. Proc. Natl. Acad. Sci. 96: 564-569.
22. Hsieh, J.C., Kodjabachian, L., Rebbert, M.L., Rattner, A., Smallwood, P.M., Samos, C.H., Nusse, R., Dawid, I.B., and Nathans, J. 1999. A new secreted protein that binds to Wnt proteins and inhibits their activities. Nature 398: 431-436.
23. Jang, C.C., Chao, J.L., Jones, N., Yao, L.C., Bessarab, D.A., Kuo, Y.M., Jun, S., Desplan, C., Beckendorf, S.K., and Sun, Y.H. 2003. Two Pax genes, eye gone and eyeless, act cooperatively in promoting Drosophila eye development. Development 130: 2939-2951.
24. Jarman, A.P., Grell, E.H., Ackerman, L., Jan, L.Y., and Jan, Y.N. 1994. Atonal is the proneural gene for Drosophila photoreceptors. Nature 369: 398-400.
25. Klipper-Aurbach, Y., Wasserman, M., Braunspiegel-Weintrob, N., Borstein, D., Peleg, S., Assa, S., Karp, M., Benjamini, Y., Hochberg, Y., and Laron, Z. 1995. Mathematical formulae for the prediction of the residual beta cell function during the first two years of disease in children and adolescents with insulin-dependent diabetes mellitus. Med. Hypotheses 45: 486-490.
26. Lawrence, P.A. 1989. Cell lineage and cell states in the Drosophila embryo. Ciba Foundation Symposium. 144: 131-140; discussion 140-149, 150-155.
27. Loosli, F., Koster, R.W., Carl, M., Krone, A., and Wittbrodt, J. 1998. Six3, a medaka homologue of the Drosophila homeobox gene sine oculis is expressed in the anterior embryonic shield and the developing eye. Mech. Dev. 74: 159-164.
28. Mardon, G., Solomon, N.M., and Rubin, G.M. 1994. dachshund encodes a nuclear protein required for normal eye and leg development in Drosophila. Development 120: 3473-3486.
29. Markstein, M. and Levine, M. 2002. Decoding cis-regulatory DNAs in the Drosophila genome. Curr. Opin. Genet. Dev. 12: 601.
30. Marquardt, T., Ashery-Padan, R., Andrejewski, N., Scardigli, R., Guillemot, F., and Gruss, P. 2001. Pax6 is required for the multipotent state of retinal progenitor cells. Cell 105: 43-55.
31. Michaut, L., Flister, S., Neeb, M., White, K.P., Certa, U., and Gehring, W.J. 2003. Analysis of the eye developmental pathway in Drosophila using DNA microarrays. Proc. Natl. Acad. Sci. 100: 4024-4029.
32. Moses, A.M., Chiang, D.Y., Pollard, D.A., Iyer, V.N., and Eisen, M.B. 2004. MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol. 5: R98.
33. Niimi, T., Seimiya, M., Kloter, U., Flister, S., and Gehring, W.J. 1999. Direct regulatory interaction of the eyeless protein with an eye-specific enhancer in the sine oculis gene during eye induction in Drosophila. Development 126: 2253-2260.
34. Pappu, K.S. and Mardon, G. 2004. Genetic control of retinal specification and determination in Drosophila. Int. J. Dev. Biol. 48: 913-924.
35. Pignoni, F., Hu, B., Zavitz, K.H., Xiao, J., Garrity, P.A., and Zipursky, S.L. 1997. The eye-specification proteins So and Eya form a complex and regulate multiple steps in Drosophila eye development. Cell 91: 881-891.
36. Punzo, C., Seimiya, M., Flister, S., Gehring, W.J., and Plaza, S. 2002. Differential interactions of eyeless and twin of eyeless with the sine oculis enhancer. Development 129: 625-634.
37. Punzo, C., Plaza, S., Seimiya, M., Schnupf, P., Kurata, S., Jaeger, J., and Gehring, W.J. 2004. Functional divergence between eyeless and twin of eyeless in Drosophila melanogaster. Development 131: 3943-3953
38. Rayapureddi, J.P., Kattamuri, C., Steinmetz, B.D., Frankfort, B.J., Ostrin, E.J., Mardon, G., and Hegde, R.S. 2003. Eyes absent represents a class of protein tyrosine phosphatases. Nature 426: 295-298.
39. Ready, D.F., Hanson, T.E., and Benzer, S. 1976. Development of the Drosophila retina, a neurocrystalline lattice. Dev. Biol. 53: 217-240.
40. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
41. Renaud, O. and Simpson, P. 2002. Movement of bristle precursors contributes to the spacing pattern in Drosophila. Mech. Dev. 119: 201-211.
42. Schroeder, M.D., Pearce, M., Fak, J., Fan, H., Unnerstall, U., Emberly, E., Rajewsky, N., Siggia, E.D., and Gaul, U. 2004. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2: E271.
43. Seimiya, M. and Gehring, W.J. 2000. The Drosophila homeobox gene optix is capable of inducing ectopic eyes by an eyeless-independent mechanism. Development 127: 1879-1886.
44. Stathopoulos, A. and Levine, M. 2002. Whole-genome expression profiles identify gene batteries in Drosophila. Dev. Cell 3: 464-465.
45. Storey, J.D. and Tibshirani, R. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. 100: 9440-9445.
46. Stormo, G.D., Schneider, T.D., Gold, L., and Ehrenfeucht, A. 1982. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli. Nucleic Acids Res. 10: 2997-3011.
47. Tamura, K., Subramanian, S., and Kumar, S. 2004. Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21: 36-44.
48. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J., and Church, G.M. 1999. Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
49. Thaker, H.M. and Kankel, D.R. 1992. Mosaic analysis gives an estimate of the extent of genomic involvement in the development of the visual system in Drosophila melanogaster. Genetics 131: 883-894.
50. Tootle, T.L., Silver, S.J., Davies, E.L., Newman, V., Latek, R.R., Mills, I.A., Selengut, J.D., Parlikar, B.E., and Rebay, I. 2003. The transcription factor Eyes absent is a protein tyrosine phosphatase. Nature 426: 299-302.
51. Toy, J., Yang, J.M., Leppert, G.S., and Sundin, O.H. 1998. The optx2 homeobox gene is expressed in early precursors of the eye and activates retina-specific genes. Proc. Natl. Acad. Sci. 95: 10643-10648.
52. Wolff, T. and Ready, D.F. 1993. Pattern formation in the Drosophila retina. In The Development of Drosophila melanogaster (eds. M. Bate and A. Martinez Arias), pp. 1277-1326. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
53. Zhang, L., Miles, M.F., and Aldape, K.D. 2003. A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol. 21: 818-821.
54. Zhu, Z., Pilpel, Y., and Church, G.M. 2002. Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J. Mol. Biol. 318: 71-81.