Identification of motifs that are conserved in 12 drosophila species and regulate midline glia vs. neuron expression

Genetics

Volumn 178, Issue 2, 2008, Pages 787-799

  Estes, Patricia ^a   Fulkerson, Eric ^a   Zhang, Yi ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; BRAIN NERVE CELL; CELL INTERACTION; CELL VIABILITY; CONTROLLED STUDY; DROSOPHILA; GENE; GENE CONTROL; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC CONSERVATION; GLIA CELL; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN MOTIF; WRAPPER GENE;

ANIMALS; CONSERVED SEQUENCE; DNA PRIMERS; DROSOPHILA; GENE EXPRESSION REGULATION; GENES, REPORTER; GERM-LINE MUTATION; NERVOUS SYSTEM PHYSIOLOGY; NEUROGLIA; NEURONS; RATS; SPECIES SPECIFICITY; VARIATION (GENETICS);

EID: 40849138175     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.107.080440     Document Type: Article

References (51)

1. AMBROSETTI, D. C., H. R. SCHOLER, L. DAILEY and C. BASILICO, 2000 Modulation of the activity of multiple transcriptional activation domains by the DNA binding domains mediates the synergistic action of Sox2 and Oct-3 on the fibroblast growth factor-4 enhancer. J. Biol. Chem. 275: 23387-23397.
2. BAILEY, P. J., J. M. KLOS, E. ANDERSSON, M. KARLEN, M. KALLSTROM et al., 2006 A global genomic transcriptional code associated with CNS-expressed genes. Exp. Cell Res. 312: 3108-3119.
3. BAROLO, S., L. A. CARVER and J. W. POSAKONY, 2000 GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques 29: 726-732.
4. BERGMANN, A., M. TUGENTMAN, B.-Z. SHILO and H. STELLER, 2002 Regulation of cell number by MAPK-dependent control of apoptosis: a mechanism for trophic survival signaling. Dev. Cell 2: 159-170.
5. BERMAN, B. P., B. D. PFEIFFER, T. R. LAVERTY, S. L. SALZBERG, G. M. RUBIN et al., 2004 Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 5: R61.
6. BOSSING, T., and G. M. TECHNAU, 1994 The fate of the CNS midline progenitors in Drosophila as revealed by a new method for single cell labelling. Development 120: 1895-1906.
7. BRAND, A. H., and N. PERRIMON, 1993 Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118: 401-415.
8. CAMPBELL, G., H. GÖRING, T. LIN, E. SPANA, S. ANDERSSON et al., 1994 RK2, a glial-specific homeodomain protein required for embryonic nerve cord condensation and viability in Drosophila. Development 120: 2957-2966.
9. CERTEL, K., M. G. ANDERSON, R. J. SHRIGLEY and W. A. JOHNSON, 1996 Distinct variant DNA-binding sites determine cell-specific autoregulated expression of the Drosophila POU domain transcription factor drifter in midline glia or trachea. Mol. Cell. Biol. 4: 1813-1823.
10. DICKSON, B. J., 2002 Molecular mechanisms of axon guidance. Science 298: 1959-1964.
11. ESTES, P. A., J. MOSHER and S. T. CREWS, 2001 Drosophila single-minded represses gene transcription by activating the expression of repressive factors. Dev. Biol. 232: 157-175.
12. FREEMAN, M. R., J. DELROW, J. KIM, E. JOHNSON and C. Q. DOE, 2003 Unwrapping glial biology: Gcm target genes regulating glial development, diversification and function. Neuron 38: 567-580.
13. GABAY, L., R. SEGER and B. Z. SHILO, 1997a MAP kinase in situ activation atlas during Drosophila embryogenesis. Development 124: 3535-3541.
14. GABAY, L., R. SEGER and B. Z. SHILO, 1997b In situ activation pattern of Drosophila EGF receptor pathway during development. Science 277: 1103-1106.
15. GARBE, D. S., and G. J. BASHAW, 2004 Axon guidance at the midline: from mutants to mechanisms. Crit. Rev. Biochem. Mol. Biol. 39: 319-341.
16. GIEBEL, B., I. STUTTEM, U. HINZ and J. A. CAMPOS-ORTEGA, 1997 Lethal of scute requires overexpression of daughterless to elicit ectopic neuronal development during embryogenesis in Drosophila. Mech. Dev. 63: 75-87.
17. HALTER, D. A., J. URBAN, C. RICKERT, S. S. NER, K. ITO et al., 1995 The homeobox gene repo is required for the differentiation and maintenance of glia function in the embryonic nervous system of Drosophila melanogaster. Development 121: 317-332.
18. JACOBS, J. R., 2000 The midline glia of Drosophila: a molecular genetic model for the developmental functions of glia. Prog. Neurobiol. 62: 475-508.
19. KALIONIS, B., and P. H. O'FARRELL, 1993 A universal target sequence is bound in vitro by diverse homeodmains. Mech. Dev. 43: 57-70.
20. KEARNEY, J. B., S. B. WHEELER, P. ESTES, B. PARENTE and S. T. CREWS, 2004 Gene expression profiling of the developing Drosophila CNS midline cells. Dev. Biol. 275: 473-492.
21. KLÄMBT, C., 1993 The Drosophila gene pointed encodes two ETS-like proteins which are involved in the development of the midline glial cells. Development 117: 163-176.
22. MA, Y., K. CERTEL, Y. GAO, E. NIEMITZ, J. MOSHER et al., 2000 Functional interactions between Drosophila bHLH/PAS, Sox, and POU transcription factors regulate CNS midline expression of the slit gene. J. Neurosci. 20: 4596-4605.
23. NAMBU, P. A., and J. R. NAMBU, 1996 The Drosophila fish-hook gene encodes a HMG domain protein essential for segmentation and CNS development. Development 122: 3467-3475.
24. NAMBU, J. R., R. G. FRANKS, S. HU and S. T. CREWS, 1990 The single-minded gene of Drosophila is required for the expression of genes important for the development of CNS midline cells. Cell 63: 63-75.
25. NAMBU, J. R., J. O. LEWIS, K. A. WHARTON and S. T. CREWS, 1991 The Drosophila single-minded gene encodes a helix-loop-helix protein that acts as a master regulator of CNS midline development. Cell 67: 1157-1167.
26. NOORDERMEER, J. N., C. C. KOPCZYNSKI, R. D. FETTER, K. S. BLAND, W. Y. CHEN et al., 1998 Wrapper, a novel member of the Ig superfamily, is expressed by midline glia and is required for them to ensheath commissural axons in Drosophila. Neuron 21: 991-1001.
27. OHSHIRO, T., and K. SAIGO, 1997 Transcriptional regulation of breathless FGF receptor gene by binding of TRACHEALESS/dARNT heterodimers to three central midline elements in Drosophila developing trachea. Development 124: 3975-3986.
28. PANKRATOVA, E. V., and O. L. POLANOVSKY, 1998 Oct-1 promoter region contains octamer sites and TAAT motifs recognized by Oct proteins. FEBS Lett. 426: 81-85.
29. PAPATSENKO, D., A. KISLYUK, M. LEVINE and I. DUBCHAK, 2006 Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics 88: 431-442.
30. PATEL, N. H., 1994 Imaging neuronal subsets and other cell types in whole-mount Drosophila embryos and larvae using antibody probes. In: Drosophila melanogaster: Practical uses in cell and molecular biology. Methods Cell Biol. 44: 445-487.
31. PENNACCHIO, L. A., N. AHITUV, A. M. MOSES, S. PRABHAKAR, M. A. NOBREGA et al., 2006 In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499-502.
32. RAJEWSKY, N., M. VERGASSOLA, U. GAUL and E. D. SIGGIA, 2002 Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3: 30.
33. REBEIZ, M., T. STONE and J. W. POSAKONY, 2005 An ancient transcriptional regulatory linkage. Dev. Biol. 281: 299-308.
34. RUBIN, G. M., and A. C. SPRADLING, 1982 Genetic transformation of Drosophila with transposable element vectors. Science 218: 348-353.
35. SALZBERG, A., D. D'EVELYN, K. L. SCHULZE, J. K. LEE, D. STRUMPF et al., 1994 Mutations affecting the pattern of the PNS in Drosophila reveal novel aspects of neuronal development. Neuron 13: 269-287.
36. SCHROEDER, M. D., M. PEARCE, J. FAK, H. FAN, U. UNNERSTALL et al., 2004 Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 9: E271.
37. SCHWEITZER, R., M. SHAHARABANY, R. SEGER and B. Z. SHILO, 1995 Secreted Spitz triggers the DER signaling pathway and is a limiting component in embryonic ventral ectoderm determination. Genes Dev. 9: 1518-1529.
38. SHARROCKS, A. D., A. L. BROWN, Y. LING and P. R. YATES, 1997 The ETS-domain transcription factor family. Int. J. Biochem. Cell Bio. 29: 1371-1387.
39. SHILO, B.-Z., 2005 Regulating the dynamics of EGF receptor signaling in space and time. Development 132: 4017-4027.
40. SINHA, S., M. D. SCHROEDER, U. UNNERSTALL, U. GAULand E. D. SIGGIA, 2004 Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics 5: 129.
41. SONNENFELD, M., M. WARD, G. NYSTROM, J. MOSHER, S. STAHL et al., 1997 The Drosophila tango gene encodes a bHLH-PAS protein that is orthologous to mammalian Arnt and controls CNS midline and tracheal development. Development 124: 4571-4582.
42. STARK, A., M. F. LIN, P. KHERADPOUR, J. S. PEDERSEN, L. PARTS et al., 2007 Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-232.
43. TANAKA, S., Y. KAMACHI, A. TANOUCHI, H. HAMADA, N. JING et al., 2004 Interplay of SOX and POU factors in regulation of the Nestin gene in neural primordial cells. Mol. Cell. Biol. 24: 8834-8846.
44. TEARLE, R. G., and C. NUSSLEIN-VOLHARD, 1987 Tubingen mutants and stock list. Dros. Inf. Serv. 66: 209-269.
45. THOMAS, J. B., S. T. CREWS and C. S. GOODMAN, 1988 Molecular genetics of the single-minded locus: a gene involved in the development of the Drosophila nervous system. Cell 52: 133-141.
46. WARD, M. P., J. T. MOSHER and S. T. CREWS, 1998 Regulation of bHLH-PAS protein subcellular localization during Drosophila embryogenesis. Development 125: 1599-1608.
47. WEGNER, M., 1999 From head to toes: the multiple facets of Sox proteins. Nucleic Acids Res. 27: 1409-1420.
48. WENICK, A. S., and O. HOBERT, 2004 Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in C. elegans. Dev. Cell 6: 757-770.
49. WHEELER, S. R., J. B. KEARNEY, A. R. GUARDIOLA and S. T. CREWS, 2006 Single-cell mapping of neural and glial gene expression in the developing Drosophila CNS midline cells. Dev. Biol. 294: 509-524.
50. XIONG, W. C., H. OKANO, N. H. PATEL, J. A. BLENDY and C. MONTELL, 1994 repo encodes a glial-specific homeo domain protein required in the Drosophila nervous system. Genes Dev. 8: 981-994.
51. ZINZEN, R. P., K. SENGER, M. LEVINE and D. PAPATSENKO, 2006 Computational models for neurogenic gene expression in the Drosophila embryo. Curr. Biol. 16: 1358-1365.