Analysis and Function of Transcriptional Regulatory Elements: Insights from Drosophila

Annual Review of Entomology

Volumn 48, Issue , 2003, Pages 579-602

  Arnosti, David N ^a  

^a Michigan State University   (United States)

Author keywords

Enhancer; Promoter; Transcription; Transcriptional regulation

Indexed keywords

GENE EXPRESSION; INSECT;

DIPTERA; DROSOPHILA MELANOGASTER; DROSOPHILIDAE; HEXAPODA; INSECTA; MELANOGASTER; TRANSPOSONS;

DNA;

ANIMAL; BIOLOGICAL MODEL; BIOLOGY; DROSOPHILA; ENHANCER REGION; EVOLUTION; GENE; GENETIC TRANSCRIPTION; GENETICS; GENOMICS; INSECT; MALE; PHYLOGENY; PROMOTER REGION; REVIEW; TRANSGENIC ANIMAL;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; COMPUTATIONAL BIOLOGY; DNA; DROSOPHILA; ENHANCER ELEMENTS (GENETICS); EVOLUTION; GENES, INSECT; GENOMICS; INSECTS; MALE; MODELS, GENETIC; PHYLOGENY; PROMOTER REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

EID: 0037209074     PISSN: 00664170     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.ento.48.091801.112749     Document Type: Review

References (122)

1. An W, Wensink PC. 1995. Integrating sex- and tissue-specific regulation within a single Drosophila enhancer. Genes Dev. 9:256-66
2. Aoyagi N, Wassarman DA. 2000. Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: diversity in TFIIA and TFIID components contributes to gene-specific traniscriptional regulation. J. Cell Biol. 150:F45-50
3. Arnone MI, Davidson EH. 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851-64
4. Arnosti DN. 2002. Design and function of transcriptional switches in Drosophila. Insect Biochem. Mol. Biol. 32(10):1257-73
5. Atkinson PW, Pinkerton AC, O'Brochta DA. 2001. Genetic transformation systems in insects. Annu. Rev. Entomol. 46:317-46
6. Averof M, Patel NH. 1997. Crustacean appendage evolution associated with changes in Hox gene expression. Nature 388:682-86
7. Banerji J, Rusconi S, Schaffner W. 1981. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell 27:299-308
8. Barolo S, Carver LA, Posakony JW. 2000. GFP and beta-galactosidase transformation vectors for promoter/enhancer analysis in Drosophila. Biotechniques 29:726-32
9. Barolo S, Posakony JW. 2002. Three habits of highly effective signaling pathways; principles of transcriptional control by developmental cell signaling. Genes Dev. 16:1167-81
10. Berghammer AJ, Klingler M, Wimmer EA. 1999. A universal marker for transgenic insects. Nature 402:370-71
11. Bergman CM, Kreitman M. 2001. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11:1335-45
12. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, et al. 2002. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA 99:757-62
13. Blackwood EM, Kadonaga JT. 1998. Going the distance: a current view of enhancer action. Science 281:60-63
14. Blümer N, Schreiter K, Hempel L, Santel A, Hollmann M, et al. 2002. A new translational repression element and unusual transcriptional control regulate expression of don juan during Drosophila spermatogenesis. Mech. Dev. 110:97-112
15. Bownes M. 1994. The regulation of the yolk protein genes, a family of sex differentiation genes in Drosophila melanogaster. BioEssays 16:745-52
16. Brand AH, Perrimon N. 1993. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118:401-15
17. Brodu V, Mugat B, Fichelson P, Lepesant JA, Antoniewski C. 2001. A UAS site substitution approach to the in vivo dissection of promoters: interplay between the GATAb activator and the AEF-1 repressor at a Drosophila ecdysone response unit. Development 128:2593-602
18. Brown SJ, Fellers JP, Shippy TD, Richardson EA, Maxwell M, et al. 2002. Sequence of the Tribolium castaneum homeotic complex. The region corresponding to the Drosophila melanogaster Antennapedia complex. Genetics 160:1067-74
19. Burke TW, Willy PJ, Kutach AK, Butler JE, Kadonaga JT. 1998. The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box. Cold Spring Harbor Symp. Quant. Biol. 63:75-82
20. Butler JE, Kadonaga JT. 2001. Enhancer-promoter specificity mediated by DPE or TATA core promoter motifs. Genes Dev. 15:2515-19
21. Cann MJ, Chung E, Levin LR. 2000. A new family of adenylyl cyclase genes in the male germline of Drosophila melanogaster. Dev. Genes Evol. 210:200-6
22. Carlson J. 2002. Odor and taste receptors: genetics and e-genetics. Presented at Annu. Drosophila Res. Conf., 43rd, San Diego, CA
23. Chalkley GE, Verrijzer CP. 1999. DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the initiator. EMBO J. 18:4835-45
24. Cherbas L, Cherbas P. 1993. The arthropod initiator: the capsite consensus plays an important role in transcription. Insect Biochem. Mol. Biol. 23:81-90
25. Courey AJ. 2001. Cooperativity in transcriptional control. Curr. Biol. 11:R250-52
26. Courey AJ, Jia S. 2001. Transcriptional repression: the long and the short of it. Genes Dev. 15:2786-96
27. De Gregorio E, Spellman PT, Rubin GM, Lemaitre B. 2001. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proc. Natl. Acad. Sci. USA 98:12590-95
28. Denell R, Shippy T. 2001. Comparative insect developmental genetics: phenotypes without mutants. BioEssays 23:379-82
29. Eckert C, Wolff C, Wimmer E, Tautz D. 2002. Functional analysis of the regulatory region of the pair-rule gene hairy in Tribolium suggests regulatory divergence in spite of conserved expression. Submitted
30. Feyereisen R. 1999. Insect P450 enzymes. Annu. Rev. Entomol. 44:507-33
31. Francis NJ, Kingston RE. 2001. Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell. Biol. 2:409-21
32. Fridell YW, Searles LL. 1992. In vivo transcriptional analysis of the TATA-less promoter of the Drosophila melanogaster vermilion gene. Mol. Cell. Biol. 12:4571-77
33. Fujioka M, Emi-Sarker Y, Yusibova GL, Goto T, Jaynes JB. 1999. Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients. Development 126:2527-38
34. Fuller MT. 1993. Spermatogenesis. In The Development of Drosophila melanogaster, ed. M Bate, A Martinez Arias, 1:71-147. New York: Cold Spring Harbor Press
35. Furlong EE, Andersen EC, Null B, White KP, Scott MP. 2001. Patterns of gene expression during Drosophila mesoderm development. Science 293:1629-33
36. Gerasimova TI, Corces VG. 2001. Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annu. Rev. Genet. 35:193-208
37. Gowher H, Leismann O, Jeltsch A. 2000. DNA of Drosophila melanogaster contains 5-methylcytosine. EMBO J. 19:6918-23
38. Gray S, Levine M. 1996. Transcriptional repression in development. Curr. Opin. Cell. Biol. 8:358-64
39. Guss KA, Nelson CE, Hudson A, Kraus ME, Carroll SB. 2001. Control of a genetic regulatory network by a selector gene. Science 292:1164-67
40. Han W, Yu Y, Su K, Kohanski RA, Pick L. 1998. A binding site for multiple transcriptional activators in the fushi tarazu proximal enhancer is essential for gene expression in vivo. Mol. Cell. Biol. 18:3384-94
41. Hearn MG, Hedrick A, Grigliatti TA, Wakimoto BT. 1991. The effect of modifiers of position-effect variegation on the variegation of heterochromatic genes of Drosophila melanogaster. Genetics 128:785-97
42. Henikoff S. 2000. Heterochromatin function in complex genomes. Biochim. Biophys. Acta 1470:1-8
43. Hewitt GF, Strunk BS, Margulies C, Priputin T, Wang X-D, et al. 1999. Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. Development 126:1201-10
44. Hiller MA, Lin TY, Wood C, Fuller MT. 2001. Developmental regulation of transcription by a tissue-specific TAF homolog. Genes Dev. 15:1021-30
45. Hoch M, Schröder C, Seifert E, Jäckle H. 1990. cis-acting control elements for Krüppel expression in the Drosophila embryo. EMBO J. 9:2587-95
46. Hooper KL, Parkhurst SM, Ish-Horowicz D. 1989. Spatial control of hairy protein expression during embryogenesis. Development 107:489-504
47. Hung MS, Karthikeyan N, Huang B, Koo HC, Kiger J, Shen CJ. 1999. Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases. Proc. Natl. Acad. Sci. USA 96:11940-45
48. Imam FB, Johnson EJ, Arbeitman M, Furlong E, Null B, et al. 2002. A transcriptional view of Drosophila development. Presented at Annu. Drosophila Res. Conf., 43rd, San Diego, CA
49. Jiang J, Hoey T, Levine M. 1991. Autoregulation of a segmentation gene in Drosophila: combinatorial interaction of the even-skipped homeo box protein with a distal enhancer element. Genes Dev. 5:265-77
50. Jost W, Yu Y, Pick L, Preiss A, Maier D. 1995. Structure and regulation of the fushi tarazu gene from Drosophila hydei. Roux's Arch. Dev. Biol. 205:160-70
51. Kermekchiev M, Pettersson M, Matthias P, Schaffner W. 1991. Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling? Gene Exp. 1:71-81
52. Klingler M, Soong J, Butler B, Gergen JP. 1996. Disperse versus compact elements for the regulation of runt stripes in Drosophila. Dev. Biol. 177:73-84
53. Kokoza VA, Martin D, Mienaltowski MJ, Ahmed A, Morton CM, Raikhel AS. 2001. Transcriptional regulation of the mosquito vitellogenin gene via a blood meal-triggered cascade. Gene 274:47-65
54. Kravariti L, Thomas J, Sourmeli S, Rodakis GC, Mauchamp B, et al. 2001. The biolistic method as a tool for testing the differential activity of putative silkmoth chorion gene promoters. Insect Biochem. Mol. Biol. 31:473-79
55. Kulkarni M, Arnosti DN. 2002. Parallel signaling by transcriptional enhancers. Submitted
56. Kutach AK, Kadonaga JT. 2000. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20:4754-64
57. Lawson R, Mestril R, Schiller P, Voellmy R. 1984. Expression of heat shock-beta-galactosidase hybrid genes in cultured Drosophila cells. Mol. Gen. Genet. 198:116-24
58. Lee TI, Young RA. 2000. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34:77-137
59. Lehmann M. 1996. Drosophila Sgs genes: stage and tissue specificity of hormone responsiveness. BioEssays 18:47-54
60. Lewis EB. 1998. The bithorax complex: the first fifty years. Int. J. Dev. Biol. 42:403-15
61. Li TR, White KP. 2002. Developmental gene expression profiles of individual tissues and organs in Drosophila. Presented at Annu. Drosophila Res. Conf., 43rd, San Diego, CA
62. Li X, Noll M. 1994. Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo. EMBO J. 13:400-6
63. Li X, Noll M. 1994. Evolution of distinct developmental functions of three Drosophila genes by acquisition of different cis-regulatory regions. Nature 367:83-87
64. Lu J, Oliver B. 2001. Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site. Development 128:1671-86
65. Ludwig MZ, Bergman C, Patel NH, Kreitman M. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403:564-67
66. Ludwig MZ, Kreitman M. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125:949-58
67. Lyko F, Ramsahoye BH, Jaenisch R. 2000. DNA methylation in Drosophila melanogaster. Nature 408:538-40
68. Mackay TF. 2001. Quantitative trait loci in Drosophila. Nat. Rev. Genet. 2:11-20
69. Mahmoudi T, Verrijzer CP. 2001. Chromatin silencing and activation by Polycomb and trithorax group proteins. Oncogene 20:3055-66
70. Maier D, Preiss A, Powell JR. 1990. Regulation of the segmentation gene fushi tarazu has been functionally conserved in Drosophila. EMBO J. 9:3957-66
71. Markstein M, Markstein P, Markstein V, Levine MS. 2002. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl. Acad. Sci. USA 99:763-68
72. Martin D, Wang SF, Raikhel AS. 2001. The vitellogenin gene of the mosquito Aedes aegypti is a direct target of ecdysteroid receptor. Mol. Cell. Endocrinol. 173:75-86
73. Meister M, Braun A, Kappler C, Reichhart JM, Hoffmann JA. 1994. Insect immunity. A transgenic analysis in Drosophila defines several functional domains in the diptericin promoter. EMBO J. 13:5958-66
74. Merika M, Thanos D. 2001. Enhanceosomes. Curr. Opin. Genet. Dev. 11:205-8
75. Merli C, Bergstrom DE, Cygan JA, Blackman RK. 1996. Promoter specificity mediates the independent regulation of neighboring genes. Genes Dev. 10:1260-70
76. Mihaly J, Hogga I, Barges S, Galloni M, Mishra RK, et al. 1998. Chromatin domain boundaries in the Bithorax complex. Cell. Mol. Life Sci. 54:60-70
77. Mitsialis SA, Kafatos FC. 1985. Regulatory elements controlling chorion gene expression are conserved between flies and moths. Nature 317:453-56
78. Mitsialis SA, Spoerel N, Leviten M, Kafatos FC. 1987. A short 5′-flanking DNA region is sufficient for developmentally correct expression of moth chorion genes in Drosophila. Proc. Natl. Acad. Sci. USA 84:7987-91
79. Mougneau E, von Seggern D, Fowler T, Rosenblatt J, Jongens T, et al. 1993. A transcriptional switch between the Pig-1 and Sgs-4 genes of Drosophila melanogaster. Mol. Cell. Biol. 13:184-95
80. Näär AM, Lemon BD, Tjian R. 2001. Transcriptional coactivator complexes. Annu. Rev. Biochem. 70:475-501
81. Ohler U. 2000. Promoter prediction on a genomic scale: the Adh experience. Genome Res. 10:539-42
82. Ohtsuki S, Levine M. 1998. GAGA mediates the enhancer blocking activity of the eve promoter in the Drosophila embryo. Genes Dev. 12:3325-30
83. Ohtsuki S, Levine M, Cai HN. 1998. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev. 12:547-56
84. Orphanides G, Reinberg D. 2002. A unified theory of gene expression. Cell 108:439-51
85. Papatsenko DA, Makeev VJ, Lifanov AP, Regnier M, Nazina AG, Desplan C. 2002. Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. Genome Res. 12:470-81
86. Piano F, Parisi MJ, Karess R, Kambysellis MP. 1999. Evidence for redundancy but not trans factor-cis element coevolution in the regulation of Drosophila Yp genes. Genetics 152:605-16
87. Purnell BA, Emanuel PA, Gilmour DS. 1994. TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes. Genes Dev. 8:830-42
88. Ren B, Maniatis T. 1998. Regulation of Drosophila Adh promoter switching by an initiator-targeted repression mechanism. EMBO J. 17:1076-86
89. Renault N, King-Jones K, Lehmann M. 2001. Downregulation of the tissue-specific transcription factor Fork head by Broad-Complex mediates a stage-specific hormone response. Development 128:3729-37
90. Roth SY, Denu JM, Allis CD. 2001. Histone acetyltransferases. Annu. Rev. Biochem. 70:81-120
91. Rushlow C, Colosimo PF, Lin MC, Xu M, Kirov N. 2001. Transcriptional regulation of the Drosophila gene zen by competing Smad and Brinker inputs. Genes Dev. 15:340-51
92. Santel A, Kaufmann J, Hyland R, Renkawitz-Pohl R. 2000. The initiator element of the Drosophila β2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression. Nucleic Acids Res. 28:1439-46
93. Schulz RA, Xie XL, Miksch JL. 1990. cis-acting sequences required for the germ line expression of the Drosophila gonadal gene. Dev. Biol. 140:455-58
94. Sheng G, Thouvenot E, Schmucker D, Wilson DS, Desplan C. 1997. Direct regulation of rhodopsin 1 by Pax-6/eyeless in Drosophila: evidence for a conserved function in photoreceptors. Genes Dev. 11:1122-31
95. Schier AF, Gehring WJ. 1993. Analysis of a fushi tarazu autoregulatory element: multiple sequence elements contribute to enhancer activity. EMBO J. 12:1111-19
96. Schwyter DH, Huang JD, Dubnicoff T, Courey AJ. 1995. The decapentaplegic core promoter region plays an integral role, in the spatial control of transcription. Mol. Cell. Biol. 15:3960-68
97. Scott KS, Geyer PK. 1995. Effects of the su(Hw) insulator protein on the expression of the divergently transcribed Drosophila yolk protein genes. EMBO J. 14:6258-67
98. Skavdis G, Siden-Kiamos I, Muller HM, Crisanti A, Louis C. 1996. Conserved function of Anopheles gambiae midgut-specific promoters in the fruitfly. EMBO J. 15:344-50
99. Smale ST. 2001. Core promoters: active contributors to combinatorial gene regulation. Genes Dev. 15:2503-8
100. Small S, Arnosti DN, Levine M. 1993. Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter. Development 119:767-72
101. Small S, Blair A, Levine M. 1992. Regulation of even-skipped stripe 2 in the Drosophila embryo. EMBO J. 11:4047-57
102. Stanojevic D, Small S, Levine M. 1991. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254:1385-87
103. Struhl K. 2001. Gene regulation. A paradigm for precision. Science 293:1054-55
104. Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, et al. 2001. Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Genome Res. 11:677-84
105. Tautz D. 2000. A genetic uncertainty problem. Trends Genet. 16:475-77
106. Tautz D. 2000. Evolution of transcriptional regulation. Curr. Opin. Genet. Dev. 10:575-79
107. Tingvall TO, Roos E, Engstrom Y. 2001. The GATA factor Serpent is required for the onset of the humoral immune response in Drosophila embryos. Proc. Natl. Acad. Sci. USA 98:3884-88
108. Tomancak P, Beaton A, Weiszmann R, Kwan E, Celniker S, Rubin GM. 2002. Patterns of gene expression in development-embryology meets bioinformatics. Presented at the Annu. Drosophila Res. Conf., 43rd, San Diego, CA
109. Tweedie S, Ng HH, Barlow AL, Turner BM, Hendrich B, Bird A. 1999. Vestiges of a DNA methylation system in Drosophila melanogaster? Nat. Genet. 23:389-90
110. Verrijzer CP. 2001. Transcription factor IID: not so basal after all. Science 293:2010-11
111. Weiler KS, Wakimoto BT. 1995. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 29:577-605
112. White KP, Rifkin SA, Hurban P, Hogness DS. 1999. Microarray analysis of Drosophila development during metamorphosis. Science 286:2179-84
113. Willy PJ, Kobayashi R, Kadonaga JT. 2000. A basal transcription factor that activates or represses transcription. Science 290:982-85
114. Wolff C, Pepling M, Gergen P, Klingler M. 1999. Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis. Mech. Dev. 80:87-99
115. Workman JL, Kingston RE. 1998. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67:545-79
116. Woychik NA, Hampsey M. 2002. The RNA polymerase II machinery: structure illuminates function. Cell 108:453-63
117. Wu CH, Madabusi L, Nishioka H, Emanuel P, Sypes M, et al. 2001. Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster. Mol. Cell. Biol. 21:1593-602
118. Xiong B, Jacobs-Lorena M. 1995. Gut-specific transcriptional regulatory elements of the carboxypeptidase gene are conserved between black flies and Drosophila. Proc. Natl. Acad. Sci. USA 92:9313-17
119. Yanicostas C, Lepesant JA. 1990. Transcriptional and translational cis-regulatory sequences of the spermatocyte-specific Drosophila janusB gene are located in the 3′ exonic region of the overlapping janusA gene. Mol. Gen. Genet. 224:450-58
120. rd Annu. Drosophila Res. Conf., San Diego, CA
121. Zenzie-Gregory B, O'Shea-Greenfield A, Smale ST. 1992. Similar mechanisms for transcription initiation mediated through a TATA box or an initiator element. J. Biol. Chem. 267:2823-30
122. Zhu J, Kokoza V, Raikhel A. 2002. Analysis of stage- and tissue-specific gene expression in insect vectors. In The Biology of Disease Vectors, pp. xx-xx, ed. WC Marquardt. Niwot: Univ. Colorado Press. 2nd ed.