The evolution of transcriptional regulation in eukaryotes

Molecular Biology and Evolution

Volumn 20, Issue 9, 2003, Pages 1377-1419

  Wray, Gregory A ^a   Hahn, Matthew W ^a   Abouheif, Ehab ^a   Balhoff, James P ^a   Pizer, Margaret ^a   Rockman, Matthew V ^a   Romano, Laura A ^a  

^a NONE

Author keywords

Binding site; Enhancer; Evolution of development; Genotype phenotype relationship; Promoter; Transcription factor

Indexed keywords

CIS ACTING ELEMENT; PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; BIOCHEMISTRY; CLADISTICS; EUKARYOTE EVOLUTION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC SELECTION; GENETIC VARIABILITY; GENOTYPE; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHENOTYPE; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS; REVIEW; TRANSCRIPTION REGULATION;

EUKARYOTA;

EID: 0042697343     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg140     Document Type: Review

References (432)

1. Abouheif, E. H., and G. A. Wray. 2002. The developmental genetic basis for the evolution of wing polyphenism in ants. Science 297:249-252.
2. Abraham, I., and W. W. Doane. 1978. Genetic regulation of tissue-specific expression of amylase structural genes in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 75:4446-4450.
3. Abu-Shaar, M., H. D. Ryoo, and R. S. Mann. 1999. Control of the nuclear localization of extradenticle by competing nuclear import and export signals. Genes Dev. 13:935-945.
4. Abzhanov, A., and T. C. Kaufman. 2000. Crustacean (malacostracan) Hox genes and the evolution of the arthropod trunk. Development 127:2239-2248.
5. Akashi, H. 2001. Gene expression and molecular evolution. Curr. Opin. Genet. Dev. 11:660-666.
6. Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. The molecular biology of the cell. Garland Publishing, New York.
7. Allendorf, F. W., K. L. Knudsen, and R. F. Leary. 1983. Adaptive significance of differences in the tissue-specific expression of a phosphoglucomutase gene in rainbow trout. Proc. Natl. Acad. Sci. USA 80:1397-1400.
8. Allendorf, F. W., K. L. Knudsen, and S. R. Phelps. 1982. Identification of a gene regulating the tissue expression of a phosphoglucomutase locus in rainbow trout. Genetics 102:259-268.
9. Andersson, C. R., E. O. Jensen, D. J. Llewellyn, E. S. Dennis, and W. J. Peacock. 1996. A new hemoglobin gene from soybean: a role for hemoglobin in all plants. Proc. Natl. Acad. Sci. USA 93:5682-5687.
10. Angerer, L. M., D. W. Oleksyn, A. M. Levine, X. Li, W. H. Klein, and R. C. Angerer. 2001. Sea urchin goosecoid function links fate specification along the animal-vegetal and oral-aboral embryonic axes. Development 128:4393-4404.
11. Anisimov, S. V., M. V. Volkova, L. V. Lenskaya, V. K. Khavinson, D. V. Solovieva, and E. I. Schwartz. 2001. Age-associated accumulation of the apolipoprotein C-III gene T-455C polymorphism C allele in a Russian population. J. Gerontol. A. Biol. Sci. Med. Sci. 56:B27-B32.
12. Aparicio, S., A. Morrison, A. Gould, J. Gilthorpe, C. Chaudhuri, P. Rigby, R. Krumlauf, and S. Brenner. 1995. Detecting conserved regulatory elements with the model genome of the Japanese pufferfish, Fugu rubipes. Proc. Natl. Acad. Sci. USA 92:1684-1688.
13. Arbeitman, M. N., E. E. Furlong, F. Imam, E. Johnson, B. H. Null, B. S. Baker, M. A. Krasnow, M. P. Scott, R. W. Davis, and K. P. White. 2002. Gene expression during the life cycle of Drosophila melanogaster. Science 297:2270-2275.
14. Arnone, M. I., and E. H. Davidson. 1997. The hardwiring of development: organization and function of genomic regulatory systems. Development 124:1851-1864.
15. Arnone, M. I., E. L. Martin, and E. H. Davidson. 1998. Cis-regulation downstream of cell type specification: a single compact element controls the complex expression of the Cylla gene in sea urchin embryos. Development 125:1381-1395.
16. Atchison, M. L. 1988. Enhancers: mechanisms of action and cell specificity. Annu. Rev. Cell Biol. 4:127-153.
17. Averof, M., and N. H. Patel. 1997. Crustacean appendage evolution associated with changes in Hox gene expression. Nature 388:682-686.
18. Avila, S., M. C. Casero, R. Fernandez-Canton, and L. Sastre. 2002. Transactivation domains are not functionally conserved between vertebrate and invertebrate serum response factors. Eur. J. Biochem. 269:3669-3677.
19. Babich, V., N. Aksenov, V. Alexeenko, S. L. Oei, G. Buchlow, and N. Tomilin. 1999. Association of some potential hormone response elements in human genes with the Alu family repeats. Gene 239:341-349.
20. Bamshad, M. J., S. Mummidi, E. Gonzalez et al. (11 co-authors). 2002. A strong signature of balancing selection in the 5′ cis-regulatory region of CCR5. Proc. Natl. Acad. Sci. USA 99:10539-10544.
21. Barrier, M., R. H. Robichaux, and M. D. Purugganan. 2001. Accelerated regulatory gene evolution in an adaptive radiation. Proc. Natl. Acad. Sci. USA 98:10208-10213.
22. Beckers, J., and D. Duboule. 1998. Genetic analysis of a conserved sequence in the HoxD complex: regulatory redundancy or limitations of the transgenic approach? Dev. Dyn. 213:1-11.
23. Beldade, P., P. M. Brakefield, and A. D. Long. 2002. Contribution of Distal-less to quantitative variation in butterfly eyespots. Nature 415:315-318.
24. Bell, A. C., and G. Felsenfeld. 1999. Stopped at the border: boundaries and insulators. Curr. Opin. Genet. Dev. 9:191-198.
25. Bell, S. D., and S. P. Jackson. 1998. Transcription in Archaea. Cold Spring Harbor Symp. Quant. Biol. 63:41-51.
26. Belting, H.-G., C. S. Shashikant, and F. H. Ruddle. 1998. Modification of expression and cis-regulation of Hoxc8 in the evolution of diverged axial morphology. Proc. Natl. Acad. Sci. USA 95:2355-2360.
27. Benbrook, D. M., and N. C. Jones. 1990. Heterodimer formation between CREB and JUN proteins. Oncogene 5:295-302.
28. Bender, W., M. Akam, F. Karch, P. A. Beachy, M. Peifer, P. Spierer, E. B. Lewis, and D. S. Hogness. 1983. Molecular-genetics of the bithorax complex in Drosophila melanogaster. Science 221:23-29.
29. Benecke, A., C. Gaudon, and H. Gronemeyer. 2001. Transcriptional integration of hormone and metabolic signals by nuclear receptors. Pp. 167-214 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
30. Benezra, R., R. L. Davis, D. Lockshon, D. L. Turner, and H. Weintraub. 1990. The protein Id: a negative regulator of helix-loop-helix DNA-binding proteins. Cell 61:49-59.
31. Bergman, C. M., and M. Kreitman. 2001. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11:1335-1345.
32. Berman, B. P., Y. Nibu, B. D. Pfeiffer, P. Tomancak, S. E. Celnick, M. Levine, G. M. Rubin, and M. B. Eisen. 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 99:757-767.
33. Bernstein, B. E., J. K. Tong, and S. L. Schreiber. 2000. Genome-wide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97:13708-13713.
34. Berthelsen, J., V. Zappavigna, E. Feretti, F. Mavilio, and F. Blasi. 1998. The novel homeoprotein Prepl modulates Pbx-Hox protein cooperativity. EMBO J. 17:1434-1445.
35. Betran, E., K. Thornton, and M. Long. 2002. Retroposed new genes out of the X in Drosophila. Genome Res. 12:1854-1859.
36. Bharathan, G., T. E. Goliber, C. Moore, S. Kessler, T. Pham, and N. R. Sinha. 2002. Homologies in leaf form inferred from KNOXI gene expression during development. Science 296:1858-1860.
37. Bharathan, G., B.-J. Janssen, E. A. Kellogg, and N. Sinha. 1997. Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa? Proc. Natl. Acad. Sci. USA 94:13749-13753.
38. Biggin, M. D., and W. McGinnis. 1997. Regulation of segmentation and segmental identity by Drosophila homeoproteins: the role of DNA binding in functional activity and specificity. Development 124:4425-4433.
39. Birnbaum, K., P. N. Benfey, and D. E. Shasha. 2001. cis element/transcription factor analysis (cis/TF): a method for discovering transcription factor/cis element relationships. Genome Res. 11:1567-1573.
40. Blumenthal, T. 1998. Gene clusters and polycistronic transcription in eukaryotes. Bioessays 20:480-487.
41. Bonifer, C. 2000. Developmental regulation of eukaryotic gene loci: which cis-regulatory information is required? Trends Genet. 16:310-315.
42. Brakefield, P. M., J. Gates, D. Keys, F. Kesbeke, P. J. Wijngaarden, A. Monteiro, V. French, and S. B. Carroll. 1996. Development, plasticity and evolution of butterfly eyespot patterns. Nature 384:236-242.
43. Brem, R. B., G. Yvert, R. Clinton, and L. Kruglyak. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296:752-755.
44. Brickman, J. M., M. Clements, R. Tyrell, D. McNay, K. Woods, J. Warner, A. Stewart, R. S. P. Beddington, and M. Dattani. 2001. Molecular effects of novel mutations in Hesx1/HESX1 associated with human pituitary disorders. Development 128:5189-5199.
45. Britten, R. J. 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205:177-182.
46. Britten, R. J., and E. H. Davidson. 1969. Gene regulation for higher cells: a theory. Science 165:349-357.
47. -. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q. Rev. Biol. 46:111-138.
48. Brosius, J. 1999. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 238:115-134.
49. Brunetti, C. R., J. E. Selegue, A. Monteiro, V. French, P. M. Brakefield, and S. B. Carroll. 2001. The generation and diversification of butterfly eyespot color patterns. Curr. Biol. 11:1578-1585.
50. Buckwold, V. E., Z. C. Xu, T. S. B. Yen, and J. H. Ou. 1997. Effects of a frequent double-nucleotide basal core promoter mutation and its putative single-nucleotide precursor mutations on hepatitis B virus gene expression and replication. J. Gen. Virol. 78:2055-2065.
51. Budd, G. E. 1999. Does evolution in body patterning genes drive morphological change - or vice versa? Bioessays 21:326-332.
52. Buggs, C., N. Nasrin, A. Mode, P. Tollet, H.-F. Zhao, J.-Å. Gustafsson, and M. Alexander-Bridges. 1998. IRE-ABP (insulin response element-A binding protein), An SRY-like protein, inhibits C/EBPα (CCAAT/enhancer-binding protein α)-stimulated expression of the sex-specific cytochrome P450 2C12 gene. Mol. Endocrinol. 12:1294-1309.
53. Bürglin, T. 1997. Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iriquois, TGIF) reveals a novel domain conserved between plants and animals. Nucleic Acids Res. 25:4173-4180.
54. Burke, A. C., C. E. Nelson, B. A. Morgan, and C. Tabin. 1995. Hox genes and the evolution of vertebrate axial morphology. Development 121:333-346.
55. Burstin, J., D. De Vienne, P. Dubreuil, and C. Damerval. 1994. Molecular markers and protein quantities as genetic descriptors in maize. I. Genetic diversity among 21 inbred lines. Theor. Appl. Genet. 89:943-950.
56. Bush, R. M., and K. Paigen. 1992. Evolution of β-glucuronidase regulation in the genus Mus. Evolution 46:1-15.
57. Calhoun, V. C., A. Stathopoulos, and M. Levine. 2002. Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex. Proc. Natl. Acad. Sci. USA 99:9243-9247.
58. Carey, M., and S. T. Smale. 2000. Transcriptional regulation in eukaryotes: concepts, strategies, and techniques. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
59. 2+-regulated transcriptional repressor. Nature 398:80-84.
60. Carroll, S. B. 1995. Homeotic genes and the evolution of arthropods and chordates. Nature 376:479-485.
61. -. 2000. Endless forms: the evolution of gene regulation and morphological diversity. Cell 101:577-580.
62. Carroll, S. B., J. K. Grenier, and S. D. Weatherbee. 2001. From DNA to diversity: molecular genetics and the evolution of animal design. Blackwell Science, Malden, Mass.
63. Caspi, A., J. McClay, T. E. Moffitt, J. Mill, J. Martin, I. W. Craig, A. Taylor, and R. Poulton. 2002. Role of genotype in the cycle of violence in maltreated children. Science 297:851-854.
64. Cavalieri, D., J. P. Townsend, and D. L. Hartl. 2000. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc. Natl. Acad. Sci. USA 97:12369-12374.
65. Cavener, D. R. 1992. Transgenic animal studies on the evolution of genetic regulatory circuitries. Bioessays 14:237-244.
66. Cereb, N., and S. Y. Yang. 1994. The regulatory complex of HLA class I promoters exhibits locus-specific conservation with limited allelic variation. J. Immunol. 152:3873-3883.
67. Chen, G., and A. J. Courey. 2000. Groucho/TLE family proteins and transcriptional repression. Gene 249:1-16.
68. Chiu, C. H., H. Schneider, J. L. Slightom, D. L. Gumucio, and M. Goodman. 1997. Dynamics of regulatory evolution in primate beta-globin gene clusters: cis-mediated acquisition of simian gamma fetal expression patterns. Gene 205:47-57.
69. Choo, Y., and A. Klug. 1997. Physical basis of a protein-DNA recognition code. Curr. Opin. Struct. Biol. 7:117-125.
70. Christophides, G. K., I. Livadras, C. Savakis, and K. Komitopolou. 2000. Two medfly promoters that have originated by recent gene duplications drive distinct sex, tissue and temporal expression patterns. Genetics 156:173-182.
71. Chung, Y. D., H. C. Kwon, K. W. Chung, S. J. Kim, K. J. Kim, and C. C. Lee. 1996. Identification of ovarian enhancer-binding factors which bind to ovarian enhancer 1 of the Drosophila genes yp1 and yp2. Mol. Gen. Genet. 251:347-351.
72. Clark, A. G. 1990. Genetic components of variation in energy storage in Drosophila melanogaster. Evolution 44:637-650.
73. Coller, H. A., C. Grandori, P. Tamayo, T. Colbert, E. S. Lander, R. N. Eisenman, and T. R. Golub. 2000. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion. Proc. Natl. Acad. Sci. USA 97:3260-3265.
74. Conlon, F. L., L. Fairclough, B. M. J. Price, E. S. Casey, and J. C. Smith. 2001. Determinants of T box protein specificity. Development 128:3749-3758.
75. Cooper, D. N. 1999. Human gene evolution. Academic Press, San Die go, Calif.
76. Core, N., B. Charroux, A. McCormick, C. Vola, L. Fasano, M. P. Scott, and S. Kerridge. 1997. Transcriptional regulation of the Drosophila homeotic gene teashirt by the homeodomain protein Fushi tarazu. Mech. Dev. 68:157-172.
77. Costa, P., and C. Plomion. 1999. Genetic analysis of needle proteins in maritime pine. 2. Variation in protein accumulation. Silvae Genet. 48:146-150.
78. Courey, A. J. 2001. Regulatory transcription factors and cis-regulatory regions. Pp. 17-34 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
79. Cowell, L. G., T. B. Kepler, M. Janitz, R. Lauster, and N. A. Mitchison. 1998. The distribution of variation in regulatory gene segments, as present in MHC class II promoters. Genome Res. 8:124-134.
80. Cowen, L. E., D. Sanglard, D. Calabrese, C. Sirjusingh, J. B. Anderson, and L. M. Kohn. 2000. Evolution of drug resistance in experimental populations of Candida albicans. J. Bacteriol. 182:1515-1522.
81. Cowles, C. R., J. N. Hirshhom, D. Altshuler, and E. S. Lander. 2002. Detection of regulatory variation in mouse genes. Nat. Genet. 32:432-437.
82. Crawford, D. L., J. A. Segal, and J. L. Barnett. 1999. Evolutionary analysis of TATA-less proximal promoter function. Mol. Biol. Evol. 16:194-207.
83. Czerny, T., G. Schaffner, and M. Busslinger. 1993. DNA sequence recognition by pax proteins: bipartite structure of the paired domain and its binding site. Genes Dev. 7:2048-2061.
84. Daborn, P. J., J. L. Yen, M. R. Bogwitz, G. L. Goff, E. Feil, S. Jeffers, N. Tijet, T. Perry, D. Heckel, P. Batterham, R. Feyereisen, T. G. Wilson, and R. H. French-Constant. 2002. A single P450 allele associated with insecticide resistance in Drosophila. Science 297:2253-2225.
85. Dailey, L., and C. Basilico. 2001. Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes. J. Cell. Physiol. 186:315-328.
86. Damerval, C., A. Maurice, J. M. Josse, and D. De Vienne. 1994. Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137:289-301.
87. Darwin, C. 1859. On the origin of species by means of natural selection. John Murray, London.
88. Davidson, E. H. 2001. Genomic regulatory systems: development and evolution. Academic Press, San Diego, Calif.
89. Dawes, R., I. Dawson, F. Falciani, G. Tear, and M. Akam. 1994. Dax, a locust hox gene related to fushi-tarazu but showing no pair-rule expression. Development 120:1561-1572.
90. Dawson, S. J., P. J. Morris, and D. S. Latchman. 1996. A single amino acid change converts a repressor into an activator. J. Biol. Chem. 271:11631-11633.
91. De Vienne, D., B. Bost, J. Fievet, M. Zivy, and C. Dillmann. 2001. Genetic variability of proteome expression and metabolic control. Plant Physiol. Biochem. 39:271-283.
92. D'Elia, A. V., G. Tell, I. Paron, L. Pellizzari, R. Lonigro, and G. Damante. 2002. Missense mutations of human homeoboxes: a review. Hum. Mutat. 18:361-374.
93. Denizot, Y., E. Pinaud, C. Aupetit, C. Le Morvan, E. Magnoux, J. C. Aldigier, and M. Cogne. 2001. Polymorphism of the human alpha1 immunoglobulin gene 3′ enhancer hs1,2 and its relation to gene expression. Immunology 103:35-40.
94. Dermitzakis, E. T., and A. G. Clark. 2002. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19:1114-1121.
95. DeRobertis, E. M., and Y. Sasai. 1996. A common plan for dorsoventral patterning in Bilateria. Nature 380:37-40.
96. Di Gregorio, A., J. C. Corbo, and M. Levine. 2001. The regulation of forkhead/HNf-3 beta expression in the Ciona embryo. Dev. Biol. 229:31-43.
97. Dickinson, W. J. 1988. On the architecture of regulatory systems: evolutionary insights and implications. Bioessays 8:204-208.
98. DiLeone, R. J., L. B. Russell, and D. M. Kingsley. 1998. An extensive 3′ regulatory region controls expression of Bmp5 in specific anatomical structures of the mouse embryo. Genetics 148:401-408.
99. Dillon, N., and P. Sabbattini. 2000. Functional gene expression domains: defining the functional unit of eukaryotic gene regulation. Bioessays 22:657-665.
100. Dobzhansky, T. 1936. Studies on hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 21:113-135.
101. Doebley, J., and L. Lukens. 1998. Transcriptional regulators and the evolution of plant form. Plant Cell 10:1075-1082.
102. Droge, P., and B. Muller-Hill. 2001. High local protein concentrations at promoters: strategies in prokaryotic and eukaryotic cells. Bioessays 23:179-183.
103. Duboule, D. 1994. Guidebook to the homeobox genes. Oxford University Press, Oxford.
104. Duboule, D., and A. S. Wilkins. 1998. The evolution of 'bricolage.' Trends Genet. 14:54-59.
105. Dudareva, N., L. Cseke, V. M. Blanc, and E. Pichersky. 1996. Evolution of floral scent in Clarkia: novel patterns of S-linalool synthase gene expression in the C. breweri flower. Plant Cell 8:1137-1148.
106. Dynan, W. S. 1989. Modularity in promoters and enhancers. Cell 58:1-4.
107. Enard, W., P. Khaitovich, J. Klose et al. (13 co-authors). 2002a. Intra- and interspecific variation in primate gene expression patterns. Science 296:340-343.
108. Enard, W., M. Przeworski, S. E. Fisher, C. S. L. Lai, V. Wiebe, T. Kitano, A. P. Monaco, and S. Pääbo. 2002b. Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418:869-872.
109. Fairall, L., and J. W. R. Schwabe. 2001. DNA binding by transcription factors. Pp. 65-84 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
110. Falciani, F., B. Hausdorf, R. Schröder, M. Akam, D. Tautz, R. Denell, and S. Brown. 1996. Class 3 Hox genes in insects and the origin of zen. Proc. Natl. Acad. Sci. USA 93:8479-8484.
111. Fang, H., and B. P. Brandhorst. 1996. Expression of the actin gene family in embryos of the sea urchin Lytechinus pictus. Dev. Biol. 173:306-317.
112. Fang, S., A. Takahashi, and C.-I. Wu. 2002. A mutation in the promoter of desaturase 2 is correlated with sexual isolation between Drosophila behavioral races. Genetics 162:781-784.
113. Ferea, T. L., D. Botstein, P. O. Brown, and R. F. Rosenzweig. 1999. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc. Natl. Acad. Sci. USA 96:9721-9726.
114. Ferkowicz, M. J., and R. Raff. 2001. Wnt gene expression in sea urchin development: heterochronies associated with the evolution of developmental mode. Evol. Dev. 3:24-33.
115. Ferrigno, O., T. Virolle, Z. Djabari, J. P. Ortonne, R. J. White, and D. Aberdam. 2001. Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat. Genet. 28:77-81.
116. Ferris, S. D., and G. S. Whitt. 1979. Evolution of the differential regulation of duplicate genes following polyploidization. J. Mol. Evol. 12:267-317.
117. Fisher, R. A. 1930. The genetical theory of natural selection. Clarendon Press, Oxford.
118. Fitch, D. H. A. 1997. Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans. Syst. Biol. 46:145-179.
119. Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
120. Flores-Saaib, R. D., S. Jia, and A. J. Courey. 2001. Activation and repression by the C-terminal domain of Dorsal. Development 128:1869-1879.
121. Force, A., M. Lynch, F. B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531-1545.
122. Foulkes, N. S., and P. Sassone-Corsi. 1992. More is better: activators and repressors from the same gene. Cell 68:411-414.
123. Frasch, M., X. Chen, and T. Lufkin. 1995. Evolutionary-conserved enhancers direct region-specific expression of the murine Hoxa-1 and Hoxa-2 loci in both mice and Drosophila. Development 121:957-974.
124. Frazer, K. A., J. B. Sheehan, R. P. Stokowski, X. Chen, R. Hosseini, J. F. Cheng, S. P. Fodor, D. R. Cox, and N. Patil. 2001. Evolutionarily conserved sequences on human chromosome 21. Genome Res. 11:1651-1659.
125. Fry, C. J., and P. J. Farnham. 1999. Context-dependent transcriptional regulation. J. Biol. Chem. 274:29583-29586.
126. Fu, Y.-X., and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
127. Fullerton, S. M., A. Bartoszewicz, G. Ybazeta, Y. Horikawa, G. I. Bell, K. K. Kidd, N. J. Cox, R. R. Hudson, and A. Di Rienzo. 2002. Geographic and haplotype structure of candidate type 2 diabetes-susceptibility variants at the calpain-10 locus. Am. J. Hum. Genet. 70:1096-1106.
128. Galant, R., and S. B. Carroll. 2002. Evolution of a transcriptional repression domain in an insect Hox protein. Nature 415:910-913.
129. Gehring, W. J., and K. Ikeo. 1999. Pax6: mastering eye morphogenesis and eye evolution. Trends Genet. 15:371-377.
130. Gerard, M., J. Zakany, and D. Duboule. 1997. Interspecies exchange of a Hoxd enhancer in vivo induces premature transcription and anterior shift of the sacrum. Dev. Biol. 190:32-40.
131. Gerber, S., F. Fabre, and C. Planchon. 2000. Genetics of seed quality in soybean analysed by capillary gel electrophoresis. Plant Sci. 152:181-189.
132. Gerhart, J., and M. Kirschner. 1997. Cells, embryos, and evolution: toward a cellular and developmental understanding of phenotypic variation and evolutionary adaptability. Blackwell Science, Malden, Mass.
133. Gibson, G. 1996. Epistasis and pleiotropy as natural properties of transcriptional regulation. Theor. Popul. Biol. 49:58-89.
134. Gilbert, S. F. 2000. Developmental biology. Sinauer Associates, Sunderland, Mass.
135. -. 2001. Ecological developmental biology: developmental biology meets the real world. Dev. Biol. 233:1-12.
136. Gill, G., and M. Ptashne. 1987. Mutants of GAL4 protein altered in an activation function. Cell 51:121-126.
137. Gillespie, J. H. 1991. The causes of molecular evolution. Oxford University Press, New York.
138. Giordano, M., C. Marchetti, E. Chiorboli, G. Bona, and P. Momigliano Richiardi. 1997. Evidence for gene conversion in the generation of extensive polymorphism in the promoter of the growth hormone gene. Hum. Genet. 100:249-255.
139. Glass, C. K., D. W. Rose, and M. G. Rosenfeld. 1997. Nuclear receptor coactivators. Curr. Opin. Cell Biol. 9:222-232.
140. Gonzalez, P., P. V. Rao, S. B. Nunez, and J. S. Zigler, Jr. 1995. Evidence for independent recruitment of zeta-crystallin/quinone reductase (CRYZ) as a crystallin in camelids and hystricomorph rodents. Mol. Biol. Evol. 12:773-781.
141. Goodyer, C. G., G. Zogopolos, G. Schwartzbauer, H. Zheng, G. N. Hendy, and R. K. Menon. 2001. Organization and evolution of the human growth hormone receptor 5′-flanking region. Endocrinology 142:1923-1934.
142. Grandori, C., S. M. Cowley, L. P. James, and R. N. Eisenman. 2000. The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu. Rev. Cell. Dev. Biol. 16:653-699.
143. Gray, S., and M. Levine. 1996. Transcriptional repression in development. Curr. Opin. Cell Biol. 8:358-364.
144. Grbic, M., L. M. Nagy, and M. R. Strand. 1998. Polyembryonic insect development: insect pattern formation in a cellularised environment. Dev. Genes Evol. 208:69-81.
145. Grosveld, F., M. Antoniou, M. Berry et al. (16 co-authors). 1993. The regulation of human globin gene switching. Phil. Trans. R. Soc. Lond. Ser. B 339:183-191.
146. Gstaiger, M., L. Knoepfl, O. Georgiev, W. Schaffner, and C. M. Hovens. 1995. A B-cell co-activator of octamer-binding transcription factors. Nature 373:360-362.
147. Gu, W., and R. G. Roeder. 1997. Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell 90:595-606.
148. Gu, Z., D. Nicolae, H. H.-S. Lu, and W.-H. Li. 2002. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18:609-613.
149. Guardiola, J., A. Maffei, R. Lauster, N. A. Mitchison, R. S. Accolla, and S. Sartoris. 1996. Functional significance of polymorphism among MHC class II gene promoters. Tissue Antigens 48:615-625.
150. Hahn, M. W., M. D. Rausher, and C. W. Cunningham. 2002. Distinguishing between selection and population expansion in an experimental lineage of bacteriophage T7. Genetics 161:11-20.
151. Hahn, M. W., J. E. Stajich, and G. A. Wray. 2003. The effects of selection against spurious transcription factor binding sites. Mol. Biol. Evol. (in press).
152. Hamblin, M. T., and A. DiRienzo. 2000. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am. J. Hum. Genet. 66:1669-1679.
153. Hancock, J., P. Shaw, F. Benneton, and G. Dover. 1999. High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. Mol. Biol. Evol. 16:253-265.
154. Hanes, S. D., G. Riddihough, D. Ish-Horowicz, and R. Brent. 1994. Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen. Mol. Cell. Biol. 14:3364-3375.
155. Hanna-Rose, W., and U. Hansen. 1996. Active repression mechanisms of eukaryotic transcription factors. Trends Genet. 12:229-234.
156. Hardison, R. C. 2000. Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet. 16:369-372.
157. Hariri, A. R., V. S. Mattay, A. Tessitore, B. Kolachana, F. Fera, D. Goldman, M. F. Egan, and D. R. Weinberger. 2002. Serotonin transporter genetic variation and the response of the human amygdala. Science 297:400-403.
158. Harrison, S. C. 1991. A structural taxonomy of DNA-binding domains. Nature 353:715-719.
159. Haudek, S. B., B. E. Natmessnig, H. Redl, G. Schlag, and B. P. Giroir. 1998. Genetic sequences and transcriptional regulation of the TNFA promoter: comparison of human and baboon. Immunogenetics 48:202-207.
160. Hill, T. A., C. D. Day, S. C. Zondlo, A. G. Thackeray, and V. F. Irish. 1998. Discrete spatial and temporal cis-acting elements regulate transcription of the Arabidopsis floral homeotic gene APETELA3. Development 125:1711-1721.
161. Hizver, J., H. Rozenberg, F. Frolow, D. Rabinovich, and Z. Shakked. 2001. DNA bending by an adenine-thymine tract and its role in gene regulation. Proc. Natl. Acad. Sci. USA 98:8490-8495.
162. Hodgkin, J. 1992. Genetic sex determination mechanisms and evolution. Bioessays 14:253-261.
163. Holland, N. D., and L. Z. Holland. 1999. Amphioxus and the utility of molecular genetic data for hypothesizing body part homologies between distantly related animals. Am. Zool. 39:630-640.
164. Holstege, F. C. P., E. G. Jennings, J. J. Wyrick, T. I. Lee, C. J. Hengartner, M. R. Green, T. R. Golub, E. S. Lander, and R. A. Young. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95:717-728.
165. Hope, I. A., and K. Struhl. 1986. Functional dissection of a eukaryotic transcriptional activator, GCN4 of yeast. Cell 46:885-894.
166. Houchens, C. R., W. Montigny, L. Zeltser, L. Dailey, J. M. Gilbert, and N. H. Heintz. 2000. The dhfr ori beta-binding protein RIP60 contains 15 zinc fingers: DNA binding and looping by the central three fingers and an associated proline-rich region. Nucleic Acids Res. 28:570-581.
167. Hudson, R. R., M. Kreitman, and M. Aguade. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
168. Hunt, G. M., D. Johnson, and C. T. Tiemesse. 2001. Characterisation of the long terminal repeat regions of South African human immunodeficiency virus type 1 isolates. Virus Genes 23:27-34.
169. Indovina, P., F. Megiorni, P. Ferrante, I. Apollonio, F. Petronzelli, and M. C. Mazzilli. 1998. Different binding of NF-Y transcriptional factor to DQA1 promoter variants. Hum. Immunol. 59:758-767.
170. Iyer, V. R., C. E. Horak, C. S. Scafe, D. Botstein, M. Snyder, and P. O. Brown. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409:533-538.
171. Jackson, S. P., and R. Tjian. 1988. O-glycosylation of eukaryotic transcription factors: implications for mechanisms of transcriptional regulation. Cell 55:125-133.
172. Jackson-Fisher, A. J., C. Chitikila, M. Mitra, and B. F. Pugh. 1999. A role for TBP dimerization in preventing unregulated gene expression. Mol. Cell 3:717-727.
173. Jacob, F. 1977. Evolution and tinkering. Science 196:1161-1166.
174. Jacob, F., and J. Monod. 1961. On the regulation of gene activity. Cold Spring Harbor Symp. Quant. Biol. 26:193-211.
175. Jacobs, J. J., and M. Van Lohuizen. 1999. Cellular memory of transcriptional states by polycomb-group proteins. Semin. Cell. Dev. Biol. 10:227-235.
176. James, L., and R. N. Eisenman. 2002. Myc and Mad bHLHZ domains possess identical DNA-binding specificities but only partially overlapping functions in vivo. Proc. Natl. Acad. Sci. USA 99:10429-10434.
177. Jareborg, N., E. Bimey, and R. Durbin. 1999. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res. 9:815-824.
178. Jaynes, J. B., and P. H. O'Farrell. 1991. Active repression of transcription by the engrailed homeodomain protein. EMBO J. 10:1427-1433.
179. Jeeninga, R. E., M. Hoogenkamp, M. Armand-Ugon, M. De Baar, K. Verhoef, and B. Berkhout. 2000. Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G. J. Virol. 74:3740-3751.
180. Jenkins, D. L., C. A. Ortori, and J. F. Y. Brookfield. 1995. A test for adaptive change in DNA sequences controlling transcription. Proc. R. Soc. Lond. Ser. B Biol. Sci. 261:203-207.
181. Jin, W., R. M. Riley, R. D. Wolfinger, K. P. White, G. Passador-Gurgel, and G. Gibson. 2001. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat. Genet. 29:389-395.
182. Johnson, N. A., and A. H. Porter. 2000. Rapid speciation via parallel, directional selection on regulatory genetic pathways. J. Theor. Biol. 205:527-542.
183. Jones, P. A., and D. Takai. 2001. The role of DNA methylation in mammalian epigenetics. Science 293:1068-1070.
184. Jones, S., P. Van Heyningen, H. M. Berman, and J. M. Thornton. 1999. Protein-DNA interactions: a structural analysis. J. Mol. Biol. 287:877-896.
185. Jordan, I. K., and J. F. McDonald. 1998. Interelement selection in the regulator region of the copia retrotransposon. J. Mol. Evol. 47:670-676.
186. Kadosh, D., and K. Struhl. 1998. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol. Cell. Biol. 18:5121-5127.
187. Kajiya, Y., K. Hamasaki, K. Nakata et al. (11 co-authors). 2001. A long-term follow-up analysis of serial core promoter and precore sequences in Japanese patients chronically infected by hepatitis B virus. Digest. Dis. Sci. 46:509-515.
188. Kammandel, B., K. Chowdhury, A. Stoykova, S. Aparicio, S. Brenner, and P. Gruss. 1999. Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. Dev. Biol. 205:79-97.
189. Karp, C. L., A. Grupe, E. Schadt et al. (13 co-authors). 2000. Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma. Nat. Immunol. 1:221-226.
190. Kayo, T., D. B. Allison, R. Weindruch, and T. A. Prolla. 2001. Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proc. Natl. Acad. Sci. USA 98:5093-5098.
191. Kazazian, H. H. 1990. The thalassemia syndromes: molecular basis and prenatal diagnosis in 1990. Semin. Hematol. 27:209-228.
192. Keys, D. N., D. L. Lewis, J. E. Selegue, B. J. Pearson, L. V. Goodrich, R. L. Johnson, J. Gates, M. P. Scott, and S. B. Carroll. 1999. Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. Science 283:532-534.
193. Kidwell, M. G., and D. Lisch. 1997. Transposable elements as sources of variation in animals and plants. Proc. Natl. Acad. Sci. USA 94:7704-7711.
194. Kim, J. 2001. Macro-evolution of the hairy enhancer in Drosophila species. J. Exp. Zool. 291:175-185.
195. Kim, J., J. Q. Kerr, and G.-S. Min. 2000. Molecular heterochrony in the early development of Drosophila. Proc. Natl. Acad. Sci. USA 97:212-216.
196. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge.
197. King, M. C., and A. C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188:107-116.
198. Kirchhamer, C. V., L. D. Bogarad, and E. H. Davidson. 1996. Dvelopmental expression of synthetic cis-regulatory systems composed of spatial control elements from two different genes. Proc. Natl. Acad. Sci. USA 93:13849-13854.
199. Kirchhamer, C. V., C.-H. Yuh, and E. H. Davidson. 1996. Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples. Proc. Natl. Acad. Sci. USA 93:9322-9328.
200. Kissinger, J. C., and R. A. Raff. 1998. Evolutionary changes in sites and timing of actin gene expression in embryos of the direct- and indirect-developing sea urchins, Heliocidaris erythrogramma and H. tuberculata. Dev. Genes Evol. 208:82-93.
201. Klarenberg, A. J., K. Sikkema, and W. Scharloo. 1987. Functional significance of regulatory map and structural amy variants in Drosophila melanogaster. Heredity 58:383-389.
202. Klein, W. H., and X. T. Li. 1999. Function and evolution of Otx proteins. Biochem. Biophys. Res. Commun. 258:229-233.
203. Klose, J., C. Nock, M. Herrmann et al. (13 co-authors). 2002. Genetic analysis of the mouse brain proteome. Nat. Genet. 30:385-393.
204. Kmita, M., T. Kondo, and D. Duboule. 2000. Targeted inversion of a polar silencer within the HoxD complex re-allocates domains of enhancer sharing. Nat. Genet. 26:451-454.
205. Knoepfler, P. S., and M. P. Kamps. 1995. The pentapeptide motif of hox proteins is required for cooperative DNA binding with pbx1, physically contacts pbx1 and enhances DNA binding by pbx1. Mol. Cell. Biol. 15:5811-5819.
206. Kopp, A., I. Duncan, and S. B. Carroll. 2000. Genetic control and evolution of sexually dimorphic characters in Drosophila. Nature 408:553-559.
207. Korneev, S., and M. O'Shea. 2002. Evolution of nitric oxide synthase regulatory genes by DNA inversion. Mol. Biol. Evol. 19:1228-1233.
208. Kramer, S. G., T. M. Jinks, P. Schedl, and J. P. Gergen. 1999. Direct activation of Sex-lethal transcription by the Drosophila runt protein. Development 126:191-200.
209. Kuras, L., and K. Struhl. 1999. Binding of TBP to promoters in vivo is stimulated by activators and requires Pol 11 holoenzyme. Nature 399:609-613.
210. Lander, E. S., L. M. Linton, and B. Birren et al. (242 co-authors). 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
211. Latchman, D. S. 1998. Eukaryotic transcription factors. Academic Press, San Diego, Calif.
212. Laurie-Ahlberg, C. C., and G. C. Bewley. 1983. Naturally occurring genetic variation affecting the expression of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster. Biochem. Genet. 21:943-961.
213. Laurie-Ahlberg, C. C., G. Maroni, G. C. Bewley, J. C. Lucchesi, and B. S. Weir. 1980. Quantitative genetic variation of enzyme activities in natural populations of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 77:1073-1077.
214. Lawton-Rauh, A. L., E. R. Alvarez-Buylla, and M. D. Purugganan. 2000. Molecular evolution of flower development. Trends Ecol. Evol. 15:144-149.
215. Lee, H., S. N. Cho, H. E. Bang, J. H. Lee, G. H. Bai, S. J. Kim, and J. D. Kim. 2000. Exclusive mutations related to isoniazid and ethionamide resistance among Mycobacterium tuberculosis isolates from Korea. Eur. J. Clin. Microbiol. Infect. Dis. 17:508-511.
216. Lee, J. E. 1997. Basic helix-loop-helix genes in neural development. Curr. Opin. Neurobiol. 7:13-20.
217. Lee, T. I., N. J. Rinaldi, R. Robert et al. (20 co-authors). 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
218. Lee, T. I., and R. A. Young. 2000. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34:77-137.
219. Lemon, B., and R. Tjian. 2000. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev. 14:2551-2569.
220. Lerman, D. N., P. Michalak, A. B. Helin, B. R. Bettencourt, and M. E. Feder. 2003. Modification of heat-shock gene expression in Drosophila melanogaster populations via transposable elements. Mol. Biol. Evol. 20:135-144.
221. Lescot, M., P. Dehais, G. Thijs, K. Marchal, Y. Moreau, Y. van de Peer, P. Rouze, and S. Rombauts. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30:325-327.
222. Lettice, L. A., T. Horikoshi, S. J. H. Heaney et al. (18 co-authors). 2002. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc. Natl. Acad. Sci. USA 99:7548-7553.
223. Lewin, B. 2000. Genes VII. Oxford University Press, Oxford.
224. Lewis, E. B. 1978. Gene complex controlling segmentation in Drosophila. Nature 276:565-570.
225. Li, Q. M., and S. A. Johnston. 2001. Are all DNA binding and transcription regulation by an activator physiologically relevant? Mol. Cell. Biol. 21:2467-2474.
226. Li, W.-H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
227. Li, W. W., M. M. Dammerman, J. D. Smith, S. Metzger, J. L. Breslow, and T. Leff. 1995. Common genetic variation in the promoter of the human apo CIII gene abolishes regulation by insulin and may contribute to hypertriglyceridemia. J. Clin. Invest. 96:2601-2605.
228. Li, X., and M. Noll. 1994. Evolution of distinct developmental functions of three Drosophila genes by acquisition of different cis-regulatory regions. Nature 367:83-87.
229. Li, Y., J. P. Bernot, C. Illingworth et al. (10 co-authors). 2001. Gene conversion within regulatory sequences generates maize r alleles with altered gene expression. Genetics 159:1727-1740.
230. Liang, Z., and M. D. Biggin. 1998. Eve and ftz regulate a wide array of genes in blastoderm embryos: the selector homeoproteins directly or indirectly regulate most genes in Drosophila. Development 125:4471-4482.
231. Lieb, J. D., X. Liu, D. Botstein, and P. O. Brown. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:327-334.
232. Liu, T., J. Wu, and F. He. 2000. Evolution of cis-acting elements in 5′ flanking regions of vertebrate actin genes. J. Mol. Evol. 50:22-30.
233. Locker, J. 2001. Transcription factors. Academic Press, San Diego, Calif.
234. Long, M., W. Wang, and J. Zhang. 1999. Origin of new genes and source for N-terminal domain of the chimerical gene, jingwei, in Drosophila. Gene 238:135-141.
235. Loots, G. G., R. M. Locksley, C. M. Blankespoor, Z. E. Wang, W. Miller, E. M. Rubin, and K. A. Frazer. 2000. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288:136-140.
236. Love, J. J., X. Li, D. A. Case, K. Geise, R. Grosschedl, and P. E. Wright. 1995. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376:791-795.
237. Lowe, C. J., and G. A. Wray. 1997. Radical alterations in the roles of homeobox genes during echinoderm evolution. Nature 389:718-721.
238. Ludwig, M. Z. 2002. Functional evolution of noncoding DNA. Curr. Opin. Genet. Dev. 12:634-639.
239. Ludwig, M. Z., C. Bergman, N. H. Patel, and M. Kreitman. 2000. Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403:564-567.
240. Ludwig, M. Z., and M. Kreitman. 1995. Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. Mol. Biol. Evol. 12:1002-1011.
241. Ludwig, M. Z., N. H. Patel, and M. Kreitman. 1998. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 125:949-958.
242. Lufkin, T. 2001. Developmental control by Hox transcriptional regulators and their cofactors. Pp. 215-235 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
243. Lutz, B., H. C. Lu, G. Eichele, D. Miller, and T. C. Kaufman. 1996. Rescue of Drosophila labial null mutant by the chicken ortholog Hoxb-1 demonstrates that the function of Hox genes is phylogenetically conserved. Genes Dev. 10:176-184.
244. Ma, X., D. Yuan, K. Diepold, T. Scarborough, and J. Ma. 1996. The Drosophila morphogenic protein bicoid binds DNA cooperatively. Development 122:1195-1206.
245. Maduro, M., and D. Pilgrim. 1996. Conservation of function and expression of unc-119 from two Caenorhabditis species despite divergence of non-coding DNA. Gene 183:77-85.
246. Mahmoudi, T., and C. P. Verrijzer. 2001. Chromatin silencing and activation by Polycomb and trithorax group proteins. Oncogene 20:3055-3066.
247. Manzanares, M., H. Wada, N. Itasaki, P. A. Trainor, R. Krumlauf, and P. W. Holland. 2000. Conservation and elaboration of Hox gene regulation during evolution of the vertebrate head. Nature 408:854-857.
248. Margarit, E., A. Guillén, C. Bebordosa, J. Vidal-Taboada, M. Sánchez, F. Ballesta, and R. Oliva. 1998. Identification of conserved potentially regulatory sequences of the SRY gene from 10 different species of mammals. Biochem. Biophys. Res. Commun. 245:370-377.
249. Markstein, M., and M. Levine. 2002. Decoding cis-regulatory DNAs in the Drosophila genome. Curr. Opin. Genet. Dev. 12:601-606.
250. Mastick, G. S., R. McKay, T. Oligino, K. Donovan, and A. J. López. 1995. Identification of target genes regulated by homeotic proteins in Drosophila melanogaster through genetic selection of Ultrabithorax protein-binding sites in yeast. Genetics 139:349-363.
251. Mathias, J. R., H. L. Zhong, H. H. Jin, and A. K. Vershon. 2001. Altering the DNA-binding specificity of the yeast Mat alpha 2 homeodomain protein. J. Biol. Chem. 276:32696-32703.
252. Matsuo, Y., and T. Yamazaki. 1984. Genetic analysis of natural populations of Drosophila melanogaster in Japan. IV. Natural selection on the inducibility, but not on the structural genes, of amylase loci. Genetics 108:879-896.
253. McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
254. McKinney, M. L., and K. J. McNamara. 1991. Heterochrony: the evolution of ontogeny. Plenum Press, New York.
255. Metherall, J. E., F. P. Gillespie, and B. G. Forget. 1988. Analyses of linked beta-globin genes suggest that nondeletion forms of hereditary persistence of fetal hemoglobin are bona fide switching mutants. Am. J. Hum. Genet. 42:476-481.
256. -308A associated with shorter intervals of Plasmodium falciparum reinfections. Tissue Antigens 59:287-292.
257. Milo, R., S. Shen-Orr, S. Itzkovitz, D. Kashtan, D. Chklovskii, and U. Alon. 2002. Network motifs: simple building blocks of complex networks. Science 298:824-827.
258. Mitsialis, S. A., and F. C. Kafatos. 1985. Regulatory elements controlling chorion gene expression are conserved between flies and moths. Nature 317:453-456.
259. Miyashita, N. T. 2001. DNA variation in the 5′ upstream region of the Adh locus of the wild plants Arabidopsis thaliana and Arabis gemmifera. Mol. Biol. Evol. 18:164-171.
260. Mody, M., Y. Cao, Z. Cui et al. (10 co-authors). 2001. Genome-wide gene expression profiles of the developing mouse hippocampus. Proc. Natl. Acad. Sci. USA 98:8862-8867.
261. Montano, M. A., C. P. Nixon, T. Ndung'u, H. Bussmann, V. A. Novitsky, D. Dickman, and M. Essex. 2000. Elevated tumor necrosis factor-alpha activation of human immunodeficiency virus type 1 subtype C in southern Africa is associated with an NF-kappaB enhancer gain-of-function. J. Infect. Dis. 181:76-81.
262. Montano, M. A., V. A. Novitsky, J. T. Blackard, N. L. Cho, D. A. Katzenstein, and M. Essex. 1997. Divergent transcriptional regulation among expanding human immunodeficiency virus type 1 subtypes. J. Virol. 71:8657-8665.
263. Morishima, A. 1998. Identification of preferred binding sites of a light-inducible DNA-binding factor (MNF1) within 5′-upstream sequence of c4-type phosphoenolpyruvate carboxylase gene in maize. Plant Mol. Biol. 38:633-646.
264. Mouchel-Vielh, E., M. Blin, C. Rigolot, and J. S. Deutsch. 2002. Expression of a homologue of the fushi-tarazu (fiz) gene in a cirriped crustacean. Evol. Dev. 4:76-85.
265. Müller, G. B., and G. P. Wagner. 1991. Novelty in evolution: restructuring the concept. Annu. Rev. Ecol. Syst. 22:229-256.
266. Muller, H. J. 1942. Isolating mechanisms, evolution, and temperature. Biol. Symp. 6:71-125.
267. Naganawa, S., H. N. Ginsberg, R. M. Glickman, and G. S. Ginsburg. 1997. Intestinal transcription and synthesis of apolipoprotein AI is regulated by five natural polymorphisms upstream of the apolipoprotein CIII gene. J. Clin. Invest. 99:1958-1965.
268. Nakayama, E. E., L. Meyer, A. Iwamoto, A. Persoz, Y. Nagai, C. Rouzioux, J. F. Delfraissy, P. Debre, D. McIlroy, I. Theodorou, T. Shioda, and S. S. Group. 2002. Protective effect of interleukin-4-589T polymorphism on human immunodeficiency virus type 1 disease progression: relationship with virus load. J. Infect. Dis. 185:1183-1186.
269. Narlikar, G. J., H.-Y. Fan, and R. E. Kingston. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108:475-487.
270. Naylor, L. H., and E. M. Clark. 1990. d(TG)n.d(CA)n sequences upstream of the rat prolactin gene form Z-DNA and inhibit gene transcription. Nucleic Acids Res. 18:1595-1601.
271. Neznanov, N., A. Umezawa, and R. G. Oshima. 1997. A regulatory element within a coding exon modulates keratin 18 gene expression in transgenic mice, J. Biol. Chem. 272:27549-27557.
272. Nielsen, L. B., D. Kahn, T. Duell, H. U. Weier, S. Taylor, and S. G. Young. 1998. Apolipoprotein B gene expression in a series of human apolipoprotein B transgenic mice generated with recA-assisted restriction endonuclease cleavage-modified bacterial artificial chromosomes. An intestine-specific enhancer element is located between 54 and 62 kilobases 5′ to the structural gene. J. Biol. Chem. 273:21800-21807.
273. Nurminsky, D. I., E. N. Moriyama, E. R. Lozovskaya, and D. L. Hartl. 1996. Molecular phylogeny and genome evolution in the Drosophila virilis species group: duplications of the alcohol dehydrogenase gene. Mol. Biol. Evol. 13:132-149.
274. Nurminsky, D. I., M. V. Nurminskaya, D. Deaguiar, and D. L. Hartl. 1998. Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396:572-575.
275. Odgers, W. A., M. J. Healy, and J. G. Oakeshott. 1995. Nucleotide polymorphism in the 5′ promoter region of esterase 6 in Drosophila melanogaster and its relationship to enzyme activity variation. Genetics 141:215-222.
276. Ohler, U., and H. Niemann. 2001. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 17:56-60.
277. Ohta, T. 1992. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23:263-286.
278. Ohtsuki, S., M. Levine, and H. N. Cai. 1998. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev. 12:547-556.
279. Oleksiak, M. F., G. A. Churchill, and D. L. Crawford. 2002. Variation in gene expression within and among natural populations. Nat. Genet. 32:261-266.
280. Onyango, P., W. Miller, J. Lehoczky, C. T. Leung, B. Birren, S. Wheelan, K. Dewar, and A. P. Feinberg. 2000. Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 1lp115 imprinted domain. Genome Res. 10:1697-1710.
281. Orphanides, G., T. Lagrange, and D. Reinberg. 1998. The general transcription factors of RNA polymerase II. Genes Dev. 10:2657-2683.
282. Orr, H. A., and D. C. Presgraves. 2000. Speciation by postzygotic isolation: forces, genes and molecules. Bioessays 22:1085-1094.
283. Osada, S., H. Yamamoto, T. Nishihara, and M. Imagawa. 1996. DNA binding specificity of the CCAAT/enhancer-binding protein transcription factor family. J. Biol. Chem. 271:3891-3896.
284. Paigen, K. 1989. Experimental approaches to the study of regulatory evolution. Am. Nat. 134:440-458.
285. Panganiban, G., S. M. Irvine, C. Lowe et al. (14 co-authors). 1997. The origin and evolution of animal appendages. Proc. Natl. Acad. Sci. USA 94:5162-5166.
286. Papenbrock, T., R. L. Peterson, R. S. Lee, T. Hsu, A. Kuroiwa, and A. Awgulewitsch. 1998. Murine Hoxc-9 gene contains a structurally and functionally conserved enhancer. Dev. Dyn. 212:540-547.
287. Paquette, J., N. Giannoukakis, C. Polychronakos, P. Vafiadis, and C. Deal. 1998. The INS 5′ variable number of tandem repeats is associated with IGF2 expression in humans. J. Biol. Chem. 273:14158-14164.
288. Parks, A. L., B. A. Parr, J.-E. Chin, D. S. Leaf, and R. A. Raff. 1988. Molecular analysis of heterochronic changes in the evolution of direct developing sea urchins. J. Evol. Biol. 1:27-44.
289. Patrinos, G. P., P. Kollia, A. Loutradi-Anagnostou, D. Loukopoulos, and M. N. Papadakis. 1998. The Cretan type of non-deletional hereditary persistence of fetal hemoglobin [A gamma-158C->T] results from two independent gene conversion events. Hum. Genet. 102:629-634.
290. Petronzelli, F., A. Kimura, P. Ferrante, and M. C. Mazzilli. 1995. Polymorphism in the upstream regulatory region of DQA1 gene in the Italian population. Tissue Antigens 45:258-263.
291. Pfister K., K. Paigen, G. Watson, and V. Chapman. 1982. Expression of beta-glucuronidase haplotypes in prototype and congenic mouse strains. Biochem. Genet. 20:519-536.
292. Piano, F., M. J. Parisi, R. Karess, and M. P. Kambysellis. 1999. Evidence for redundancy but not trans factor-cis element co-evolution in the regulation of Drosophila Yp genes. Genetics 152:605-616.
293. Pinsonneault, J., B. Florence, H. Vaessin, and W. McGinnis. 1997. A model for extradenticle function as a switch that changes Hox proteins from repressors to activators. EMBO J. 16:2032-2042.
294. Pirkkala, L., P. Nykanen, and L. Sistonen. 2001. Roles of the heat shock transcription factors in regulation of the heat shock response and beyond. FASEB J. 15:1118-1131.
295. Plaza, S., S. Saule, and C. Dozier. 1999. High conservation of cis-regulatory elements between quail and human for the Pax-6 gene. Dev. Genes Evol. 209:165-173.
296. Powell, J. R. 1979. Population genetics of Drosophila amylase. II. Geographic patterns in D. pseudoobscura. Genetics 92:613-622.
297. Powell, J. R., and J. M. Lichtenfels. 1979. Population genetics of Drosophila amylase. I. genetic control of tissue-specific expression in D. pseudoobscura. Genetics 92:603-612.
298. Praz, V., R. Perier, C. Bonnard, and P. Bucher. 2002. The Eukaryotic Promoter Database, EPD: new entry types and links to gene expresion data. Nuclic Acids Res. 30:322-324.
299. Pugh, B. F. 2001. RNA polymerase II transcription machinery. Pp. 1-16 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
300. Purugganan, M. D. 2000. The molecular population genetics of regulatory genes. Mol. Ecol. 9:1451-1461.
301. Quiring, R., U. Walldorf, U. Kloter, and W. J. Gehring. 1994. Homology of the eyeless gene of Drosophila to the small eye gene in mice and aniridia in humans. Science 265:785-789.
302. Raff, R. A. 1996. The shape of life: genes, development, and the evolution of animal form. The University Of Chicago Press, Chicago.
303. Raff, R. A., and T. C. Kaufman. 1983. Embryos, genes, and evolution: the developmental-genetic basis of evolutionary change. Macmillan, New York.
304. Rebeiz, M., N. L. Reeves, and J. W. Posakony. 2002. SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Proc. Natl. Acad. Sci. USA 99:9888-9893.
305. Regier, J. C., and N. S. Vlahos. 1988. Heterochrony and the introduction of novel modes of morphogenesis during the evolution of moth choriogenesis. J. Mol. Evol. 28:19-31.
306. Reinberg, D., G. Oprhanides, R. Ebright et al. (29 co-authors). 1998. The RNA polymerase II general transcription factors: past, present, and future. Cold Spring Harbor Symp. Quant. Biol. 63:83-103.
307. Ren, B., F. Robert, J. J. Wyrick et al. (14 co-authors). 2000. Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
308. Richards, E. J., and S. C. R. Elgin. 2002. Epigenetic codes for heterochromatin silencing: rounding up the usual suspects. Cell 108:489-500.
309. Riechmann, J. L., M. Wang, and E. M. Meyerowitz. 1996. DNA-binding properties of Arabidopsis Mads domain homeotic proteins APETALA1, APETALA3, PISTILLATA and AGAMOUS. Nucleic Acids Res. 24:3134-3141.
310. Rifkin, S. A., J. Kim, and K. P. White. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 33:138-144.
311. Rinder, H., A. Thomschke, S. Rusch-Gerdes, G. Bretzel, K. Feldmann, M. Rifai, and T. Loscher. 1998. Significance of ahpC promoter mutations for the prediction of isoniazid resistance in Mycobacterium tuberculosis. Eur. J. Clin. Microbiol. Infect. Dis. 17:508-511.
312. Roberts, S. B., N. Segil, and H. Heintz. 1991. Differential phosphorylation of the transcription factor Oct1 during the cell cycle. Science 253:1022-1026.
313. Robin, C., R. F. Lyman, A. D. Long, C. H. Langley, and T. F. C. Mackay. 2002. hairy: a quantitative trait locus for Drosophila sensory bristle number. Genetics 162:155-164.
314. Rockman, M. V., and G. A. Wray. 2002. Abundant raw material for cis-regulatory evolution in humans. Mol. Biol. Evol. 19:1981-1990.
315. Romano, L. A., and G. A. Wray. 2003. Conservation of Endo16 expression in sea urchins despite divergence in both cis and trans-acting components of transcriptional regulation. Development (in press).
316. Romey, M. C., C. Guittard, J. P. Chazalette et al. (14 co-authors). 1999. Complex allele [-102T>A+s549r (T>G)] is associated with milder forms of cystic fibrosis than allele s549r[T>G] alone. Hum. Genet. 105:145-150.
317. Romey, M. C., N. Pallares-Ruiz, A. Mange, C. Mettling, R. Peytavi, J. Demaille, and M. Claustres. 2000. A naturally occurring sequence variation that creates a YY1 element is associated with increased cystic fibrosis transmembrane conductance regulator gene expression. J. Biol. Chem. 275:3561-3567.
318. Ronshaugen, M., N. McGinnis, and W. McGinnis. 2002. Hox protein mutation and macroevolution of the insect body plan. Nature 415:914-917.
319. Ross, J. L., P. P. Fong, and D. R. Cavener. 1994. Correlated evolution of the cis-acting regulatory elements and developmental expression of the Drosophila Gld gene in seven species from the subgroup melanogaster. Dev. Genet. 15:38-50.
320. Rothenburg, S., F. Koch-Nolte, A. Rich, and F. Haag. 2001. A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity. Proc. Natl. Acad. Sci. USA 98:8985-8990.
321. Ruez, C., F. Payre, and A. Vincent. 1998. Transcriptional control of Drosophila bicoid by Serendipity delta: cooperative binding sites, promoter context, and co-evolution. Mech. Dev. 78:125-134.
322. Saccone, G., I. Peluso, D. Artiaco, E. Giordano, D. Bopp, and L. C. Polito. 1998. The Ceratitis capitata homologue of the Drosophila sex-determining gene Sex-lethal is structurally conserved, but not sex-specifically regulated. Development 125:1495-1500.
323. Sackerson, C., M. Fujioka, and T. Goto. 1999. The even-skipped locus is contained in a 16-kb chromatin domain. Dev. Biol. 211:39-52.
324. Saito, T., H. M. Lachman, L. Diaz et al. (12 co-authors). 2002. Analysis of monoamine oxidase a (MAOA) promoter polymorphism in Finnish male alcoholics. Psych. Res. 109:113-119.
325. Sandrelli, F., S. Campesan, M. G. Rossetto, C. Benna, E. Zieger, A. Megighian, M. Couchman, C. P. Kyriacou, and R. Costa. 2001. Molecular dissection of the 5′ region of no-on-transientA of Drosophila melanogaster reveals cis-regulation by adjacent dGpi1 sequences. Genetics 157:765-775.
326. Sauer, F., S. K. Hansen, and R. Tjian. 1995. DNA Template requirement and activator-coactivator requirements for transcriptional synergism by Drosophila bicoid. Science 270:1825-1827.
327. Scaffidi, P., and M. E. Bianchi. 2001. Spatially precise DNA bending is an essential activity of the Sox2 transcription factor. J. Biol. Chem. 276:47296-47302.
328. Scemama, J. L., M. Hunter, J. McCallam, V. Prince, and E. Stellwag. 2002. Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. J. Exp. Zool. 294:285-299.
329. Schadt, E. E., S. A. Monks, T. A. Drake et al. (14 co-authors). 2003. Genetics of gene expression surveyed in maize, mouse and man. Nature 422:297-302.
330. Schiff, N. M., Y. Feng, J. A. Quine, P. A. Krasney, and D. R. Cavener. 1992. Evolution of the expression of the Gld gene in the reproductive tract of Drosophila. Mol. Biol. Evol. 9:1029-1049.
331. Schlichting, C. D., and M. Pigliucci. 1998. Phenotypic evolution: a reaction norm perspective. Sinauer Associates, Sunderland, Mass.
332. Segal, J. A., J. L. Barnett, and D. L. Crawford. 1999. Functional analysis of natural variation in Sp1 binding sites of a TATA-less promoter. J. Mol. Evol. 49:736-749.
333. Segil, N., S. B. Roberts, and N. Heitz. 1991. Mitotic phosphorylation of the Oct-1 homeodomain and regulation of Oct-1 DNA binding activity. Science 254:1814-1816.
334. Seoighe, C., N. Federspiel, T. Jones et al. (29 co-authors). 2000. Prevalence of small inversions in yeast gene order evolution. Proc. Natl. Acad. Sci. USA 97:14433-14437.
335. Serfling, E., M. Jasin, and W. Schaffner. 1985. Enhancers and eukaryotic gene-transcription. Trends Genet. 1:224-230.
336. Shabalina, S. A., and A. S. Kondrashov. 1999. Pattern of selective constraint in C. elegans and C. briggsae genomes. Genet. Res. 74:23-30.
337. Shabalina, S. A., A. Y. Ogurtsov, V. A. Kondrashov, and A. S. Kondrashov. 2001. Selective constraint in intergenic regions of human and mouse genomes. Trends Genet. 17:373-376.
338. Shashikant, C. S., C. B. Kim, M. A. Borbely, W. C. Wang, and F. H. Ruddle. 1998. Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element. Proc. Natl. Acad. Sci. USA 95:12364-12369.
339. Shaw, P. J., N. S. Wratten, A. P. McGregor, and G. A. Dover. 2002. Coevolution in bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera. Evol. Dev. 4:265-277.
340. Shikama, N., J. Lyon, and N. B. La Thangue. 1997. The p300/CBP family: integrating signals with transcription factors and chromatin. Trends Cell Biol. 7:230-236.
341. Shin, H. D., C. Winkler, J. C. Stephens et al. (15 co-authors). 2000. Genetic restriction of HIV-1 pathogenesis to AIDS by promoter alleles of IL10. Proc. Natl. Acad. Sci. USA 97:14467-14472.
342. Shore, P., and A. D. Sharrocks. 2001. Regulation of transcription by extracellular signals. Pp. 113-135 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
343. Simon, J., M. Peifer, W. Bender, and M. O'Connor. 1990. Regulatory elements of the bithorax complex that control expression along the anterior-posterior axis. EMBO J. 9:3945-3956.
344. Singh, N., K. W. Barbour, and F. G. Berger. 1998. Evolution of transcriptional regulatory elements within the promoter of a mammalian gene. Mol. Biol. Evol. 15:312-325.
345. Singh, N., and F. G. Berger. 1998. Evolution of a mammalian promoter through changes in patterns of transcription factor binding. J. Mol. Evol. 46:639-648.
346. 4 photosynthesis in the grass family. Am. J. Bot. 83:1458-1470.
347. Sinha, S., and M. Tompa. 2002. Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res. 30:5549-5560.
348. Sjostrand, J. O., A. Kegel, and S. U. Astrom. 2002. Functional diversity of silencers in budding yeasts. Eukaryot. Cell 1:548-557.
349. Sjottem, E., C. Andersen, and T. Johansen. 1997. Structural and functional analysis of DNA bending by Sp1 family transcription factors. J. Mol. Biol. 267:490-504.
350. Skaer, N., D. Pistillo, and P. Simpson. 2002. Transcriptional heterochrony of scute and changes in bristle pattern between two closely related species of blowfly. Dev. Biol. 252:31-45.
351. Skaer, N., and P. Simpson. 2000. Genetic analysis of bristle loss in hybrids between Drosophila melanogaster and D. simulans provides evidence for divergence of cis-regulatory sequences in the achaete-scute gene complex. Dev. Biol. 221:148-167.
352. Smale, S. T., A. Jain, J. Kaufmann, K. H. Emamai, K. Lo, and I. P. Garraway. 1998. The initiator element: a paradigm for core promoter heterogeneity within metazoan protein-coding genes. Cold Spring Harbor Symp. Quant. Biol. 63:21-31.
353. Small, S., A. Blair, and M. Levine. 1992. Regulation of even-skipped stripe-2 in the Drosophila embryo. EMBO J. 11:4047-4057.
354. Spek, C. A., R. M. Bertina, and P. H. Reitsma. 1999. Unique distance- and DNA-turn-dependent interactions in the human protein C gene promoter confer submaximal transcriptional activity. Biochem. J. 340:513-518.
355. Stauber, M., H. Jackle, and U. Schmidt-Ott. 1999. The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene. Proc. Natl. Acad. Sci. USA 96:3786-3789.
356. Stauber, M., A. Prell, and U. Schmidt-Ott. 2002. A single Hox3 gene with composite bicoid and zerknult expression characteristics in non-Cyclorrhaphan flies. Proc. Natl. Acad. Sci. USA 99:274-279.
357. Stern, D. L. 1998. A role of Ultrabithorax in morphological difference between Drosophila species. Nature 396:463-466.
358. -. 2000. Perspective: evolutionary developmental biology and the problem of variation. Evolution 54:1079-1091.
359. Stockhaus, J., U. Schlue, M. Koczor, J. A. Chitty, W. C. Taylor, and P. Westhoff. 1997. The promoter of the gene encoding the C4 form of phoshpoenolpyruvate carboxylase directs mesophyll-specific expression in transgenic C4 Flaveria spp. Plant Cell 9:479-489.
360. Stone, J. R., and G. A. Wray. 2001. Rapid evolution of cis-regulatory sequences via local point mutations. Mol. Biol. Evol. 18:1764-1770.
361. Storgaard, T., J. Christensen, B. Aasted, and S. Alexandersen. 1993. Cis-acting sequences in the Aleutian mink disease parvovirus late promoter important for transcription: comparison to the canine parvovirus and minute virus of mice. J. Virol. 67:1887-1895.
362. Stormo, G. D. 2000. DNA binding sites: representation and discovery. Bioinformatics 16:16-23.
363. Stougaard, J., N. N. Sandal, A. Grøn, A. Kuhle, and K. A. Marcker. 1987. 5′ analysis of the soybean leghaemoglobin lbc3 gene: regulatory elements required for promoter activity and organ specificity. EMBO J. 6:3565-3569.
364. Streelman, J. T., and T. D. Kocher. 2002. Microsatellite variation associated with prolactin expression and growth of salt-challenged Tilapia. Physiol. Genomics 9:1-4.
365. Struhl, K. 1999. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98:1-4.
366. Sucena, E., and D. L. Stern. 2000. Divergence of larval morphology between Drosophila sechellia and its sibling species caused by cis-regulatory evolution of ovo/shaven-baby. Proc. Natl. Acad. Sci. USA 97:4530-4534.
367. Suske, G. 1999. The Sp-family of transcription factors. Gene 238:291-300.
368. Sutton, K. A., and M. Wilkinson. 1997. Rapid evolution of a homeodomain: evidence for positive selection. J. Mol. Evol. 45:579-588.
369. Swalla, B. J., and W. R. Jeffery. 1996. Requirement of the Manx gene for expression of chordate features in a tailless ascidian larva. Science 274:1205-1208.
370. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
371. Takahashi, A., S. C. Tsaur, J. A. Coyne, and C. I. Wu. 2001. The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 98:3920-3925.
372. Takahashi, H., Y. Mitani, G. Satoh, and N. Satoh. 1999. Evolutionary alterations of the minimal promoter for notochord-specific Brachyury expression in ascidian embryos. Development 126:3725-3734.
373. Takahata, N. 1987. On the overdispersed molecular clock. Genetics 116:169-179.
374. Tamarina, N. A., M. Z. Ludwig, and R. C. Richmond. 1997. Divergent and conserved features in the spatial expression of the Drosophila pseudoobscura esterase-5B gene and the esterase-6 gene of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 94:7735-7741.
375. Tautz, D. 2000. Evolution of transcriptional regulation. Curr. Opin. Genet. Dev. 10:575-579.
376. Thanos, D., and T. Maniatis. 1995. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83:1091-1100.
377. Theissen, G., A. Becker, A. Di Rosa, A. Kanno, J. T. Kim, T. Munster, K. U. Winter, and H. Saedler. 2000. A short history of MADS-box genes in plants. Plant Mol. Biol. 42:115-149.
378. Thompson, J. R., S. W. Chen, L. Ho, A. W. Langston, and L. J. Gudas. 1998. An evolutionary conserved element is essential for somite and adjacent mesenchymal expression of the Hoxal gene. Dev. Dyn. 211:97-108.
379. Thurz, M. 2001. Genetic susceptibility in chronic viral hepatitis. Antiviral Res. 52:113-116.
380. Ting, C. T., S. C. Tsaur, M. L. Wu, and C. I. Wu. 1998. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science 282:1501-1504.
381. Tomarev, S. I., M. K. Duncan, H. J. Roth, A. Cvekl, and J. Piatagorsky. 1994. Convergent evolution of crystallin gene regulation in squid and chicken: the AP-1/ARE connection. J. Mol. Evol. 39:134-143.
382. Torchia, J., C. K. Glass, and M. G. Rosenfeld. 1998. Co-activators and co-repressors in the integration of transcriptional responses. Curr. Opin. Cell Biol. 10:373-383.
383. Tournamille, C., Y. Colin, J. P. Cartron, and C. Le Van Kim. 1995. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat. Genet. 10:224-228.
384. Trefilov, A., J. Berard, M. Krawczak, and J. Schmidtke. 2000. Natal dispersal in rhesus macaques is related to serotonin transporter gene promoter variation. Behav. Genet. 30:295-301.
385. Treisman, J., P. Gönczy, M. Vashishtha, E. Harris, and C. Desplan. 1989. A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell 59:553-562.
386. Triezenberg, S. J. 1995. Structure and function of transcriptional activation domains. Curr. Opin. Genet. Dev. 5:190-196.
387. Tümpel, S., M. Maconochie, L. M. Wiedemann, and R. Krumlauf. 2002. Conservation and diversity in the cisregulatory networks that integrate information controlling expression of Hoxa2 in hindbrain and cranial neural crest cells in vertebrates. Dev. Biol. 246:45-56.
388. Varga-Weisz, P. 2001. ATP-dependent chromatin remodeling factors: nucleosome shuffiers with many missions. Oncogene 20:3076-3085.
389. Venter, J. C., M. D. Adams, E. W. Myers et al. (274 co-authors). 2001. The sequence of the human genome. Science 291:1304-1351.
390. Vidigal, P., J. J. Gemner, and N. N. Zein. 2002. Polymorphisms in the interleukin-10, tumor necrosis factor-a, and transforming growth factor-b1 genes in chronic hepatitis C patients treated with interferon and ribavarin. J. Hepatol. 36:271-277.
391. Vogelauer, M., J. Wu, N. Suka, and M. Grunstein. 2000. Global histone acetylation and deacetylation in yeast. Nature 408:495-498.
392. Von Dassow, G., E. Meir, E. M. Munro, and G. M. Odell. 2000. The segment polarity network is a robust developmental module. Nature 406:188-192.
393. Wagner, A. 2001. The yeast protein interaction network evolves rapidly and contains few duplicate genes. Mol. Biol. Evol. 18:1283-1292.
394. Wallace, B. 1963. Genetic diversity, genetic uniformity, and heterosis. Can. J. Genet. Cytol. 5:239-253.
395. Walter, J., and M. D. Biggin. 1996. DNA binding specificity of two homeodomain proteins in vitro and in Drosophila embryos. Proc. Natl. Acad. Sci. USA 93:2680-2685.
396. Wang, R. L., A. Stec, J. Hey, L. Lukens, and J. Doebley. 1999. The limits of selection during maize domestication. Nature 398:236-239.
397. Wang, W., F. G. Brunet, E. Nevo, and M. Long. 2002. Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99:4448-4453.
398. Wassermann, W. W., M. Palumbo, W. Thompson, J. W. Fickett, and C. E. Lawrence. 2000. Human-mouse genome comparisons to locate regulatory sites. Nat. Genet. 26:225-228.
399. Waterston, R. H., K. Lindblad-Toh, E. Bimey et al. (219 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
400. Wei, Z., L. M. Angerer, M. L. Gagnon, and R. C. Angerer. 1995. Characterization of the SpHE promoter that is spatially regulated along the animal-vegetal axis of the sea urchin embryo. Dev. Biol. 171:195-211.
401. Weinzierl, R. O. J. 1999. Mechanisms of gene expression. Imperial College Press, London.
402. G. Mol. Cell. Biol. 4:2467-2478.
403. Wheeler, J. C., K. Shigesada, J. P. Gergen, and Y. Ito. 2000. Mechanisms of transcriptional regulation by Runt domain proteins. Semin. Cell. Dev. Biol. 11:369-375.
404. White, K. P., S. A. Rifkin, P. Hurban, and D. S. Hogness. 1999. Microarray analysis of Drosophila development during metamorphosis. Science 286:2179-2184.
405. White, R. J. 2001. Gene transcription: mechanisms and control. Blackwell Science, Malden, Mass.
406. Wilkins, A. S. 1993. Genetic analysis of animal development. Wiley-Liss, Inc., New York.
407. -. 2002. The evolution of developmental pathways. Sinauer Associates, Sunderland, Mass.
408. Wilson, A. C. 1975. Evolutionary importance of gene regulation. Stadler Symp. 7:117-134.
409. Wilton, A. N., C. C. Laurie-Ahlberg, T. H. Emigh, and J. W. Curtsinger. 1982. Naturally occurring enzyme activity variation in Drosophila melanogaster. II. Relationships among enzymes. Genetics 102:207-221.
410. Wingender, E., X. Chen, E. Fricke et al. (14 co-authors). 2001. The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29:281-283.
411. Wolff, C., M. Pepling, P. Gergen, and M. Klingler. 1999. Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis. Mech. Dev. 80:87-99.
412. Wolffe, A. P. 1994. Insulating chromatin. Curr. Biol. 4:85-87.
413. -. 2001. Chromatin structure and the regulation of transcription. Pp. 35-64 in J. Locker, ed. Transcription factors. Academic Press, San Diego, Calif.
414. Wray, G. A., and A. E. Bely. 1994. The evolution of echinoderm development is driven by several distinct factors. Development 120(Suppl):97-106.
415. Wray, G. A., and C. J. Lowe. 2000. Developmental regulatory genes and echinoderm evolution. Syst. Biol. 49:28-51.
416. Wray, G. A., and D. R. McClay. 1989. Molecular heterochronies and heterotopies in early echinoid development. Evolution 43:803-813.
417. 3 and evidence for an upstream enhancer. Am. J. Physiol. 276:C883-C891.
418. Wright, S. 1982. Character change, speciation, and the higher taxa. Evolution 36:427-443.
419. Wu, C. Y., and M. D. Brennan. 1993. Similar tissue-specific expression of the Adh genes from different Drosophila species is mediated by distinct arrangements of cis-acting sequences. Mol. Gen. Genet. 240:58-64.
420. Xu, P.-X., X. Zhang, S. Heaney, A. Yoon, A. M. Michelson, and R. L. Maas. 1999. Regulation of Pax6 expression is conserved between mice and flies. Development 126:383-395.
421. Yamamoto, K. R., B. D. Darimont, R. L. Wagner, and J. A. Iñiguez-Lluhf. 1998. Building transcriptional regulatory complexes: signals and surfaces. Cold Spring Harbor Symp. Quant. Biol. 63:587-598.
422. Yamamoto, Y., and W. R. Jeffery. 2000. Central role for the lens in cave fish eye degeneration. Science 289:631-633.
423. Yan, H., W. S. Yuan, V. E. Velculescu, B. Vogelstein, and K. W. Kinzler. 2002. Allelic variation in human gene expression. Science 297:1143-1143.
424. Yu, H., S. H. Yang, and C. J. Goh. 2002. Spatial and temporal expression of the orchid floral homeotic gene DOMADS1 is mediated by its upstream regulatory regions. Plant Mol. Biol. 49:225-237.
425. Yuh, C. H., H. Bolouri, and E. H. Davidson. 1998. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279:1896-1902.
426. -. 2001. Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control. Development 128:617-629.
427. Yuh, C.-H., C. T. Brown, C. B. Livi, L. Rowen, P. J. C. Clarke, and E. H. Davidson. 2002. Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin. Dev. Biol. 246:148-161.
428. Yun, K. S., and B. Wold. 1996. Skeletal muscle determination and differentiation: story of a core regulatory network and its context. Curr. Opin. Cell Biol. 8:877-889.
429. Zeller, R. W., J. D. Griffith, J. G. Moore, C. V. Kirchhamer, R. J. Britten, and E. H. Davidson. 1995. A multimerizing transcription factor of sea urchin embryos capable of looping DNA. Proc. Natl. Acad. Sci. USA 92:2989-2993.
430. Zerucha, T., T. Stuhmer, G. Hatch, B. K. Park, Q. M. Long, G. Y. Yu, A. Gambarotta, J. R. Schultz, J. L. R. Rubenstein, and M. Ekker. 2000. A highly conserved enhancer in the Dlx5/Dlx6 region is the site of cross-regulatory interactions between Dlx genes in the embryonic forebrain. J. Neuro. 20:709-721.
431. Zhu, J., and M. Q. Zhang. 1999. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 15:607-611.
432. Zuckerkandl, E. 1963. Perspectives in molecular anthropology. Pp. 256-274 in A. Rich and N. Davidson, eds. Structural chemistry and molecular biology. W.H. Freeman, San Francisco.