The Plant Genome: Decoding the Transcriptional Hardwiring

Annual Plant Reviews

Volumn 35, Issue , 2009, Pages 196-228

  Grotewold, Erich ^a   Springer, Nathan ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Chromatin; cis regulatory element; Promoter; Regulatory motif; TATA; Transcription factor

Indexed keywords

EID: 70350429218     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781444312249.ch6     Document Type: Chapter

References (202)

1. Adhikary, S. and Eilers, M. (2005) Transcriptional regulation and transformation by Myc proteins. Nat Rev Mol Cell Biol 6, 635-645.
2. Alexandrov, N.N., Troukhan, M.E., Brover, V.V., Tatarinova, T., Flavell, R.B. and Feldmann, K.A. (2006) Features of Arabidopsis genes and genome discovered using full-length cDNAs. Plant Mol Biol 60, 69-85.
3. Ali, S. and Taylor, W.C. (2001) The 3' non-coding region of a C4 photosynthesis gene increases transgene expression when combined with heterologous promoters. Plant Mol Biol 46, 325-333.
4. Andrau, J.C., Van Oevelen, C.J., Van Teeffelen, H.A., Weil, P.A., Holstege, F.C. and Timmers, H.T. (2002) Mot1p is essential for TBP recruitment to selected promoters during in vivo gene activation. EMBO J 21, 5173-5183.
5. Aravind, L., Anantharaman, V., Balaji, S., Babu, M.M. and Iyer, L.M. (2005) The many faces of the helix-turn-helix domain: transcription regulation and beyond. FEMS Microbiol Rev 29, 231-262.
6. Arnone, M.I. and Davidson, E.H. (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.
7. Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. and Teichmann, S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14, 283-291.
8. Bailey, T.L. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3, 21-29.
9. Baldwin, D.A. and Gurley, W.B. (1996) Isolation and characterization of cDNAs encoding transcription factor IIB from Arabidopsis and soybean. Plant J 10, 561-568.
10. Bao, X., Franks, R.G., Levin, J.Z. and Liu, Z. (2004) Repression of AGAMOUS by BELLRINGER in floral and inflorescence meristems. Plant Cell 16, 1478-1489.
11. Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5, 101-113.
12. Basehoar, A.D., Zanton, S.J. and Pugh, B.F. (2004) Identification and distinct regulation of yeast TATA box-containing genes. Cell 116, 699-709.
13. Beltran, A.C., Dawson, P.E. and Gottesfeld, J.M. (2005) Role of DNA sequence in the binding specificity of synthetic basic-helix-loop-helix domains. Chembiochem 6, 104-113.
14. Benfey, P.N. and Chua, N.-H. (1990) The cauliflower mosaic virus 35S Promoter:combinatorial regulation of transcription in plants. Science 250, 959-966.
15. Berk, A.J. (2000) TBP-like factors come into focus. Cell 103, 5-8.
16. Berman, B.P., Nibu, Y., Pfeiffer, B.D., Tomancak, P., Celniker, S.E., Levine, M., et al. (2002) Exploiting transcription factor binding site clustering to identify cisregulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA 99, 757-762.
17. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., et al. (2003) A gene expression map of the Arabidopsis root. Science 302, 1956-1960.
18. Blais, A. and Dynlacht, B.D. (2005) Constructing transcriptional regulatory networks. Genes Dev 19, 1499-1511.
19. Blanc, G. and Wolfe, K.H. (2004) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16, 1679-1691.
20. Bodeau, J.P. and Walbot, V. (1992) Regulated transcription of the maize Bronze-2 promoter in electroporated protoplasts requires the C1 and R gene products. Mol Gen Genet 233, 379-387.
21. Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956.
22. Braun, E.L. and Grotewold, E. (1999a) Diversification of the R2R3 Myb gene family and the segmental allotetraploid origin of the maize genome. Maize Genet Coop Newsl 73, 26-27.
23. Braun, E.L. and Grotewold, E. (1999b) Newly discovered plant c-myb-like genes rewrite the evolution of the plant myb gene family. Plant Physiol 121, 21-24.
24. Bray, D. (2003) Molecular networks: the top-down view. Science 301, 1864-1865.
25. Britten, R.J. and Davidson, E.H. (1969) Gene regulation for higher cells: a theory. Science 165, 349-357.
26. Buchanan, B., Gruissem, W. and Jones, R. (2000) Biochemistry and Molecular Biology of Plants (Rockville: ASPP).
27. Buratowski, S., Hahn, S., Guarente, L. and Sharp, P.A. (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56, 549-561.
28. Butler, J.E. and Kadonaga, J.T. (2002) The RNA polymerase II core promoter: a key component in the regulation of gene expression. Genes Dev 16, 2583-2592.
29. Cao, X., Costa, L.M., Biderre-Petit, C., Kbhaya, B., Dey, N., Perez, P., et al. (2007) Abscisic Acid and stress signals induce viviparous1 expression in seed and vegetative tissues of maize. Plant Physiol 143, 720-731.
30. Cardon, L.R. and Stormo, G.D. (1992) Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J Mol Biol 223, 159-170.
31. Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 38, 626-635.
32. Cheng, W.H., Taliercio, E.W. and Chourey, P.S. (1999) Sugars modulate an unusual mode of control of the cell-wall invertase gene (Incw1) through its 3' untranslated region in a cell suspension culture of maize. Proc Natl Acad Sci USA 96, 10512-10517.
33. Clancy, M. and Hannah, L.C. (2002) Splicing of the maize Sh1 first intron is essential for enhancement of gene expression, and a T-rich motif increases expression without affecting splicing. Plant Physiol 130, 918-929.
34. Clark, R.M., Wagler, T.N., Quijada, P. and Doebley, J. (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38, 594-597.
35. Colinas, J., Birnbaum, K. and Benfey, P.N. (2002) Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiol 129, 451-454.
36. Davidson, E.H. (2001) Genomic Regulatory Systems: Development and Evolution (San Diego: Academic Press).
37. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M., et al. (2003) AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4, 25.
38. De Bodt, S., Maere, S. and Van de Peer, Y. (2005) Genome duplication and the origin of angiosperms. Trends Ecol Evol 20, 591-597.
39. Decary, S., Decesse, J.T., Ogryzko, V., Reed, J.C., Naguibneva, I., Harel-Bellan, A., et al. (2002) The retinoblastoma protein binds the promoter of the survival gene bcl-2 and regulates its transcription in epithelial cells through transcription factor AP-2. Mol Cell Biol 22, 7877-7888.
40. Dekker, J. (2006) The three 'C's of chromosome conformation capture: controls, controls, controls. Nat Methods 3, 17-21.
41. Dekker, J., Rippe, K., Dekker, M. and Kleckner, N. (2002) Capturing chromosome conformation. Science 295, 1306-1311.
42. Dias, A.P., Braun, E.L., McMullen, M.D. and Grotewold, E. (2003) Recently duplicated maize R2R3 Myb genes provide evidence for distinct mechanisms of evolutionary divergence after duplication. Plant Physiol 131, 610-620.
43. Djordjevic, M. and Sengupta, A.M. (2006) Quantitative modeling and data analysis of SELEX experiments. Phys Biol 3, 13-28.
44. Djordjevic, M., Sengupta, A.M. and Shraiman, B.I. (2003) A biophysical approach to transcription factor binding site discovery. Genome Res 13, 2381-2390.
45. Dostie, J., Richmond, T.A., Arnaout, R.A., Selzer, R.R., Lee, W.L., Honan, T.A., et al. (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16, 1299-1309.
46. Dynan, W.S. (1989) Modularity in promoters and enhancers. Cell 58, 1-4.
47. Ehlert, A., Weltmeier, F., Wang, X., Mayer, C.S., Smeekens, S., Vicente-Carbajosa, J., et al. (2006) Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts:establishment of a heterodimerization map of group C and group S bZIP transcription factors. Plant J 46, 890-900.
48. Eulgem, T., Rushton, P.J., Robatzek, S. and Somssich, I.E. (2000) TheWRKY superfamily of plant transcription factors. Trends Plant Sci 5, 199-206.
49. Fernandez, P.C., Frank, S.R., Wang, L., Schroeder, M., Liu, S., Greene, J., et al. (2003) Genomic targets of the human c-Myc protein. Genes Dev 17, 1115-1129.
50. Florquin, K., Saeys, Y., Degroeve, S., Rouze, P. and Van de Peer, Y. (2005) Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res 33, 4255-4264.
51. Fujimori, S., Washio, T., Higo, K., Ohtomo, Y., Murakami, K., Matsubara, K., et al. (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554, 17-22.
52. Gao, Y., Li, J., Strickland, E., Hua, S., Zhao, H., Chen, Z., et al. (2004) An Arabidopsis promoter microarray and its initial usage in the identification of HY5 binding targets in vitro. Plant Mol Biol 54, 683-699.
53. Garvie, C.W., Hagman, J. and Wolberger, C. (2001) Structural studies of Ets-1/Pax5 complex formation on DNA. Mol Cell 8, 1267-1276.
54. Gidekel, M., Jimenez, B. and Herrera-Estrella, L. (1996) The first intron of the Arabidopsis thaliana gene coding for elongation factor 1 beta contains an enhancer-like element. Gene 170, 201-206.
55. Goff, S.A., Cone, K.C. and Chandler, V.L. (1992) Functional analysis of the transcriptional activator encoded by the maize B gene: evidence for a direct functional interaction between two classes of regulatory proteins. Genes Dev 6, 864-875.
56. Goff, S.A., Cone, K.C. and Fromm, M.E. (1991) Identification of functional domains in the maize transcriptional activator C1: comparison of wild-type and dominant inhibitor proteins. Genes Dev 5, 298-309.
57. Goff, S.A., Klein, T.M., Roth, B.A., Fromm, M.E., Cone, K.C., Radicella, J.P., et al. (1990) Transactivation of anthocyanin biosynthetic genes following transfer of B regulatory genes into maize tissues. EMBO J 9, 2517-2522.
58. Gold, L., Brown, D., He, Y., Shtatland, T., Singer, B.S. and Wu, Y. (1997) From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops. Proc Natl Acad Sci USA 94, 59-64.
59. Grace, M.L., Chandrasekharan, M.B., Hall, T.C. and Crowe, A.J. (2004) Sequence and spacing of TATA box elements are critical for accurate initiation from the betaphaseolin promoter. J Biol Chem 279, 8102-8110.
60. Greene, B., Walko, R. and Hake, S. (1994) Mutator insertions in an intron of the maize knotted 1 gene result in dominant suppressible mutations. Genetics 138, 1275-1285.
61. Grotewold, E. (2005) Plant metabolic diversity: a regulatory perspective. Trends Plant Sci 10, 57-62.
62. Grotewold, E. (2006) The genetics and biochemistry of floral pigments. Annu Rev Plant Biol 57, 761-780.
63. Grotewold, E., Drummond, B.J., Bowen, B. and Peterson, T. (1994) The mybhomologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell 76, 543-553.
64. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L., et al. (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics 21, 2568-2569.
65. Guo, H. and Moose, S.P. (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15, 1143-1158.
66. Haberer, G., Mader, M.T., Kosarev, P., Spannagl, M., Yang, L. and Mayer, K.F. (2006) Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol 142, 1589-1602.
67. Haerizadeh, F., Singh, M.B. and Bhalla, P.L. (2006) Transcriptional repression distinguishes somatic from germ cell lineages in a plant. Science 313, 496-499.
68. Haga, N., Kato, K., Murase, M., Araki, S., Kubo, M., Demura, T., et al. (2007) R1R2R3-Myb proteins positively regulate cytokinesis through activation of KNOLLE transcription in Arabidopsis thaliana. Development 134, 1101-1110.
69. Hake, S., Vollbrecht, E. and Freeling, M. (1989) Cloning knotted, the dominant morphological mutant in maize using Ds2 as a transposon tag. EMBO J 8, 15-22.
70. Haralampidis, K., Milioni, D., Rigas, S. and Hatzopoulos, P. (2002) Combinatorial interaction of cis elements specifies the expression of the Arabidopsis AtHsp90-1 gene. Plant Physiol 129, 1138-1149.
71. Hartmann, U., Sagasser, M., Mehrtens, F., Stracke, R. and Weisshaar, B. (2005) Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes. Plant Mol Biol 57, 155-171.
72. Haverty, P.M., Hansen, U. and Weng, Z. (2004) Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res 32, 179-188.
73. Heine, G.F., Malik, V., Dias, A.P. and Grotewold, E. (2007) Expression and molecular characterization of ZmMYB-IF35 and related R2R3-MYB transcription factors. Mol Biotechnol 37, 155-164.
74. Hernandez, J., Heine, G., Irani, N.G., Feller, A., Kim, M.-G., Matulnik, T., et al. (2004) Different mechanisms participate in the R-dependent activity of the R2R3 MYB transcription factor C1. J Biol Chem 279, 48205-48213.
75. Herr, A.J., Jensen, M.B., Dalmay, T. and Baulcombe, D.C. (2005) RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118-120.
76. Hertz, G.Z. and Stormo, G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15, 563-577.
77. Higo, K., Ugawa, Y., Iwamoto, M. and Higo, H. (1998) PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Res 26, 358-359.
78. Higo, K., Ugawa, Y., Iwamoto, M. and Korenaga, T. (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27, 297-300.
79. Hill, T.A., Day, C.D., Zondlo, S.C., Thackeray, A.G. and Irish, V.F. (1998) Discrete spatial and temporal cis-acting elements regulate transcription of the Arabidopsis floral homeotic gene APETALA3. Development 125, 1711-1721.
80. Hiratsu, K., Matsui, K., Koyama, T. and Ohme-Takagi, M. (2003) Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J 34, 733-739.
81. Holt, K.E., Millar, A.H. and Whelan, J. (2006) ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. Plant Methods 2, 8.
82. Huang, H., Mizukami, Y., Hu, Y. and Ma, H. (1993) Isolation and characterization of the binding sequence for the product of the Arabidopsis floral homeotic gene AGAMOUS. Nucleic Acids Res 21, 4769-4776.
83. Huang, H., Tudor, M., Su, T., Zhang, Y., Hu, Y. and Ma, H. (1996) DNA binding properties of two arabidopsis MADS domain proteins: binding consensus and dimer formation. Plant Cell 8, 81-94.
84. Inada, D.C., Bashir, A., Lee, C., Thomas, B.C., Ko, C., Goff, S.A., et al. (2003) Conserved noncoding sequences in the grasses. Genome Res 13, 2030-2041.
85. Ito, M. (2005) Conservation and diversification of three-repeat Myb transcription factors in plants. J Plant Res 118, 61-69.
86. Ito, M., Araki, S., Matsunaga, S., Itoh, T., Nishihama, R., Machida, Y., et al. (2001) G2/Mphase- specific transcription during the plant cell cycle is mediated by c-Myb-like transcription factors. Plant Cell 13, 1891-1905.
87. Itzkovitz, S., Tlusty, T. and Alon, U. (2006) Coding limits on the number of transcription factors. BMC Genomics 7, 239.
88. Jeong, Y.M., Mun, J.H., Lee, I., Woo, J.C. Hong, C.B. and Kim, S.G. (2006) Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members. Plant Physiol 140, 196-209.
89. Jia, J., Fu, J., Zheng, J., Zhou, X., Huai, J., Wang, J., et al. (2006) Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J 48, 710-727.
90. Jiang, C., Gu, J., Chopra, S., Gu, X. and Peterson, T. (2004) Ordered origin of the typical two- and three-repeat Myb genes. Gene 326, 13-22.
91. Jin, H. and Martin, C. (1999) Multifunctionality and diversity within the plant MYBgene family. Plant Mol Biol 41, 577-585.
92. Kanei-Ishii, C., Sarai, A., Sawazaki, T., Nakagoshi, H., He, D.-N., Ogata, K., et al. (1990) The tryptophan cluster: a hypothetical structure of the DNA-binding domain of the myb protooncogene product. J Biol Chem 265, 19990-19995.
93. Kazan, K. (2006) Negative regulation of defence and stress genes by EAR-motifcontaining repressors. Trends Plant Sci 11, 109-112.
94. Keegan, L., Gill, G. and Ptashne, M. (1986) Separation of DNA binding from the transcription-activating function of a eukaryotic regulatory protein. Science 231, 699-704.
95. Kiran, K., Ansari, S.A., Srivastava, R., Lodhi, N., Chaturvedi, C.P., Sawant, S.V., et al. (2006) The TATA-box sequence in the basal promoter contributes to determining light-dependent gene expression in plants. Plant Physiol 142, 364-376.
96. Klempnauer, K.-H., Gonda, T.J. and Bishop, J.M. (1982) Nucleotide sequence of the retroviral leukemia gene v-myb and its cellular progenitor c-myb: the architecture of a transduced oncogene. Cell 31, 453-463.
97. Klempnauer, K.-H., Ramsay, G., Bishop, J.M., Moscovici, M.G., Moscovici, C., Mc-Grath, J.P., et al. (1983) The product of the retroviral transforming gene v-myb is a truncated version of the protein encoded by the cellular oncogene c-myb. Cell 33, 345-355.
98. Koch, M.A., Weisshaar, B., Kroymann, J., Haubold, B. and Mitchell-Olds, T. (2001) Comparative genomics and regulatory evolution: conservation and function of the Chs and Apetala3 promoters.Mol Biol Evol 18, 1882-1891.
99. Kranz, H., Scholz, K. and Weisshaar, B. (2000) c-MYB oncogene-like genes encoding three MYB repeats occur in all major plant lineages. Plant J 21, 231-235.
100. Kuhlemeier, C., Cuozzo, M., Green, P.J., Goyvaerts, E., Ward, K. and Chua, N.H. (1988) Localization and conditional redundancy of regulatory elements in rbcS-3A, a pea gene encoding the small subunit of ribulose-bisphosphate carboxylase. Proc Natl Acad Sci USA 85, 4662-4666.
101. Lago, C., Clerici, E., Dreni, L., Horlow, C., Caporali, E., Colombo, L., et al. (2005) The Arabidopsis TFIID factor AtTAF6 controls pollen tube growth. Dev Biol 285, 91-100.
102. Lagrange, T., Hakimi, M.A., Pontier, D., Courtois, F., Alcaraz, J.P., Grunwald, D., et al. (2003) Transcription factor IIB (TFIIB)-related protein (pBrp), a plant-specific member of the TFIIB-related protein family. Mol Cell Biol 23, 3274-3286.
103. Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D. and Ebright, R.H. (1998) New core promoter element in RNA polymerase II-dependent transcription: sequencespecific DNA binding by transcription factor IIB. Genes Dev 12, 34-44.
104. Lam, E., Benfey, P.N., Gilmartin, P.M., Fang, R.X. and Chua, N.H. (1989) Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. Proc Natl Acad Sci USA 86, 7890-7894.
105. Lamb, R.S., Hill, T.A., Tan, Q.K. and Irish, V.F. (2002) Regulation of APETALA3 floral homeotic gene expression by meristem identity genes. Development 129, 2079-2086.
106. Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A. and Freeling, M. (2004) Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166, 935-945.
107. Lawit, S.J., O'Grady, K., Gurley, W.B. and Czarnecka-Verner, E. (2007) Yeast twohybrid map of Arabidopsis TFIID. Plant Mol Biol 64, 73-87.
108. Lee, J., He, K., Stolc, V., Lee, H., Figueroa, P., Gao, Y., et al. (2007) Analysis of transcription factor HY5 genomic binding sites revealed its hierarchical role in light regulation of development. Plant Cell 19, 731-749.
109. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804.
110. Lescot, M., Dehais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., et al. (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.
111. Lesnick, M.L. and Chandler, V.L. (1998) Activation of the maize anthocyanin gene a2 is mediated by an element conserved in many anthocyanin promoters. Plant Physiol 117, 437-445.
112. Lesnick, M.L. (1997) Analysis of the cis-Acting Sequences Required for C1/B Activation of the Maize Anthocyanin Biosynthetic Pathway. PhD Thesis, University of Oregon, Eugene, OR, pp. 32-53.
113. Levesque, M.P., Vernoux, T., Busch, W., Cui, H., Wang, J.Y., Blilou, I., et al. (2006) Wholegenome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol 4, e143.
114. Levine, H.A. and Nilsen-Hamilton, M. (2007) A mathematical analysis of SELEX. Comput Biol Chem 31, 11-35.
115. Lipsick, J.S. (1996) One billion years of Myb. Oncogene 13, 223-235.
116. Locke, J.C., Kozma-Bognar, L., Gould, P.D., Feher, B., Kevei, E., Nagy, F., et al. (2006) Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol 2, 59.
117. Locke, J.C., Southern, M.M., Kozma-Bognar, L., Hibberd, V., Brown, P.E., Turner, M.S., et al. (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 1, 0013.
118. Luscombe, N.M., Austin, S.E., Berman, H.M. and Thornton, J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol 1, REVIEWS001.
119. Maere, S., De Bodt, S., Raes, J., Casneuf, T., Van Montagu, M., Kuiper, M., et al. (2005) Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102, 5454-5459.
120. Maniatis, T., Falvo, J.V., Kim, T.H., Kim, T.K., Lin, C.H., Parekh, B.S., et al. (1998) Structure and function of the interferon-beta enhanceosome. Cold Spring Harb Symp Quant Biol 63, 609-620.
121. Maniatis, T. and Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature 416, 499-506.
122. Martin, C. and Paz-Ares, J. (1997) MYB transcription factors in plants. Trends Genet 13, 67-73.
123. Massari, M.E. and Murre, C. (2000) Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol Cell Biol 20, 429-440.
124. Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34, D108-D110.
125. Menossi, M., Rabaneda, F., Puigdomenech, P. and Martinez-Izquierdo, J.A. (2003) Analysis of regulatory elements of the promoter and the 3' untranslated region of the maize Hrgp gene coding for a cell wall protein. Plant Cell Rep 21, 916-923.
126. Merika, M. and Thanos, D. (2001) Enhanceosomes. Curr Opin Genet Dev 11, 205-208.
127. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. and Alon, U. (2002) Networkmotifs: simple building blocks of complex networks. Science 298, 824-827.
128. Molina, C. and Grotewold, E. (2005) Genome wide analysis of Arabidopsis core promoters. BMC Genomics 6, 25.
129. Morishige, D.T., Childs, K.L., Moore, L.D. and Mullet, J.E. (2002) Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing. Plant Physiol 130, 1614-1625.
130. Morohashi, K., Zhao, M., Yang, M., Read, B., Lloyd, A., Lamb, R., et al. (2007) Participation of the Arabidopsis bHLH factor GL3 in trichome initiation regulatory events. Plant Physiol 145, 736-746.
131. Murre, C., McCaw, P.S. and Baltimore, D. (1989) A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell 56, 777-783.
132. Nakamura, M., Tsunoda, T. and Obokata, J. (2002) Photosynthesis nuclear genes generally lack TATA-boxes: a tobacco photosystem I gene responds to light through an initiator. Plant J 29, 1-10.
133. Nakazono, M., Qiu, F., Borsuk, L.A. and Schnable, P.S. (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types:identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15, 583-596.
134. Narusaka, Y., Nakashima, K., Shinwari, Z.K., Sakuma, Y., Furihata, T., Abe, H., et al. (2003) Interaction between two cis-acting elements, ABRE and DRE, in ABAdependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J 34, 137-148.
135. Ogata, K., Hojo, H., Aimoto, S., Nakai, T., Nakamura, H., Sarai, A., et al. (1992) Solution structure of a DNA-binding unit of Myb: a helix-turn-helix-related motif with conserved tryptophans forming a hydrophobic core. Proc Natl Acad Sci USA 89, 6428-6432.
136. Ogata, K., Morikawa, S., Nakamura, H., Sekikawa, A., Inoue, T., Kanai., H., et al. (1994) Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell 79, 639-648.
137. Ohler, U., Liao, G., Niemann, H. and Rubin, G.M. (2002) Computational analysis of core promoters in the Drosophila genome. Genome Biol 3, 0087.1-0087.12.
138. Ohler, U. and Niemann, H. (2001) Identification and analysis of eukaryotic promoters:recent computational approaches. Trends Genet 17, 56-60.
139. Ohtsu, K., Takahashi, H., Schnable, P.S. and Nakazono, M. (2006) Cell type-specific gene expression profiling in plants by using a combination of laser microdissection and high-throughput technologies. Plant Cell Physiol 48, 3-7.
140. Onodera, Y., Haag, J.R., Ream, T., Nunes, P.C., Pontes, O. and Pikaard, C.S. (2005) Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120, 613-622.
141. Pabo, C.O. and Sauer, R.T. (1992) Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem 61, 1053-1095.
142. Palaniswamy, K., James, S., Sun, H., Lamb, R., Davuluri, R.V. and Grotewold, E. (2006) AGRIS and AtRegNet: a platform to link cis-regulatory elements and transcription factors into regulatory networks. Plant Phyisiol 140, 818-829.
143. Pan, S., Czarnecka-Verner, E. and Gurley, W.B. (2000) Role of the TATA binding protein-transcription factor IIB interaction in supporting basal and activated transcription in plant cells. Plant Cell 12, 125-135.
144. Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., et al. (2006) in vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502.
145. Pooma, W., Gersos, C. and Grotewold, E. (2002) Transposon insertions in the promoter of the Zea mays a1 gene differentially affect transcription by the Myb factors P and C1. Genetics 161, 793-801.
146. Quattrocchio, F., Baudry, A., Lepiniec, L. and Grotewold, E. (2006) The regulation of flavonoid biosynthesis. In The Science of Flavonoids, E. Grotewold, ed. (New York, NY: Springer), pp. 97-122.
147. Quiros, C.F., Grellet, F., Sadowski, J., Suzuki, T., Li, G. and Wroblewski, T. (2001) Arabidopsis and Brassica comparative genomics: sequence, structure and gene content in the ABI-Rps2-Ck1 chromosomal segment and related regions. Genetics 157, 1321-1330.
148. Rabinowicz, P.D., Braun, E.L., Wolfe, A.D., Bowen, B. and Grotewold, E. (1999) Maize R2R3 Myb genes: sequence analysis reveals amplification in higher plants. Genetics 153, 427-444.
149. Rand, D.A., Shulgin, B.V., Salazar, D. and Millar, A.J. (2004) Design principles underlying circadian clocks. J R Soc Interface 1, 119-130.
150. Riano-Pachon, D.M., Ruzicic, S., Dreyer, I. and Mueller-Roeber, B. (2007) PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8, 42.
151. Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290, 2105-2110.
152. Riechmann, J.L. and Ratcliffe, O.J. (2000) Agenomic perspective on plant transcription factors. Curr Opin Plant Biol 3, 423-434.
153. Roberts, S.G. (2000) Mechanisms of action of transcription activation and repression domains. Cell Mol Life Sci 57, 1149-1160.
154. Rombauts, S., Florquin, K., Lescot, M., Marchal, K., Rouze, P. and Van de Peer, Y. (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol 132, 1162-1176.
155. Romero, I., Fuertes, A., Benito, M.J., Malpica, J.M., Leyva, A. and Paz-Ares, J. (1998) More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14, 273-284.
156. Rose, A.B. (2004) The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J 40, 744-751.
157. Rose, A.B. and Beliakoff, J.A. (2000) Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing. Plant Physiol 122, 535-542.
158. Roth, F.P., Hughes, J.D., Estep, P.W. and Church, G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16, 939-945.
159. Rubio, V., Shen, Y., Saijo, Y., Liu, Y., Gusmaroli, G., Dinesh-Kumar, S.P., et al. (2005) An alternative tandem affinity purification strategy applied to Arabidopsis protein complex isolation. Plant J 41, 767-778.
160. Sablowski, R.W.M. and Meyerowitz, E.M. (1998) A Homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92, 93-103.
161. Sainz, M.B., Goff, S.A. and Chandler, V.L. (1997a) Extensive mutagenesis of a transcriptional activation domain identifies single hydrophobic and acidic amino acids important for activation in vivo. Mol Cell Biol 17, 115-122.
162. Sainz, M.B., Grotewold, E. and Chandler, V.L. (1997b) Evidence for direct activation of an anthocyanin promoter by the maize C1 protein and comparison ofDNAbinding by related Myb domain proteins. Plant Cell 9, 611-625.
163. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296, 141-145.
164. Seki, M., Narusaka, M., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y., et al. (2001) Arabidopsis encyclopedia using full-length cDNAs and its application. Plant Physiol Biochem 39, 211-220.
165. Seoighe, C. and Gehring, C. (2004) Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet 20, 461-464.
166. Serfling, E., Jasin, M. and Schaffner, W. (1985) Enhancers and eukaryotic genetranscription. Trends Genet 1, 224-230.
167. Shi, W. and Zhou, W. (2006) Frequency distribution of TATA box and extension sequences on human promoters. BMC Bioinformatics 7, S2.
168. Shin, B., Choi, G., Yi, H., Yang, S., Cho, I., Kim, J., et al. (2002) AtMYB21, a gene encoding a flower-specific transcription factor, is regulated by COP1. Plant J 30, 23-32.
169. Shiu, S.H., Shih, M.C. and Li, W.H. (2005) Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiol 139, 18-26.
170. Sidorenko, L.V., Li, X., Cocciolone, S.M., Chopra, S., Tagliani, L., Bowen, B., et al. (2000) Complex structure of a maizeMyb gene promoter: functional analysis in transgenic plants. Plant J 22, 471-482.
171. Smale, S.T. and Kadonaga, J.T. (2003) The RNA polymerase II core promoter. Annu Rev Biochem 72, 449-479.
172. Spelt, C., Quattrocchio, F., Mol, J.N. and Koes, R. (2000) Anthocyanin1 of petunia encodes a basic helix-loop-helix protein that directly activates transcription of structural anthocyanin genes. Plant Cell 12, 1619-1632.
173. Springer, N.M. and Kaeppler, S.M. (2005) Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins. Plant Physiol 138, 92-104.
174. Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C., Chandler, V.L., et al. (2003) Comparative analysis of SET domain proteins inmaize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol 132, 907-925.
175. Stam, M., Belele, C., Dorweiler, J.E. and Chandler, V.L. (2002a) Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 16, 1906-1918.
176. Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J.E., Bennetzen, J.L. and Chandler, V.L. (2002b) The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
177. Stormo, G.D. (1990) Consensus patterns in DNA. Methods Enzymol 183, 211-221.
178. Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics 16, 16-23.
179. Stormo, G.D. and Hartzell, G.W., III. (1989) Identifying protein-binding sites from unaligned DNA fragments. Proc Natl Acad Sci USA 86, 1183-1187.
180. Stracke, R., Werber, M. and Weisshaar, B. (2001) The R2R3 MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4, 447-456.
181. Thibaud-Nissen, F., Wu, H., Richmond, T., Redman, J.C., Johnson, C., Green, R., et al. (2006) Development of Arabidopsis whole-genome microarrays and their application to the discovery of binding sites for the TGA2 transcription factor in salicylic acid-treated plants. Plant J 47, 152-162.
182. Tirosh, I., Weinberger, A., Carmi, M. and Barkai, N. (2006) A genetic signature of interspecies variations in gene expression. Nat Genet 38, 830-834.
183. Tompa, M., Li, N., Bailey, T.L., Church, G.M., De Moor, B., Eskin, E., et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23, 137-144.
184. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment:RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
185. Ulyanov, A.V. and Stormo, G.D. (1995) Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions. NucleicAcids Res 23, 1434-1440.
186. Vandepoele, K., Casneuf, T. and Van de Peer, Y. (2006) Identification of novel regulatory modules in dicot plants using expression data and comparative genomics. Genome Biol 7, R103.
187. Vogel, J.M., Roth, B., Cigan, M. and Freeling, M. (1993) Expression of the two maize TATA binding protein genes and function of the encoded TBP proteins by complementation in yeast. Plant Cell 5, 1627-1638.
188. Wang, D., Amornsiripanitch, N. and Dong, X. (2006) A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants. PLoS Pathog 2, e123.
189. Wang, T. and Stormo, G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19, 2369-2380.
190. Wasserman, W.W. and Sandelin, A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5, 276-287.
191. Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J.L. and Meyerowitz, E.M. (2006) Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet 2, e117.
192. West, A.G. and Fraser, P. (2005) Remote control of gene transcription. Hum Mol Genet 14 (Spec No 1), R101-R111.
193. Weston, K. (1998) Myb proteins in life, death and differentiation. Curr Opin Gen Dev 8, 76-81.
194. William, D.A., Su, Y., Smith, M.R., Lu, M., Baldwin, D.A. and Wagner, D. (2004) Genomic identification of direct target genes of LEAFY. Proc Natl Acad Sci USA 101, 1775-1780.
195. Williams, C.E. and Grotewold, E. (1997) Differences between plant and animal Myb domains are fundamental for DNA-binding, and chimericMybdomains have novel DNA-binding specificities. J Biol Chem 272, 563-571.
196. Wray, G.A., Hahn, M.W., Abouheif, E., Balhoff, J.P., Pizer, M., Rockman, M.V., et al. (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20, 1377-1419.
197. Yamaguchi-Shinozaki, K. and Shinozaki, K. (2005) Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters. Trends Plant Sci 10, 88-94.
198. Yuh, C.-H., Bolouri, H. and Davidson, E.H. (1998) Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279, 1896-1902.
199. Zhang, L., Zuo, K., Zhang, F., Cao, Y., Wang, J., Zhang, Y., et al. (2006) Conservation of noncodingmicrosatellites in plants: implication for gene regulation. BMC Genomics 7, 323.
200. Zhao, Z., Tavoosidana, G., Sjolinder, M., Gondor, A., Mariano, P., Wang, S., et al. (2006) Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet 38, 1341-1347.
201. Zhu, Q., Dabi, T. and Lamb, C. (1995) TATA box and initiator functions in the accurate transcription of a plant minimal promoter in vitro. Plant Cell 7, 1681-1689.
202. Zhu, Q., Ordiz, M.I., Dabi, T., Beachy, R.N. and Lamb, C. (2002) Rice TATA binding protein interacts functionally with transcription factor IIB and the RF2a bZIP transcriptional activator in an enhanced plant in vitro transcription system. Plant Cell 14, 795-803.