Genome-wide analysis of gene expression during early Arabidopsis flower development

PLoS Genetics

Volumn 2, Issue 7, 2006, Pages 1012-1024

  Wellmer, Frank ^a   Alves Ferreira, Márcio ^a,b   Dubois, Annick ^a,c   Riechmann, José Luis ^a   Meyerowitz, Elliot M ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c UNIVERSITÉ DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; BUD CULTURE; CORRELATION ANALYSIS; DOWN REGULATION; FLOWER DEVELOPMENT; GENE ACTIVATION; GENE EXPRESSION; GENE ISOLATION; GENETIC IDENTIFICATION; GENOME ANALYSIS; LIFE CYCLE; MICROARRAY ANALYSIS; MULTIGENE FAMILY; NONHUMAN; PRIMORDIUM; UPREGULATION; DNA MICROARRAY; FLOWER; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM; TIME;

ARABIDOPSIS;

VEGETABLE PROTEIN;

ARABIDOPSIS; FLOWERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PROTEINS; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 33746591797     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020117     Document Type: Article

References (62)

1. Smyth DR (2005) Morphogenesis of flowers-our evolving view. Plant Cell 17: 330-341.
2. Lohmann JU, Weigel D (2002) Building beauty: The genetic control of floral patterning. Dev Cell 2: 135-142.
3. Krizek BA, Fletcher JC (2005) Molecular mechanisms of flower development: An armchair guide. Nat Rev Genet 6: 688-698.
4. Jack T (2004) Molecular and genetic mechanisms of floral control. Plant Cell 16 Suppl: S1-S17.
5. Cutler S, McCourt P (2005) Dude, where's my phenotype? Dealing with redundancy in signaling networks. Plant Physiol 138: 558-559.
6. Moore RC, Purugganan MD (2005) The evolutionary dynamics of plant duplicate genes. Curr Opin Plant Biol 8: 122-128.
7. Moore RC, Grant SR, Purugganan MD (2005) Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana. Mol Biol Evol 22: 91-103.
8. Reinke V, White KP (2002) Developmental genomic approaches in model organisms. Annu Rev Genomics Hum Genet 3: 153-178.
9. Wellmer F, Riechmann JL (2005) Gene network analysis in plant development by genomic technologies. Int J Dev Biol 49: 745-759.
10. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, et al. (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
11. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
12. Ma L, Sun N, Liu X, Jiao Y, Zhao H, et al. (2005) Organ-specific expression of Arabidopsis genome during development. Plant Physiol 138: 80-91.
13. Zhang X, Feng B, Zhang Q, Zhang D, Altman N, et al. (2005) Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis. Plant Mol Biol 58: 401-419.
14. Gomez-Mena C, de Folter S, Costa MM, Angenent GC, Sablowski R (2005) Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis. Development 132: 429-438.
15. Ito T, Wellmer F, Yu H, Das P, Ito N, et al. (2004) The homeotic protein AGAMOUS controls microsporogenesis by regulation of SPOROCYTELESS. Nature 430: 356-360.
16. Wellmer F, Riechmann JL, Alves-Ferreira M, Meyerowitz EM (2004) Genome-wide analysis of spatial gene expression in Arabidopsis flowers. Plant Cell 16: 1314-1326.
17. Schmid M, Uhlenhaut NH, Godard F, Demar M, Bressan R, et al. (2003) Dissection of floral induction pathways using global expression analysis. Development 130: 6001-6012.
18. Smyth DR, Bowman JL, Meyerowitz EM (1990) Early flower development in Arabidopsis. Plant Cell 2: 755-767.
19. Bowman JL, Alvarez J, Weigel D, Meyerowitz EM, Smyth DR (1993) Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. Development 119: 721-743.
20. Ferrandiz C, Gu Q, Martienssen R, Yanofsky MF (2000) Redundant regulation of meristem identity and plant architecture by FRUITFULL, APETALA1, and CAULIFLOWER. Development 127: 725-734.
21. Mandel MA, Yanofsky MF (1995) A gene triggering flower formation in Arabidopsis. Nature 377: 522-524.
22. Yu H, Ito T, Wellmer F, Meyerowitz EM (2004) Repression of AGAMOUS-LIKE 24 is a crucial step in promoting flower development. Nat Genet 36: 157-161.
23. Yanofsky MF, Ma H, Bowman JL, Drews GN, Feldmann KA, et al. (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346: 35-39.
24. Jack T, Brockman LL, Meyerowitz EM (1992) The homeotic gene APETALA3 of Arabidopsis thaliana encodes a MADS box and is expressed in petals and stamens. Cell 68: 683-697.
25. Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev 8: 1548-1560.
26. Jofuku KD, den Boer BG, Van Montagu M, Okamuro JK (1994) Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6: 1211-1225.
27. Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, et al. (2001) A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell 105: 793-803.
28. Lenhard M, Bohnert A, Jurgens G, Laux T (2001) Termination of stem cell maintenance in Arabidopsis floral meristems by interactions between WUSCHEL and AGAMOUS. Cell 105: 805-814.
29. Siegfried KR, Eshed Y, Baum SF, Otsuga D, Drews GN, et al. (1999) Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development 126: 4117-4128.
30. Dinneny JR, Yadegari R, Fischer RL, Yanofsky MF, Weigel D (2004) The role of JAGGED in shaping lateral organs. Development 131: 1101-1110.
31. Ohno CK, Reddy GV, Heisler MG, Meyerowitz EM (2004) The Arabidopsis JAGGED gene encodes a zinc finger protein that promotes leaf tissue development. Development 131: 1111-1122.
32. Dinneny JR, Weigel D, Yanofsky MF (2006) NUBBIN and JAGGED define stamen and carpel shape in Arabidopsis. Development 133: 1645-1655.
33. Borner R, Kampmann G, Chandler J, Gleissner R, Wisman E, et al. (2000) A MADS domain gene involved in the transition to flowering in Arabidopsis. Plant J 24: 591-599.
34. Kubo M, Udagawa M, Nishikubo N, Horiguchi G, Yamaguchi M, et al. (2005) Transcription switches for protoxylem and metaxylem vessel formation. Genes Dev 19: 1855-1860.
35. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, et al. (2000) Arabidopsis transcription factors: Genome-wide comparative analysis among eukaryotes. Science 290: 2105-2110.
36. Becker A, Theissen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29: 464-489.
37. Englbrecht CC, Schoof H, Bohm S (2004) Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 5: 39.
38. Yu H, Ito T, Zhao Y, Peng J, Kumar P, et al. (2004) Floral homeotic genes are targets of gibberellin signaling in flower development. Proc Natl Acad Sci U S A 101: 7827-7832.
39. Pfluger J, Zambryski P (2004) The role of SEUSS in auxin response and floral organ patterning. Development 131: 4697-4707.
40. Reinhardt D, Pesce ER, Stieger P, Mandel T, Baltensperger K, et al. (2003) Regulation of phyllotaxis by polar auxin transport. Nature 426: 255-260.
41. Honma T, Goto K (2001) Complexes of MADS-box proteins are sufficient to convert leaves into floral organs. Nature 409: 525-529.
42. Coen ES, Meyerowitz EM (1991) The war of the whorls: Genetic interactions controlling flower development. Nature 353: 31-37.
43. Bowman JL, Smyth DR, Meyerowitz EM (1989) Genes directing flower development in Arabidopsis. Plant Cell 1: 37-52.
44. Bowman JL, Smyth DR, Meyerowitz EM (1991) Genetic interactions among floral homeotic genes of Arabidopsis. Development 112: 1-20.
45. Bey M, Stuber K, Fellenberg K, Schwarz-Sommer Z, Sommer H, et al. (2004) Characterization of antirrhinum petal development and identification of target genes of the class B MADS box gene DEFICIENS. Plant Cell 16: 3197-3215.
46. Sablowski RW, Meyerowitz EM (1998) A homolog of NO APICAL MERISTEM is an immediate target of the floral homeotic genes APETALA3/PISTILLATA. Cell 92: 93-103.
47. Riechmann JL, Wang M, Meyerowitz EM (1996) DNA-binding properties of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, and AGAMOUS. Nucleic Acids Res 24: 3134-3141.
48. Shiraishi H, Okada K, Shimura Y (1993) Nucleotide sequences recognized by the AGAMOUS MADS domain of Arabidopsis thaliana in vitro. Plant J 4: 385-398.
49. Cubas P, Lauter N, Doebley J, Coen E (1999) The TCP domain: A motif found in proteins regulating plant growth and development. Plant J 18: 215-222.
50. Palatnik JF, Allen E, Wu X, Schommer C, Schwab R, et al. (2003) Control of leaf morphogenesis by microRNAs. Nature 425: 257-263.
51. Li C, Potuschak T, Colon-Carmona A, Gutierrez RA, Doerner P (2005) Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci U S A 102: 12978-12983.
52. Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, et al. (2003) Role of duplicate genes in genetic robustness against null mutations. Nature 421: 63-66.
53. Reddy GV, Meyerowitz EM (2005) Stem-cell homeostasis and growth dynamics can be uncoupled in the Arabidopsis shoot apex. Science 310: 663-667.
54. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
55. Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347.
56. Martin D, Brun C, Remy E, Mouren P, Thieffry D, et al. (2004) GOToolBox: Functional analysis of gene datasets based on Gene Ontology. Genome Biol 5: R101.
57. Long JA, Barton MK (1998) The development of apical embryonic pattern in Arabidopsis. Development 125: 3027-3035.
58. Riechmann JL, Krizek BA, Meyerowitz EM (1996) Dimerization specificity of Arabidopsis MADS domain homeotic proteins APETALA1, APETALA3, PISTILLATA, and AGAMOUS. Proc Natl Acad Sci U S A 93: 4793-4798.
59. Huang T, Bohlenius H, Eriksson S, Parcy F, Nilsson O (2005) The mRNA of the Arabidopsis gene FT moves from leaf to shoot apex and induces flowering. Science 309: 1694-1696.
60. Longabaugh WJ, Davidson EH, Bolouri H (2005) Computational representation of developmental genetic regulatory networks. Dev Biol 283: 1-16.
61. Flanagan CA, Hu Y, Ma H (1996) Specific expression of the AGL1 MADS-box gene suggests regulatory functions in Arabidopsis gynoecium and ovule development. Plant J 10: 343-353.
62. Savidge B, Rounsley SD, Yanofsky MF (1995) Temporal relationship between the transcription of two Arabidopsis MADS box genes and the floral organ identity genes. Plant Cell 7: 721-733.