Organ-specific expression of arabidopsis genome during development

Plant Physiology

Volumn 138, Issue 1, 2005, Pages 80-91

  Ma, Ligeng ^a,b   Sun, Ning ^c   Liu, Xigang ^d   Jiao, Yuling ^b   Zhao, Hongyu ^c   Xing, Wang Deng ^a,b  

^a PEKING UNIVERSITY   (China)

^b YALE UNIVERSITY   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d HEBEI NORMAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ENVIRONMENTAL IMPACT; MICROORGANISMS; TISSUE;

ATLAS; CHROMATIN; ENVIRONMENTAL SIGNALS; PHOTOPERCEPTION;

GENES;

GENES; MICROORGANISMS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

ARABIDOPSIS; ARTICLE; CELL DIVISION; DARKNESS; DNA REPLICATION; ENVIRONMENT; GENETICS; GENOME; GERMINATION; GROWTH, DEVELOPMENT AND AGING; LIGHT;

ARABIDOPSIS; CELL DIVISION; DARKNESS; DNA REPLICATION; ENVIRONMENT; GENOME, PLANT; GERMINATION; LIGHT;

EID: 24344488725     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.054783     Document Type: Article

References (49)

1. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk K, et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657
2. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
3. Barker J, Harada JJ, Goldberg RB (1988) Cellular localization of soybean storage protein mRNA in transformed tobacco seeds. Proc Natl Acad Sci USA 85: 458-462
4. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960
5. Bowman J (1994) Arabidopsis: An Atlas of Morphology and Development. Springer-Verlag, New York
6. Campbell P, Braam J (1999) Xyloglucan endotransglycosylases: diversity of genes, enzymes and potential wall-modifying functions. Trends Plant Sci 9: 361-366
7. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, et al (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291: 1289-1292
8. Cashmore AR, Jarillo JA, Wu YJ, Liu D (1999) Cryptochromes: blue light receptors for plants and animals. Science 284: 760-765
9. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I (1998) The transcriptional program of sporulation in budding yeast. Science 282: 699-705
10. Cohen BA, Mitra RD, Hughes JD, Church GM (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26: 183-186
11. Cui X, Churchill GA (2003) Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 4: 210
12. Deng XW, Quail PH (1999) Signalling in light-controlled development. Semin Cell Dev Biol 10: 121-129
13. Eeau K (1977) Anatomy of Seed Plants, Ed 2. John Wiley & Sons, New York
14. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868
15. Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nat Genet 25: 25-29
16. Goldberg RB (1988) Plants: novel developmental processes. Science 240: 1460-1467
17. Goldberg RB, Barker SJ (1989) Regulation of gene expression during plant embryogenesis. Cell 56: 149-160
18. Goldberg RB, Hoschek G, Kamalay JC, Timberlake WE (1978) Sequence complexity of nuclear and polysomal RNA in leaves of the tobacco plant. Cell 14: 123-131
19. Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev 8: 1548-1560
20. 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
21. Jiao Y, Yang H, Ma L, Sun N, Yu H, Liu T, Gao Y, Gu H, Chen Z, Wada M, et al (2003) A genome-wide analysis of blue-light regulation of Arabidopsis transcription factor gene expression during seedling development. Plant Physiol 133: 1480-1493
22. Kamalay JC, Goldberg RB (1980) Regulation of structural gene expression in tobacco. Cell 19: 935-946
23. Kendrick RE, Kronenberg GHM (1994) Photomorphogenesis in Plants, Ed 2. Kluwer Academic Publishers, Dordrecht, The Netherlands
24. Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31: 180-183
25. Li Y, Jones L, McQueen-Mason S (2003) Expansins and cell growth. Curr Opin Plant Biol 6: 603-610
26. Ma L, Gao Y, Qu L, Chen Z, Li J, Zhao H, Deng XW (2002) Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14: 2383-2398
27. Ma L, Li J, Qu L, Hager J, Chen Z, Zhao H, Deng XW (2001) Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2607
28. Ma L, Zhao H, Deng XW (2003) Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development. Development 130: 969-981
29. Mandel MA, Gustafson-Brown C, Savidge B, Yanofsky MF (1992) Molecular characterization of the Arabidopsis floral homeotic gene APETALA1. Nature 360: 273-277
30. Martinez-Zapater JM, Salinas J (1998) Arabidopsis Protocols. Humana Press, Totowa, NJ, pp 27-30
31. Masucci JD, Rerie WG, Foreman DR, Zhang M, Galway ME, Marks MW, Schiefelbein JW (1996) The homeobox gene GLABRA2 is required for position-dependent cell differentiation in the root epidermis of Arabidopsis thaliana. Development 122: 1253-1260
32. Meyerowitz EM (2002) Plants compared to animals: the broadest comparative study of development. Science 295: 1482-1485
33. Neff MM, Fankhauser C, Chory J (2000) Light: an indicator of time and place. Genes Dev 14: 257-271
34. Quail PH (2002) Phytochrome photosensory signalling networks. Nat Rev Mol Cell Biol 3: 85-93
35. Reiser L, Modrusan Z, Margossian L, Samach A, Ohad N, Haughn GW, Fischer RL (1995) The BELL1 gene encodes a homeodomain protein involved in pattern formation in the Arabidopsis ovule primordium. Cell 83: 735-742
36. Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
37. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, et al (2003) The transcriptional activity of human Chromosome 22. Genes Dev 17: 529-540
38. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470
39. Somers DE, Quail PH (1995) Temporal and spatial expression patterns of PHYA and PHYB genes in Arabidopsis. Plant J 7: 413-427
40. Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1: 1-8
41. Tepperman JM, Zhu T, Chang HS, Wang X, Quail PH (2001) Multiple transcription-factor genes are early targets of phytochrome A signaling. Proc Natl Acad Sci USA 98: 9437-9442
42. Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15: 1749-1770
43. Wada T, Tachibana T, Shimura Y, Okada K (1997) Epidermal cell differentiation in Arabidopsis determined by a Myb homolog CPC. Science 277: 1113-1116
44. Wang Z, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EM (1997) A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9: 491-507
45. 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
46. Wu H, Kerr K, Cui X, Churchill GA (2003) MAANOVA: a software package for the analysis of spotted cDNA microarray experiments. In G Parmigiani, ES Garett, RA Irizarry, SL Zeger, eds, The Analysis of Gene Expression Data: Methods and Software. Springer-Verlag, Heidelberg, Germany, pp 313-341
47. Yamada K, Lim J, Dale JM, Chen H, Shinn P, Palm CJ, Southwick AM, Wu HC, Kim C, Nguyen M, et al (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846
48. Yanofsky MF, Ma H, Bowman JL, Feldmann GN, Meyerowitz EM (1990) The protein encoded by the Arabidopsis homeotic gene agamous resembles transcription factors. Nature 346: 35-39
49. Zhu T, Buwworth P, Han B, Brown D, Chang HS, Zou G, Wang X (2001) Toward elucidating the global gene expression patterns of developing Arabidopsis: parallel analysis of 8300 genes by a high-density oligonucleotide probe array. Plant Physiol Biochem 39: 221-242