Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: Unprecedented sensitivity reveals novel root-and shoot-specific genes

Plant Journal

Volumn 38, Issue 2, 2004, Pages 366-379

  Czechowski, Tomasz ^a   Bari, Rajendra P ^a   Stitt, Mark ^a   Scheible, Wolf Rüdiger ^a   Udvardi, Michael K ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

Arabidopsis; Real time RT PCR; Root; Shoot; Transcript profiling; Transcription factor

Indexed keywords

DNA; FLUORESCENCE; GENES;

EXPONENTIAL PHASE; TRANSCRIPTION FACTORS; TRANSCRIPTS;

PLANTS (BOTANY);

ARABIDOPSIS PROTEIN; COMPLEMENTARY DNA; PLANT DNA; PRIMER DNA; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT; PLANT ROOT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; STATISTICS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; DNA PRIMERS; DNA, COMPLEMENTARY; DNA, PLANT; GENE EXPRESSION PROFILING; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT ROOTS; PLANT SHOOTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION FACTORS;

ARABIDOPSIS; EMBRYOPHYTA;

EID: 1942475192     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2004.02051.x     Document Type: Article

References (42)

1. AGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
2. Alvarez-Buylla, E.R., Liljegren, S.J., Pelaz, S., Gold, S.E., Burgeff, C., Ditta, G.S., Vergara-Silva, F. and Yanofsky, M.F. (2000) MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J. 24, 457-466.
3. Brenner, S., Williams, S.R., Vermaas, E.H. et al. (2000a) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc. Natl. Acad. Sci. USA, 97, 1665-1670.
4. Brenner, S., Johnson, M., Bridgham, J. et al. (2000b) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18, 630-634.
5. Burgeff, C., Liljegren, S.J., Tapia-Lopez, R., Yanofsky, M.F. and Alvarez-Buylla, E.R. (2002) MADS-box gene expression in lateral primordia, meristems and differentiated tissues of Arabidopsis thaliana roots. Planta, 214, 365-372.
6. Cardon, G.H., Hohmann, S., Nettesheim, K., Saedler, H. and Huijser, P. (1997) Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition. Plant J. 12, 367-377.
7. Cardon, G., Hohmann, S., Klein, J., Nettesheim, K., Saedler, H. and Huijser, P. (1999) Molecular characterisation of the Arabidopsis SBP-box genes. Gene, 237, 91-104.
8. Chen, W., Provart, N.J., Glazebrook, J. et al. (2002) Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses. Plant Cell, 14, 559-574.
9. Davuluri, R.V., Sun, H., Palaniswamy, S.K., Matthews, N., Molina, C., Kurtz, M. and Grotewold, E. (2003) AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics, 4, 25.
10. Fujimoto, S.Y., Ohta, M., Usui, A., Shinshi, H. and Ohme-Takagi, M. (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell, 12, 393-404.
11. Haas, B.J., Volfovsky, N., Town, C.D., Troukhan, M., Alexandrov, N., Feldmann, K.A., Flavell, R.B., White, O. and Salzberg, S.L. (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol. 3, 0029.1-0029.12 (Research).
12. Hardtke, C.S. and Berleth, T. (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J. 17, 1405-1411.
13. Holland, M.J. (2002) Transcript abundance in yeast varies over six orders of magnitude. J. Biol. Chem. 277, 14363-14366.
14. Horak, C.E. and Snyder, M. (2002) Global analysis of gene expression in yeast. Funct. Integr. Genomics, 2, 171-180.
15. Huq, E. and Quail, P. (2002) PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J. 15, 2441-2450.
16. Kamalay, J.C. and Goldberg, R.B. (1980) Regulation of structural gene expression in tobacco. Cell, 19, 935-946.
17. Kiper, M. (1979) Gene numbers as measured by single-copy DNA saturation with mRNA are routinely overestimates. Nature, 278, 279-280.
18. Liljegren, S.J., Ditta, G.S., Eshed, Y., Savidge, B., Bowman, J.L. and Yanofsky, M.F. (2000) SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis. Nature, 404, 766-770.
19. Lipshutz, R.J., Fodor, S.P., Gingeras, T.R. and Lockhart, D.J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20-24.
20. Lockhart, D.J., Dong, H., Byrne, M.C. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14, 1675-1680.
21. Long, J.A., Moan, E.I., Medford, J.I. and Barton, M.K. (1996) A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of Arabidopsis. Nature, 379, 66-69.
22. Mayer, K.F., Schoof, H., Haecker, A., Lenhard, M., Jurgens, G. and Laux, T. (1998) Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem. Cell, 95, 805-815.
23. Medina, J., Bargues, M., Terol, J., Perez-Alonso, M. and Salinas, J. (1999) The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol. 119, 463-470.
24. Murashige, T. and F. Skoog (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol. Plant. 15, 473-479
25. Pelaz, S., Ditta, G.S., Baumann, E., Wisman, E. and Yanofsky, M.F. (2000) B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature, 405, 200-203.
26. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucl. Acids Res. 29, e45.
27. Putterill, J., Robson, F., Lee, K., Simon, R. and Coupland, G. (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell, 80, 847-857.
28. Quaedvlieg, N., Dockx, J., Rook, F., Weisbeek, P. and Smeekens, S. (1995) The homeobox gene ATH1 of Arabidopsis is derepressed in the photomorphogenic mutants cop1 and det1. Plant Cell, 7, 117-129.
29. Ramakers, C., Ruijter, J.M., Deprez, R.H. and Moorman, A.F. (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 13, 62-66.
30. Ratcliffe, O.J. and Riechmann, J.L. (2002) Arabidopsis transcription factors and the regulation of flowering time: a genomic perspective. Curr. Issues Mol. Biol. 4, 77-91.
31. Riechmann, J.L. (2002) Transcriptional regulation: a genomic overview (September, 30, 2002). In The Arabidopsis Book (Somerville, C.R., and Meyerowitz E.M., eds), Rockville, MD: American Society of Plant Biologists (doi/10.1199/tab.0085, http://www.aspb.org/publications/Arabidopsis/).
32. Riechmann, J.L., Heard, J., Martin, G. et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
33. Rounsley, S.D., Ditta, G.S. and Yanofsky, M.F. (1995) Diverse roles for MADS box genes in Arabidopsis development. Plant Cell, 7, 1259-1269.
34. Ruan, Y., Gilmore, J. and Conner, T. (1998) Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays. Plant J. 15, 821-833.
35. Sawa, S., Ito, T., Shimura, Y. and Okada, K. (1999) FILAMENTOUS FLOWER controls the formation and development of Arabidopsis inflorescences and floral meristems. Plant Cell, 11, 69-86.
36. Shinwari, Z.K., Nakashima, K., Miura, S., Kasuga, M., Seki, M., Yamaguchi-Shinozaki, K. and Shinozaki, K. (1998) An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression. Biochem. Biophys. Res. Commun. 250, 161-170.
37. Shiu, S.H. and Bleecker, A.B. (2001) Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc. Natl. Acad. Sci. USA, 98, 10763-10768.
38. Siegfried, K.R., Eshed, Y., Baum, S.F., Otsuga, D., Drews, G.N. and Bowman, J.L. (1999) Members of the YABBY gene family specify abaxial cell fate in Arabidopsis. Development, 126, 4117-4128.
39. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
40. Weigel, D., Alvarez, J., Smyth, D.R., Yanofsky, M.F. and Meyerowitz, E.M. (1992) LEAFY controls floral meristem identity in Arabidopsis. Cell, 69, 843-859.
41. Wilson, K., Long, D., Swinburne, J. and Coupland, G. (1996) A dissociation insertion causes a semidominant mutation that increases expression of TINY, an Arabidopsis gene related to APETALA2. Plant Cell, 8, 659-671.
42. Yamashino, T., Matsushika, A., Fujimori, T., Sato, S., Kato, T., Tabata, S. and Mizuno, T. (2003) A link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol. 44, 619-629.