Access the full text.
Sign up today, get DeepDyve free for 14 days.
G. Cardon, S. Höhmann, J. Klein, Klaus Nettesheim, H. Saedler, P. Huijser (1999)
Molecular characterisation of the Arabidopsis SBP-box genes.Gene, 237 1
K. Wilson, D. Long, J. Swinburne, G. Coupland (1996)
A Dissociation insertion causes a semidominant mutation that increases expression of TINY, an Arabidopsis gene related to APETALA2.The Plant cell, 8
J. Kamalay, R. Goldberg (1980)
Regulation of structural gene expression in tobaccoCell, 19
Susan Fujimoto, Masaru Ohta, A. Usui, H. Shinshi, M. Ohme-Takagi (2000)
Arabidopsis Ethylene-Responsive Element Binding Factors Act as Transcriptional Activators or Repressors of GCC Box–Mediated Gene ExpressionPlant Cell, 12
C. Ramakers, J. Ruijter, R. Deprez, A. Moorman (2003)
Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) dataNeuroscience Letters, 339
Ji Huang, Hongsheng Zhang, Dong Wang, Ya-Jun Cao, Jin-shui Yang (2002)
[Serial analysis of gene expression].Yi chuan = Hereditas, 24 2
D. Lockhart, Helin Dong, M. Byrne, M. Follettie, Michael Gallo, M. Chee, Mike Mittmann, Chunwei Wang, M. Kobayashi, Heidi Norton, E. Brown (1996)
Expression monitoring by hybridization to high-density oligonucleotide arraysNature Biotechnology, 14
S. Brenner, Maria Johnson, J. Bridgham, G. Golda, D. Lloyd, David Johnson, Shujun Luo, S. Mccurdy, M. Foy, Mark Ewan, Rithy Roth, Dave George, S. Eletr, G. Albrecht, Eric Vermaas, Steven Williams, Keith Moon, T. Burcham, Michael Pallas, R. Dubridge, James Kirchner, K. Fearon, J. Mao, K. Corcoran (2000)
Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arraysNature Biotechnology, 18
M. Holland (2002)
Transcript Abundance in Yeast Varies over Six Orders of Magnitude*The Journal of Biological Chemistry, 277
Shin-Han Shiu, A. Bleecker (2001)
Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinasesProceedings of the National Academy of Sciences of the United States of America, 98
S. Sawa, Toshiro Ito, Y. Shimura, K. Okada (1999)
FILAMENTOUS FLOWER Controls the Formation and Development of Arabidopsis Inflorescences and Floral MeristemsPlant Cell, 11
Ratcliffe (2002)
77Curr. Issues Mol. Biol., 4
S. Rounsley, G. Ditta, M. Yanofsky (1995)
Diverse roles for MADS box genes in Arabidopsis development.The Plant cell, 7
J.L. Riechmann (2002)
The Arabidopsis BookScience
K. Mayer, H. Schoof, Achim Haecker, Michael Lenhard, G. Jürgens, T. Laux (1998)
Role of WUSCHEL in Regulating Stem Cell Fate in the Arabidopsis Shoot MeristemCell, 95
Burgeff (2002)
365Planta, 214
J. Riechmann (2002)
Transcriptional Regulation: a Genomic OverviewThe arabidopsis book, 1
Joaquı́n Medina, M. Bargues, Javier Terol, M. Perez-Alonso, Julio Salinas (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 physiology, 119 2
J. Long, E. Moan, J. Medford, M. Barton (1996)
A member of the KNOTTED class of homeodomain proteins encoded by the STM gene of ArabidopsisNature, 379
J. Riechmann, Jacqueline Heard, George Martin, T. Reuber, C. Jiang, J. Keddie, L. Adam, O. Pineda, O. Ratcliffe, Raymond Samaha, R. Creelman, M. Pilgrim, P. Broun, James Zhang, D. Ghandehari, B. Sherman, Guo-Liang Yu (2000)
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.Science, 290 5499
Yijun Ruan, J. Gilmore, T. Conner (1998)
Towards Arabidopsis genome analysis: monitoring expression profiles of 1400 genes using cDNA microarrays.The Plant journal : for cell and molecular biology, 15 6
W. Chen, N. Provart, J. Glazebrook, F. Katagiri, Hur-Song Chang, T. Eulgem, F. Mauch, S. Luan, Guangzhou Zou, S. Whitham, P. Budworth, Yi Tao, Zhiyi Xie, Xi Chen, Steve Lam, J. Kreps, J. Harper, Azzedine Si-Ammour, B. Mauch-Mani, M. Heinlein, K. Kobayashi, T. Hohn, J. Dangl, Xun Wang, Tong Zhu (2002)
Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental StressesThe Plant Cell Online, 14
O. Ratcliffe, J. Riechmann (2002)
Arabidopsis transcription factors and the regulation of flowering time: a genomic perspective.Current issues in molecular biology, 4 3
K. Siegfried, Y. Eshed, S. Baum, Denichiro Otsuga, G. Drews, J. Bowman (1999)
Members of the YABBY gene family specify abaxial cell fate in Arabidopsis.Development, 126 18
D. Weigel, J. Alvarez, D. Smyth, M. Yanofsky, E. Meyerowitz (1992)
LEAFY controls floral meristem identity in ArabidopsisCell, 69
R. Davuluri, Hao Sun, Saranyan Palaniswamy, Nicole Matthews, Carlos Molina, M. Kurtz, E. Grotewold (2003)
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factorsBMC Bioinformatics, 4
G. Cardon, S. Höhmann, Klaus Nettesheim, H. Saedler, P. Huijser (1997)
Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition.The Plant journal : for cell and molecular biology, 12 2
E. Huq, P. Quail (2002)
PIF4, a phytochrome‐interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in ArabidopsisThe EMBO Journal, 21
Z. Shinwari, K. Nakashima, S. Miura, M. Kasuga, M. Seki, K. Yamaguchi-Shinozaki, Kazuo Shinozaki (1998)
An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low-temperature-responsive gene expression.Biochemical and biophysical research communications, 250 1
S. Liljegren, G. Ditta, Y. Eshed, Beth Savidge, J. Bowman, M. Yanofsky (2000)
SHATTERPROOF MADS-box genes control seed dispersal in ArabidopsisNature, 404
S. Pelaz, G. Ditta, Elvira Baumann, E. Wisman, M. Yanofsky (2000)
B and C floral organ identity functions require SEPALLATA MADS-box genesNature, 405
R. Lipshutz, S. Fodor, T. Gingeras, D. Lockhart (1999)
High density synthetic oligonucleotide arraysNature Genetics, 21 Suppl 1
T. Murashige, F. Skoog (1962)
A revised medium for the growth and bioassay with tobacco tissue culture
C. Burgeff, S.J. Liljegren, R. Tapia‐Lopez, M.F. Yanofsky, E.R. Alvarez‐Buylla (2002)
MADS‐box gene expression in lateral primordia, meristems and differentiated tissues of Arabidopsis thaliana rootsPlanta, 214
T. Murashige, Skoog F. (1962)
A revised medium for rapid growth and bioassays with tobacco tissue cultures.Physiol. Plant., 15
M. Pfaffl (2001)
A new mathematical model for relative quantification in real-time RT-PCR.Nucleic acids research, 29 9
N. Quaedvlieg, J. Dockx, Fred Rook, P. Weisbeek, S. Smeekens (1995)
The homeobox gene ATH1 of Arabidopsis is derepressed in the photomorphogenic mutants cop1 and det1.The Plant cell, 7
Murashige (1962)
473Physiol. Plant., 15
M. Kiper (1979)
Gene numbers as measured by single-copy DNA saturation with mRNA are routinely overestimatesNature, 278
The Initiative (2000)
Analysis of the genome sequence of the flowering plant Arabidopsis thalianaNature, 408
B. Haas, N. Volfovsky, C. Town, Maxim Troukhan, N. Alexandrov, K. Feldmann, R. Flavell, O. White, S. Salzberg (2002)
Full-length messenger RNA sequences greatly improve genome annotationGenome Biology, 3
T. Yamashino, A. Matsushika, Toru Fujimori, Shusei Sato, Tomohiko Kato, S. Tabata, T. Mizuno (2003)
A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.Plant & cell physiology, 44 6
J. Putterill, F. Robson, Karen Lee, R. Simon, G. Coupland (1995)
The CONSTANS gene of arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factorsCell, 80
C. Horak, M. Snyder (2002)
Global analysis of gene expression in yeastFunctional & Integrative Genomics, 2
S. Brenner, Steven Williams, Eric Vermaas, Thorsten Storck, Keith Moon, C. Mccollum, J. Mao, Shujun Luo, J. Kirchner, S. Eletr, R. Dubridge, T. Burcham, G. Albrecht (2000)
In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs.Proceedings of the National Academy of Sciences of the United States of America, 97 4
E. Álvarez-Buylla, E. Álvarez-Buylla, S. Liljegren, S. Pelaz, S. Gold, C. Burgeff, G. Ditta, Francisco Vergara-Silva, M. Yanofsky (2000)
MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes.The Plant journal : for cell and molecular biology, 24 4
S. Sawa, T. Ito, Y. Shimura, K. Okada (1999)
FILAMENTOUS FLOWER controls the formation and development of Arabidopsis inflorescences and floral meristemsBiochem. Biophys. Res. Commun., 11
Z.K. Shinwari, K. Nakashima, S. Miura, M. Kasuga, M. Seki, K. Yamaguchi‐Shinozaki, K. Shinozaki (1998)
An Arabidopsis gene family encoding DRE/CRT binding proteins involved in low‐temperature‐responsive gene expressionProc. Natl. Acad. Sci. USA, 250
C. Hardtke, T. Berleth (1998)
The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular developmentThe EMBO Journal, 17
To overcome the detection limits inherent to DNA array‐based methods of transcriptome analysis, we developed a real‐time reverse transcription (RT)‐PCR‐based resource for quantitative measurement of transcripts for 1465 Arabidopsis transcription factors (TFs). Using closely spaced gene‐specific primer pairs and SYBR® Green to monitor amplification of double‐stranded DNA (dsDNA), transcript levels of 83% of all target genes could be measured in roots or shoots of young Arabidopsis wild‐type plants. Only 4% of reactions produced non‐specific PCR products. The amplification efficiency of each PCR was determined from the log slope of SYBR® Green fluorescence versus cycle number in the exponential phase, and was used to correct the readout for each primer pair and run. Measurements of transcript abundance were quantitative over six orders of magnitude, with a detection limit equivalent to one transcript molecule in 1000 cells. Transcript levels for different TF genes ranged between 0.001 and 100 copies per cell. Only 13% of TF transcripts were undetectable in these organs. For comparison, 22K Arabidopsis Affymetrix chips detected less than 55% of TF transcripts in the same samples, the range of transcript levels was compressed by a factor more than 100, and the data were less accurate especially in the lower part of the response range. Real‐time RT‐PCR revealed 35 root‐specific and 52 shoot‐specific TF genes, most of which have not been identified as organ‐specific previously. Finally, many of the TF transcripts detected by RT‐PCR are not represented in Arabidopsis EST (expressed sequence tag) or Massively Parallel Signature Sequencing (MPSS) databases. These genes can now be annotated as expressed.
The Plant Journal – Wiley
Published: Apr 1, 2004
Keywords: ; ; ; ; ;
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.