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Kenneth Birnbaum,1Dennis E. Shasha,2Jean Y. Wang,3Jee W. Jung,1Georgina M. Lambert,4David W. Galbraith,4Philip N. Benfey3*
A global map of gene expression within an organ can identifygenes with coordinated expression in localized domains, therebyrelating gene activity to cell fate and tissue specialization.Here, we present localization of expression of more than 22,000genes in the Arabidopsis root. Gene expression was mapped to15 different zones of the root that correspond to cell typesand tissues at progressive developmental stages. Patterns ofgene expression traverse traditional anatomical boundaries andshow cassettes of hormonal response. Chromosomal clusteringdefined some coregulated genes. This expression map correlatesgroups of genes to specific cell fates and should serve to guidereverse genetics.
1 Department of Biology, New York University, New York, NY 10003, USA. 2 Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA. 3 Department of Biology, Duke University, Box 91000, Durham, NC 27708, USA. 4 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
* To whom correspondence should be addressed. E-mail: philip.benfey{at}duke.edu
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Science
320, 942-945
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Plant Physiology
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Genome-Enabled Approaches Shed New Light on Plant Metabolism.
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Plant Physiology
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PNAS
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To grow or not to grow: what can we learn on ethylene-gibberellin cross-talk by in silico gene expression analysis?.
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PLANT CELL
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318, 801-806
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Plant Physiology
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Plant Physiology
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PNAS
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Plant Physiology
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PLANT CELL
19, 1838-1850
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From the Cover: A gene essential for hydrotropism in roots.
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PNAS
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Development
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M. W.B. Spencer, S. A. Casson, and K. Lindsey (2007)
Plant Physiology
143, 924-940
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58, 279-289
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Cell Type-Specific Gene Expression Profiling in Plants by Using a Combination of Laser Microdissection and High-Throughput Technologies.
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48, 3-7
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Interactions among PIN-FORMED and P-Glycoprotein Auxin Transporters in Arabidopsis.
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PLANT CELL
19, 131-147
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The Acyltransferase GPAT5 Is Required for the Synthesis of Suberin in Seed Coat and Root of Arabidopsis.
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PLANT CELL
19, 351-368
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The Arabidopsis NRT1.1 transporter participates in the signaling pathway triggering root colonization of nitrate-rich patches.
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PNAS
103, 19206-19211
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PLANT CELL
18, 3502-3518
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SIAMESE, a Plant-Specific Cell Cycle Regulator, Controls Endoreplication Onset in Arabidopsis thaliana.
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PLANT CELL
18, 3145-3157
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CER4 Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis.
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Plant Physiology
142, 866-877
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Unraveling the dynamic transcriptome..
S. M. Brady, T. A. Long, and P. N. Benfey (2006)
PLANT CELL
18, 2101-2111
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The CLAVATA3/ESR Motif of CLAVATA3 Is Functionally Independent from the Nonconserved Flanking Sequences.
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Plant Physiology
141, 1284-1292
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From the Cover: AtALMT1, which encodes a malate transporter, is identified as one of several genes critical for aluminum tolerance in Arabidopsis.
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PNAS
103, 9738-9743
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Expression Profiling of Auxin-treated Arabidopsis Roots: Toward a Molecular Analysis of Lateral Root Emergence.
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47, 788-792
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SCARFACE Encodes an ARF-GAP That Is Required for Normal Auxin Efflux and Vein Patterning in Arabidopsis.
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PLANT CELL
18, 1396-1411
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LucTrap Vectors Are Tools to Generate Luciferase Fusions for the Quantification of Transcript and Protein Abundance in Vivo..
L. I. A. Calderon-Villalobos, C. Kuhnle, H. Li, M. Rosso, B. Weisshaar, and C. Schwechheimer (2006)
Plant Physiology
141, 3-14
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PNAS
103, 6055-6060
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Arabidopsis TEBICHI, with Helicase and DNA Polymerase Domains, Is Required for Regulated Cell Division and Differentiation in Meristems.
S. Inagaki, T. Suzuki, M.-a. Ohto, H. Urawa, T. Horiuchi, K. Nakamura, and A. Morikami (2006)
PLANT CELL
18, 879-892
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M. S. Pischke, E. L. Huttlin, A. D. Hegeman, and M. R. Sussman (2006)
Plant Physiology
140, 1255-1278
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Progressive Inhibition by Water Deficit of Cell Wall Extensibility and Growth along the Elongation Zone of Maize Roots Is Related to Increased Lignin Metabolism and Progressive Stelar Accumulation of Wall Phenolics.
L. Fan, R. Linker, S. Gepstein, E. Tanimoto, R. Yamamoto, and P. M. Neumann (2006)
Plant Physiology
140, 603-612
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The Arabidopsis genome: A foundation for plant research.
Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana.
P. J. Overvoorde, Y. Okushima, J. M. Alonso, A. Chan, C. Chang, J. R. Ecker, B. Hughes, A. Liu, C. Onodera, H. Quach, et al. (2005)
PLANT CELL
17, 3282-3300
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M. C. Suh, A. L. Samuels, R. Jetter, L. Kunst, M. Pollard, J. Ohlrogge, and F. Beisson (2005)
Plant Physiology
139, 1649-1665
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Multiple Type-B Response Regulators Mediate Cytokinin Signal Transduction in Arabidopsis.
M. G. Mason, D. E. Mathews, D. A. Argyros, B. B. Maxwell, J. J. Kieber, J. M. Alonso, J. R. Ecker, and G. E. Schaller (2005)
PLANT CELL
17, 3007-3018
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Plant Physiology
139, 1255-1267
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Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis.
C.-R. Xu, C. Liu, Y.-L. Wang, L.-C. Li, W.-Q. Chen, Z.-H. Xu, and S.-N. Bai (2005)
PNAS
102, 14469-14474
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A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
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46, 1202-1212
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Transcriptional Profile of the Arabidopsis Root Quiescent Center.
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PLANT CELL
17, 1908-1925
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The Maize Root Transcriptome by Serial Analysis of Gene Expression.
V. Poroyko, L.G. Hejlek, W.G. Spollen, G.K. Springer, H.T. Nguyen, R.E. Sharp, and H.J. Bohnert (2005)
Plant Physiology
138, 1700-1710
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Developmental Networks.
P. N. Benfey (2005)
Plant Physiology
138, 548-549
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Systems Biology for the Virtual Plant.
R. A. Gutierrez, D. E. Shasha, and G. M. Coruzzi (2005)
Plant Physiology
138, 550-554
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Small RNAs and Arabidopsis. A Fast Forward Look.
J. C. Carrington (2005)
Plant Physiology
138, 565-566
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High-Throughput RNA Isolation Technologies. New Tools for High-Resolution Gene Expression Profiling in Plant Systems.
J.-Y. Lee, M. Levesque, and P. N. Benfey (2005)
Plant Physiology
138, 585-590
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Immunopurification of Polyribosomal Complexes of Arabidopsis for Global Analysis of Gene Expression.
M. E. Zanetti, I.-F. Chang, F. Gong, D. W. Galbraith, and J. Bailey-Serres (2005)
Plant Physiology
138, 624-635
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Genome-Wide Analysis of Gene Expression Profiles Associated with Cell Cycle Transitions in Growing Organs of Arabidopsis.
G. T.S. Beemster, L. De Veylder, S. Vercruysse, G. West, D. Rombaut, P. Van Hummelen, A. Galichet, W. Gruissem, D. Inze, and M. Vuylsteke (2005)
Plant Physiology
138, 734-743
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Genome-Wide Identification of Genes Expressed in Arabidopsis Pistils Specifically along the Path of Pollen Tube Growth.
C.-W. Tung, K. G. Dwyer, M. E. Nasrallah, and J. B. Nasrallah (2005)
Plant Physiology
138, 977-989
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Arabidopsis thickvein Mutation Affects Vein Thickness and Organ Vascularization, and Resides in a Provascular Cell-Specific Spermine Synthase Involved in Vein Definition and in Polar Auxin Transport.
