Robert WM Sablowski, John Innes Centre, Norwich, UK
Published online: April 2007
DOI: 10.1002/9780470015902.a0002664.pub2
Changes in gene expression are central to plant development and environmental responses, and to modifying plants for practical use. Gene regulation is similar in plants and other eukaryotes, so most of the methods to study it are also comparable, including the recent emphasis on genome-wide approaches.
Keywords: expression array; cis-element; transcription factors
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Figure 1. Top view of an Arabidopsis inflorescence, showing the expression of a reporter gene (blue colour) in the stamens of developing floral buds. The reporter gene contains the coding sequence of the GUS protein, controlled by the regulatory sequences of a gene normally expressed in the developing stamens. The inflorescence has been incubated with a substrate that forms a blue precipitate after it is hydrolysed by the GUS enzyme. After this reaction, the inflorescence was treated with ethanol to remove chlorophyll and facilitate detection of the blue precipitate.
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Figure 2. Schematic view of the chromatin immunoprecipitation (ChIP) procedure. (a) In a living cell, the transcription factor (TF) under study is associated with specific DNA sequences within its target genes (marked in red). (b) The cell is treated with formaldehyde, which crosslinks the TF and the DNA with which it is in contact. (c) After crosslinking, the DNA is extracted and fragmented. (d) antibodies (in green) that recognize specifically the TF are used to precipitate the TF with its associated DNA. (e) A chemical treatment reverts the crosslinking to the TF and releases the precipitated DNA for subsequent analysis.
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Figure 3. Diagram showing how a two-component system is used to activate a gene in specific tissues of the plant. The ‘driver’ (top panel) is a transgene in which a tissue specific promoter controls the expression of an artificial transcription factor (TF). A plant containing the driver is crossed to another plant containing the ‘effector’ transgene, in which the expression of a gene of interest (marked in red) is controlled by a promoter that is normally inactive, but can be activated in the presence of the TF encoded by the driver. After crossing a plant containing the driver to the plant containing the effector, the progeny plants express the gene of interest in the same tissues where the driver is expressed. This is useful to study a gene whose activation in the plant is lethal or causes sterility; in addition, a single effector can be crossed to different drivers to study the effects of expression in different tissues.
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| References | |
| Birnbaum K, Shasha DE, Wang JY et al. (2003) A gene expression map of the Arabidopsis root. Science 302: 1956–1960. | |
| Blanchette M and Tompa M (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 12: 739–748. | |
| Clark RM, Wagler TN, Quijada P and Doebley J (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics 38: 594–597. | |
| Craft J, Samalova M, Baroux C et al. (2005) New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant Journal 41: 899–918. | |
| Freeman WM, Walker SJ and Vrana KE (1999) Quantitative RT-PCR: pitfalls and potential. Biotechniques 26: 112. | |
| Hannon GJ (2002) RNA interference. Nature 418: 244–251. | |
| Hiratsu K, Matsui K, Koyama T and Ohme-Takagi M (2003) Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. The Plant Journal 34: 733–739. | |
| Mccallum CM, Comai L, Greene EA and Henikoff S (2000) Targeted screening for induced mutations. Nature Biotechnology 18: 45–47. | |
| Nakazono M, Qiu F, Borsuk LA and Schnable PS (2003) Laser-capture microdissection, a tool for the global analysis of gene expression in specific plant cell types: identification of genes expressed differentially in epidermal cells or vascular tissues of maize. Plant Cell 15: 583–596. | |
| Parcy F, Nilsson O, Busch MA, Lee I and Weigel D (1998) Genetic framework for floral patterning. Nature 395: 561–566. | |
| Riechmann JL, Heard J, Martin G et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105–2110. | |
| Schaffer R, Landgraf J, Perez-Amador M and Wisman E (2000) Monitoring genomewide expression in plants. Current Opinion Biotechnology 11: 162–167. | |
| Wang H, Tang WN, Zhu C and Perry SE (2002) A chromatin immunoprecipitation (ChIP) approach to isolate genes regulated by AGL15, a MADS domain protein that preferentially accumulates in embryos. Plant Journal 32: 831–843. | |
| Further Reading | |
| Doebley J (2004) The genetics of maize evolution. Annual Review of Genetics 38: 37–59. | |
| Doebley J and Lukens L (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10: 1075–1082. | |
| Riechmann JL, Heard J, Martin G et al. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290: 2105–2110. | |
| Schwechheimer C, Zourelidou M and Bevan MW (1998) Plant transcription factor studies. Annual Review of Plant Physiology and Plant Molecular Biology 49: 127–150. | |
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