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Published on December 22, 2006; 10.1104/pp.106.087668

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Received July 31, 2006
Accepted December 7, 2006

Transcriptional Profiling of the Arabidopsis Embryo

Matthew W.B. Spencer , Stuart A. Casson , and Keith Lindsey *

The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK

* Corresponding author; email: keith.lindsey{at}durham.ac.uk.

We have used laser-capture microdissection to isolate RNA from discrete tissues of globular-, heart- and torpedo-stage embryos of Arabidopsis. This was amplified, and analysed by DNA microarray using the Affymetrix ATH1 GeneChip, representing ca. 22,800 Arabidopsis genes. Cluster analysis showed that spatial differences in gene expression were less significant than temporal differences. Time-course analysis reveals the dynamics and complexity of gene expression in both apical and basal domains of the developing embryo, with several classes of synexpressed genes identifiable. The transition from globular- to heart-stage is associated in particular with an up-regulation of genes involved in cell cycle control, transcriptional regulation and energetics and metabolism. The transition from heart- to torpedo-stage is associated with a repression of cell cycle genes and an up-regulation of genes encoding storage proteins, and pathways of cell growth, energy and metabolism. The torpedo-stage embryo shows strong functional differentiation in the root and cotyledon, as inferred from the classes of genes expressed in these tissues. The time-course of expression of the essential EMB genes shows that most are expressed at unchanging levels across all stages of embryogenesis. We show how identified genes can be used to generate cell type-specific markers and promoter activities, for future application in cell biology.




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