Abstract
BackgroundMicroarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix™ ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants.ResultsWe used bioinformatics methods to analyze publicly available data obtained using the ATH1 chip from Affymetrix. A total of 1887 ATH1 hybridizations were normalized and filtered to eliminate low-quality hybridizations. We classified and compared control and treatment hybridizations and determined differential gene expression. The largest differences in gene expression were observed when comparing samples obtained from different organs. On average, ten-fold more genes were differentially expressed between organs as compared to any other experimental variable. We defined "gene responsiveness" as the number of comparisons in which a gene changed its expression significantly. We defined genes with the highest and lowest responsiveness levels as hypervariable and housekeeping genes, respectively. Remarkably, housekeeping genes were best distinguished from hypervariable genes by differences in methylation status in their transcribed regions. Moreover, methylation in the transcribed region was inversely correlated (R2 = 0.8) with gene responsiveness on a genome-wide scale. We provide an example of this negative relationship using genes encoding TCA cycle enzymes, by contrasting their regulatory responsiveness to nitrate and methylation status in their transcribed regions.ConclusionOur results indicate that the Arabidopsis transcriptome is largely established during development and is comparatively stable when faced with external perturbations. We suggest a novel functional role for DNA methylation in the transcribed region as a key determinant capable of restraining the capacity of a gene to respond to internal/external cues. Our findings suggest a prominent role for epigenetic mechanisms in the regulation of gene expression in plants.
Highlights
Microarray technology is a widely used approach for monitoring genome-wide gene expression
The Arabidopsis transcriptome is robust to most perturbations but strongly influenced by organ type In an effort to discover new principles that govern gene expression in Arabidopsis thaliana, we integrated and analyzed publicly available whole-genome microarray data for this model plant
The second part of our analysis provided a weighted insight into the role of different molecular mechanisms in the global regulation of gene expression in Arabidopsis
Summary
Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on AffymetrixTM ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants. A large amount of microarray data representing many different biological conditions has accumulated over recent years This data has been used successfully to hypothesize on gene function on a global scale in different organisms, such as yeast and C. elegans [5,6,7], and to suggest shared regulatory mechanisms. We believe that this data has been underutilized as a resource to understand the basic rules of gene expression
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