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Open Access Highly Accessed Research article

The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

Felipe F Aceituno1, Nick Moseyko2, Seung Y Rhee2 and Rodrigo A Gutiérrez13*

Author Affiliations

1 Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenue Libertador Bernardo O'Higgins 340, Santiago, Chile

2 Department of Plant Biology, Carnegie Institution of Washington, 260 Panama St, Stanford, CA, 94305, USA

3 Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY 10003, USA

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BMC Genomics 2008, 9:438  doi:10.1186/1471-2164-9-438

Published: 23 September 2008

Additional files

Additional File 1:

Control vs. tests comparisons. List of the analyzed 474 comparisons in the NASCarrays database, annotated according to the experimental factor and plant structure categories. NASC experiment numbers are provided.

Format: XLS Size: 163KB Download file

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Additional File 2:

Gene responsiveness by categories. Table detailing the number of experiments, within the eight experimental categories, in which each Arabidopsis gene is regulated. The number in parenthesis in the header of the Table indicates the total number of experiments in each category.

Format: XLS Size: 3.6MB Download file

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Additional file 3:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 52KB Download file

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Additional file 4:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 24KB Download file

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Additional file 5:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 64KB Download file

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Additional file 6:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 63KB Download file

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Additional file 7:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 119KB Download file

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Additional file 8:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 157KB Download file

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Additional file 9:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 160KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 10:

Genes regulated specifically in one experimental category. Each file provides the individual genes responding exclusively in abiotic, biotic, ecotype, chemical, hormone, mutant, nutrient or organ comparisons, respectively.

Format: XLS Size: 380KB Download file

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Additional File 11:

Importance of organ type in the response to abiotic stress in Arabidopsis. Percentage of genes responding to various stresses in either roots, shoots or both. Data corresponds to the AtGenExpress Abiotic Stress series present in the NASCarrays database. The black zone indicates the percentage of genes responding only in roots; the white zone indicates those responding only in shoots, and the black squares region indicates the genes responding in both tissues

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Additional file 12:

Gene responsiveness. Gene responsiveness as determined by the Rank Products and fold-change method.

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Additional file 13:

Housekeeping and hypervariable genes and their methylation status (1). List of Housekeeping and hypervariable genes, classified according their methylation status as defined in:Zhang X, et al: Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 2006, 126(6): 1189–1201. Gene annotation was provided by the VirtualPlant system http://www.virtualplant.org webcite.

Format: XLS Size: 61KB Download file

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Additional file 14:

Housekeeping and hypervariable genes and their methylation status (2). List of Housekeeping and hypervariable genes, classified according their methylation status as defined in: Zilberman et al: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 2007, 39(1): 61–69. Gene annotation was provided by the VirtualPlant system http://www.virtualplant.org webcite

Format: XLS Size: 49KB Download file

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Additional file 15:

Function of housekeeping and hypervariable genes. Analysis of over-representation of gene ontology functional terms in housekeeping and hypervariable genes (performed in VirtualPlant – http://www.virtualplant.org webcite

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Additional file 16:

Enrichment of cis-acting motifs in the promoter of hypervariable genes. Frequency distribution of the number of predicted transcription binding sites in the promoter of housekeeping and hypervariable genes and the whole genome. The genes were ranked according to the number of cis-acting regulatory elements in their promoters according to the AGRIS database (X-axis). The points represent the fraction of genes in a bin of 10 motifs.

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Additional file 17:

Correlation between gene responsiveness as determined by the fold-change method and gene body methylation. Table listing gene responsiveness as determined by the fold-change method (≥ |2|), and the corresponding frequencies of methylated genes.

Format: XLS Size: 28KB Download file

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Additional file 18:

Plot of the correlation between gene responsiveness determined by the fod-change method versus gene body methylation. This graphs shows the linear correlation between gene responsiveness as determined by fold change ((≥ |2|) and gene body methylation.

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Additional file 19:

Results of simple regression models, given by experimental category. Description is as Table 2, see main text.

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Additional file 20:

ANOVA models for the effect of methylation and TATA-box presence on gene responsiveness, by category of experimental treatment. The models have the form Y ~ aX + b, where X was a factor encoding the presence or absence of those features as two different levels. We used the 'aov' function in R to fit the model. The F statistic estimates the significance of the contribution of the factors to the response. The differences between the levels of the factors were estimated by the Tukey procedure, using the 'glht' function from the 'multcomp' package in R. This is equivalent to comparing the coefficients of the factors. The Bayesian Information Criteria was calculated in R using the 'BIC' function in the package 'nlme'. This parameter represents the "a posteriori" probability of the model to be true, being maximized when the magnitude of the parameter is minimized.

Format: XLS Size: 28KB Download file

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Additional file 21:

Lack of linear correlation between expression levels and gene responsiveness. Box plot of the signal of a gene across the whole NASC arrays dataset (X-axis) versus gene responsiveness (the number of comparisons in which it is significantly regulated, Y-axis). A simple linear regression model cannot explain the variability in the data (R2 = 0.04).

Format: PDF Size: 3KB Download file

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