The Arabidopsis Co-expression Tool, ACT, ranks the genes across a large microarray dataset according to how closely their expression follows the expression of a query gene. A database stores pre-calculated co-expression results for approximately 21,800 genes based on data from over 300 arrays. These results can be corroborated by calculation of co-expression results for user-defined sub-sets of arrays or experiments from the NASC/GARNet array dataset. Clique Finder (CF) identifies groups of genes which are consistently co-expressed with each other across a user-defined co-expression list. The parameters can be altered easily to adjust cluster size and the output examined for optimal inclusion of genes with known biological roles. Alternatively, a Scatter Plot tool displays the correlation coefficients for all genes against two user-selected queries on a scatter plot which can be useful for visual identification of clusters of genes with similar r-values. User-input groups of genes can be highlighted on the scatter plots. Inclusion of genes with known biology in sets of genes identified using CF and Scatter Plot tools allows inferences to be made about the roles of the other genes in the set and both tools can therefore be used to generate short lists of genes for further characterization. ACT is freely available at www.Arabidopsis.leeds.ac.uk/ACT.

Summary: The herbicide isoxaben is a highly specific and potent inhibitor of cellulose synthesis in plants. Nevertheless, suspension‐cultured cells can be habituated to grow in high concentrations of isoxaben, and apparently compensate for the disruption of cellulose synthesis by the modulation of other cell wall components. We have habituated Arabidopsis cells to isoxaben and characterized the cellular and genetic consequences. Near whole‐genome transcript profiling implicated novel genes in cell wall assembly and extended our understanding of the activity of known cell wall‐related genes including glycosyltransferases involved in cellulose and pectin biosynthesis. Habituation does not appear to be mediated by stress response processes, nor by functional redundancy within the cellulose synthase (AtCesA) family. Uniquely, amongst the cellulose synthase superfamily, AtCslD5 was highly upregulated and may play a role in the biosynthesis of the novel walls of habituated cells. In silico analysis of differentially expressed genes with unknown functions identified a putative glycosyltransferase and collagen‐like putative cell wall protein.

In vitro analyses of plant GATA transcription factors have implicated some proteins in light-mediated and circadian-regulated gene expression, and, more recently, the analysis of mutants has uncovered further diverse roles for plant GATA factors. To facilitate function discovery for the 29 GATA genes in Arabidopsis (Arabidopsis thaliana), we have experimentally verified gene structures and determined expression patterns of all family members across adult tissues and suspension cell cultures, as well as in response to light and signals from the circadian clock. These analyses have identified two genes that are strongly developmentally light regulated, expressed predominantly in photosynthetic tissue, and with transcript abundance peaking before dawn. In contrast, several GATA factor genes are light down-regulated. The products of these light-regulated genes are candidates for those proteins previously implicated in light-regulated transcription. Coexpression of these genes with well-characterized light-responsive transcripts across a large microarray data set supports these predictions. Other genes show additional tissue-specific expression patterns suggesting novel and unpredicted roles. Genome-wide analysis using coexpression scatter plots for paralogous gene pairs reveals unexpected differences in cocorrelated gene expression profiles. Clustering the Arabidopsis GATA factor gene family by similarity of expression patterns reveals that genes of recent descent do not uniformly show conserved current expression profiles, yet some genes showing more distant evolutionary origins have acquired common expression patterns. In addition to defining developmental and environmental dynamics of GATA transcript abundance, these analyses offer new insights into the evolution of gene expression profiles following gene duplication events.

Using cross-linking coupled to matrix-assisted laser desorption/ionization mass spectrometry and CLIP-Seq sequencing, we determined the peptide and oligonucleotide sequences at the interfaces between the capsid proteins and the genomic RNA of bacteriophage MS2. The results suggest that the same coat protein (CP)-RNA and maturation protein (MP)-RNA interfaces are used in every viral particle. The portions of the viral RNA in contact with CP subunits span the genome, consistent with a large number of discrete and similar contacts within each particle. Many of these sites match previous predictions of the locations of multiple, dispersed and degenerate RNA sites with cognate CP affinity termed packaging signals (PSs). Chemical RNA footprinting was used to compare the secondary structures of protein-free genomic fragments and the RNA in the virion. Some PSs are partially present in protein-free RNA but others would need to refold from their dominant solution conformations to form the contacts identified in the virion. The RNA-binding peptides within the MP map to two sections of the N-terminal half of the protein. Comparison of MP sequences from related phages suggests a similar arrangement of RNA-binding sites, although these N-terminal regions have only limited sequence conservation. In contrast, the sequences of the C-termini are highly conserved, consistent with them encompassing pilin-binding domains required for initial contact with host cells. These results provide independent and unambiguous support for the assembly of MS2 virions via a PS-mediated mechanism involving a series of induced-fit viral protein interactions with RNA.