Abstract
Regulated gene expression is an important mechanism for controlling cell cycle progression in yeast and mammals, and genes involved in cell division-related processes often show transcriptional regulation dependent on cell cycle position. Analysis of cell cycle processes in plants has been hampered by the lack of synchronizable cell suspensions for Arabidopsis, and few cell cycle-regulated genes are known. Using a recently described synchrony system, we have analyzed RNA from sequential samples of Arabidopsis cells progressing through the cell cycle using Affymetrix Genearrays. We identify nearly 500 genes that robustly display significant fluctuation in expression, representing the first genomic analysis of cell cycle-regulated gene expression in any plant. In addition to the limited number of genes previously identified as cell cycle-regulated in plants, we also find specific patterns of regulation for genes known or suspected to be involved in signal transduction, transcriptional regulation, and hormonal regulation, including key genes of cytokinin response. Genes identified represent pathways that are cell cycle-regulated in other organisms and those involved in plant-specific processes. The range and number of cell cycle-regulated genes show the close integration of the plant cell cycle into a variety of cellular control and response pathways.
Highlights
Cell division is a fundamental biological process and shares conserved features and controls in all eukaryotes [1,2,3]
Regulated gene expression is an important mechanism for controlling cell cycle progression in yeast and mammals, and genes involved in cell division-related processes often show transcriptional regulation dependent on cell cycle position
We present for the first time the results of a wide scale analysis of regulated gene expression in a plant cell cycle synchronized culture
Summary
Arabidopsis Cell Suspension Culture—A suspension culture of the fast growing cell line MM2d was maintained as described [22]. Cluster Analysis of Cell Cycle Expression Patterns—Expression patterns of genes defined as having a statistically significantly (p Ͻ 0.05) greater periodic expression in the experiment than the randomized data set were imported into GeneMaths (version 1.50; Applied Maths). All of the processed values for signal log ratios after comparative analysis against the sample directly taken after block release (T0) were subjected to principal component analysis (PCA) and self-organizing map (SOM) algorithms using GeneMaths 1.50 [50]. Prior PCA and SOM analysis genes were labeled (GeneMaths) according to the annotated peak of expression found after statistical analysis for each phase as follows: S phase peak (blue), G2 (yellow), M phase (red), and G1 (green). The following consensus sequences were used to search for regulatory motifs: E2F (TTTYYCGYY), mitotic-specific activation (YCYAACGGYY), Oct (CGCGGATC), and Hex (CCACGTCA)
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