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At the onset of lateral root initiation in Arabidopsis, the phytohormone auxin activates xylem pole pericycle cells for asymmetric cell division. However, the molecular events leading from auxin to lateral root initiation are poorly understood, in part because the few responsive cells in the process are embedded in the root and are thus difficult to access. We previously described a lateral root induction system (LRIS) in which most xylem pole pericycle cells were synchronously activated by auxin transport inhibition (NPA) followed by auxin application (NAA). We used the LRIS for microarray transcript profiling and were able to identify 906 significantly differentially regulated genes out of 4600 genes analyzed. The reproducible expression profiles during a time course allowed us to define four stages preceding the cell division in the pericycle. These early stages included G1 cell cycle block at stage 0, auxin perception and signal transduction at stage I, followed by progression over G1-to-S transition at stage II, and G2-to-M transition at stage III. All these stages took place within 6 h after transfer from NPA to NAA. Three major patterns were identified representing induced, repressed, and transiently expressed genes. Analysis of the co-regulated genes specific for each stage provides new insight into the molecular regulation and signal transduction preceding lateral root initiation in Arabidopsis. Thereby, the LRIS represents a unique synchronized system that allows the systematic study of the developmental program upstream of the cell cycle regulation during lateral root initiation.
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