Spatial regulation of the gene expression response to shade in Arabidopsis seedlings

The shade avoidance response, which allows plants to escape from nearby competitors, is triggered by a reduction in the Psub(FR) form of phytochrome in response to shade. Classic physiological experiments have demonstrated that the shade signal perceived by the leaves is transmitted to the other parts of the plant. Recently, a simple method was developed to analyze the transcriptome in a single microgram tissue sample. In the present study, we adopted this method to conduct organ-specific transcriptomic analysis of the shade avoidance response in Arabidopsis seedlings. The shoot apical samples, which contained the meristem, basal parts of leaf primordia and short fragments of vasculature, were collected from the topmost part of the hypocotyl and subjected to RNA sequencing analysis. Unexpectedly, many more genes were up-regulated in the shoot apical region than in the cotyledons. Spotlight irradiation demonstrated that the apex-responsive genes were mainly controlled by phytochrome in the cotyledons. In accordance with the involvement of many auxin-responsive genes in this category, auxin biosynthesis was genetically shown to be essential for this response. In contrast, organ-autonomous regulation was more important for the genes that were up-regulated preferentially either in the cotyledons or in both the cotyledons and the apical region. Their responses to shade depended variously on auxin and PIFs (phytochrome-interacting factors), indicating the mechanistic diversity of the organ-autonomous response. Finally, we examined the expression of the auxin synthesis genes, the YUC genes, and found that three YUC genes, which were differently spatially regulated, co-ordinately elevated the auxin level within the shoot apical region.