Abstract
Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a diverse variety of processes such as cell wall biogenesis, transition through the cell cycle, or metabolism of a wide range of chemical substances. The coordination principles for such a complex orchestration are poorly understood at the systems level. Here, we perform an RNA-seq experiment to study the transcriptional response to auxin treatment within gene groups of different biological processes, molecular functions, or cell components in a quantitative fold-change-specific manner. We find for Arabidopsis thaliana roots treated with auxin for 6 h that (i) there are functional groups within which genes respond to auxin with a surprisingly similar fold changes and that (ii) these fold changes vary from one group to another. These findings make it tempting to conjecture the existence of some transcriptional logic orchestrating the coordinated expression of genes within functional groups in a fold-change-specific manner. To obtain some initial insight about this coordinated expression, we performed a motif enrichment analysis and found cis-regulatory elements TBX1-3, SBX, REG, and TCP/site2 as the candidates conferring fold-change-specific responses to auxin in Arabidopsis thaliana.
Highlights
MethodsArabidopsis Col-0 seeds were surface-sterilized and vernalized for 7 days at 4 °C
Based on the results of functional annotation of the RNA-Seq data in the knowledge domain of biological processes, we can propose a general scheme of auxin action in the root cell (Fig. 4)
While several TGTCNN hexamers are associated with auxin-responsive gene expression in general[14], we investigate here if there are motifs associated with fold-change-specific auxin response
Summary
Arabidopsis Col-0 seeds were surface-sterilized and vernalized for 7 days at 4 °C. Seedlings were grown vertically at 22 °C and 150 μmol m−2 s−1 under a 16-h light/8-h dark cycle on 1/2 Murashige and Skoog (MS) media (Sigma). Three days after germination (dag), seedlings were incubated in liquid 1/2 MS and 1/2 MS supplemented with 1 μM IAA for 6 h. Roots were collected in liquid nitrogen for three biological replicates.
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