GSE97258
Auxin regulates functional gene groups in a fold-specific manner in Arabidopsis root
Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a wide variety of processes, including cell wall biogenesis, transition through the cell cycle, and metabolism of a wide range of chemical substances, among others. The coordination principles for such complex regulation in a cell at a system level are poorly understood. Here, we apply a whole-genome approach to estimate the coherence of the auxin-regulated transcriptional response in gene groups, united by a certain biological process, molecular function or cell component, based on the fold change of the expression level. The corresponding analysis of RNA-Seq data for Arabidopsis roots treated with auxin for 6 h revealed that the intervals for the fold change of gene expression levels are quite narrow for many functional gene groups. The fold-specific manner of auxin response in most of these groups was confirmed using independent microarray data. To predict the mechanisms underlying such a coordinated expression, we performed motif enrichment analysis, which revealed TBX1-3, SBX, REG and TCP/site 2 as the candidates associated with fold-specific responses to auxin. Overall design: mRNA profiles of 3 dag wild type (WT) and 6h IAA treated Arabidopsis roots were generated by RNA sequencing, in triplicate, using AB SOLiD technology