The auxin-induced transcriptome for etiolated Arabidopsis seedlings using a structure/function approach

Funct Integr Genomics. 2003 Dec;3(4):135-43. doi: 10.1007/s10142-003-0093-7. Epub 2003 Nov 26.


To increase our understanding of the mode of action of auxin, we analyzed auxin-induced changes in the Arabidopsis transcriptome with microarrays representing 20426 Arabidopsis genes. Treatment of etiolated seedlings with low concentrations of the auxin, indole-3-acetic acid (IAA), decreased the expression levels of 23 genes, whereas it increased the expression levels of 47 genes within 20 min. After 40 min, the directional trend in genomic change was predominantly an increase in gene expression. Among the most rapidly induced changes are those in genes encoding transcription factors. Promoter regions of transiently induced genes contained DNA motifs that bind auxin response (ARFAT) and silence element binding factors whereas genes induced by IAA during the entire experimental period contained MYC and ARFAT DNA motifs at higher frequencies. Six structurally diverse auxins were analyzed to determine genes that are unique to a specific auxin, as well as a common set of genes that are rapidly regulated by all tested auxins, thus enabling the identification of shared DNA motifs. In addition to ARFAT, analysis of promoter regions of genes induced by all six auxins revealed the presence of an abscisic-acid-responsive DC3 promoter-binding factor and low temperature responsive elements suggesting a possible role for abscisic acid in modulating auxin-induced responses.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 5' Untranslated Regions
  • Arabidopsis / drug effects
  • Arabidopsis / genetics*
  • Cluster Analysis
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant / drug effects
  • Genes, Plant / drug effects
  • Indoleacetic Acids / chemistry
  • Indoleacetic Acids / pharmacology*
  • Molecular Structure
  • Oligonucleotide Array Sequence Analysis
  • Plant Growth Regulators / chemistry
  • Plant Growth Regulators / pharmacology*
  • Promoter Regions, Genetic / drug effects
  • Regulatory Sequences, Nucleic Acid
  • Seedlings / drug effects*
  • Structure-Activity Relationship
  • Time Factors
  • Transcription, Genetic / drug effects*


  • 5' Untranslated Regions
  • Indoleacetic Acids
  • Plant Growth Regulators