Genome-wide analysis of light-dependent transcript accumulation patterns during early stages of Arabidopsis seedling deetiolation

Plant Physiol. 2011 Mar;155(3):1353-66. doi: 10.1104/pp.110.166801. Epub 2011 Jan 10.


Light is among the most important exogenous factors that regulate plant development. To sense light quality, intensity, direction, and duration, plants have evolved multiple photoreceptors that enable the detection of photons from the ultraviolet B (UV-B) to the far-red spectrum. To study the effect of different light qualities on early gene expression, dark-grown Arabidopsis (Arabidopsis thaliana) seedlings were either irradiated with continuous far-red, red, or blue light or received pulses of red, UV-A, or UV-A/B light. The expression profiles of seedlings harvested at 45 min and 4 h were determined on a full genome level and compared with the profiles of dark controls. Data were used to identify light-regulated genes and to group these genes according to their light responses. While most of the genes were regulated by more than one light quality, a considerable number of UV-B-specific gene expression responses were obtained. An extraordinarily high similarity in gene expression patterns was obtained for samples that perceived continuous irradiation with either far-red or blue light for 4 h. Mutant analyses hint that this coincidence is caused by a convergence of the signaling cascades that regulate gene expression downstream of cryptochrome blue light photoreceptors and phytochrome A. Whereas many early light-regulated genes exhibited uniform responses to all applied light treatments, highly divergent expression patterns developed at 4 h. These data clearly indicate that light signaling during early deetiolation undergoes a switch from a rapid, but unspecific, response mode to regulatory systems that measure the spectral composition and duration of incident light.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / growth & development*
  • Arabidopsis / radiation effects
  • Cryptochromes / metabolism
  • Gene Expression Regulation, Developmental / radiation effects
  • Gene Expression Regulation, Plant / radiation effects*
  • Genes, Plant / genetics
  • Genetic Markers
  • Genome, Plant / genetics*
  • Light*
  • Phytochrome A / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Seedlings / genetics*
  • Seedlings / growth & development
  • Seedlings / radiation effects*
  • Time Factors
  • Up-Regulation / radiation effects


  • Cryptochromes
  • Genetic Markers
  • Phytochrome A
  • RNA, Messenger