Global gene expression profiles of photomorphogenesis in Arabidopsis seedlings

Shu-Hsing Wu1,2 and Shauna Somerville1

1Carnegie Institution of Washington, Department of Plant Biology, Stanford, CA 94305
2Institute of Botany, Academia Sinica, Nankang, Taipei, Taiwan
shuwu@gate.sinica.edu.tw

Increasing at an exponential rate, genetic sequence data opens a new avenue for biologists to explore organisms at the genome level. The DNA microarray technology is one of the recently developed technologies enabling comprehensive and high-throughput surveys of relative DNA or RNA abundance. DNA microarray first involves precise robotic gridding of thousands to tens of thousands of discrete DNA sequences onto fabricated solid support (e.g. a single 1' by 3' microscope glass slide). The most popular usage of DNA microarray is to monitor gene expression patterns in two biological samples. To achieve this, two mRNA populations could be differentially labeled with two fluorescent dyes, mixed and used to hybridize one DNA microarray. Fluorescent measurement of each DNA spot for both labeling will be acquired individually with laser excitation. The ratio of fluorescent intensity indicates the relative expression level for a specific gene between two biological samples. In the field of light-induced photomorphogenesis of Arabidopsis seedlings, DNA microarray technology can serve as a complimentary approach to current biochemical and genetic methods for identifying novel molecular components in light signaling pathways. A cDNA microarray consisting of 11,500 Arabidopsis cDNA elements was generated as part of the Arabidopsis Functional Genomics Consortium (AFGC; http://afgc.stanford.edu). Gene expression profiles of wild type and a photomorphogenic mutant, hy5, Arabidopsis seedlings were monitored at several stages during the transition from dark to light growing conditions, including de-etiolation, cotyledon expansion and inhibition of hypocotyl elongation. Cluster analyses of the expression results of these experiments will be presented. By analyzing the upstream regulatory sequences of co-expressed genes, the identification of light-responsive elements will be discussed. An overview of the public resources being developed by the AFGC project for the Arabidopsis community including microarray services and the construction of microarray gene expression database will also be highlighted.