Microarray Analysis of Diurnal and Circadian-Regulated Genes in Arabidopsis

TLDR

Plants respond to day/night cycling in various physiological ways, and at the mRNA level, some genes change expression over the 24‑hour period. The study aimed to identify novel diurnally or circadian‑regulated genes by profiling 7,800 Arabidopsis genes with microarrays at 6‑hour intervals across a day. Microarray data were collected at 6‑hour intervals and then clustered with data from 47 unrelated experiments to isolate genes regulated solely by the circadian clock. Eleven percent of genes showed diurnal patterns, about 2% displayed circadian rhythms, and clustering revealed groups containing known clock genes LHY, CCA1, and GI, indicating additional circadian regulators may reside in these clusters.

Abstract

Abstract Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional nonrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters.