Robustness of gene expression rhythmicity can identify new oscillator components in the circadian clock.

Abstract

The transcriptomes of many eukaryotic genomes exhibit rhythmic gene expression, resulting in genes that show peak expression at specific times of the day. In plants, genes that are considered to be oscillator components alter the circadian period and/or phase (time of peak expression) when misexpressed. The first plant circadian clock gene was identified almost 30 years ago, and since then additional components have been identified through forward and reverse genetic mutant screens. Over the years, mathematical modeling has helped to refine our understanding of oscillator interactions within the network and in the context of environmental cues. The complexity of the clock network suggests that additional components are yet to be discovered. In the era of genomics and genome-scale analysis, circadian research has focused on understanding the mechanisms of clock gene control of cellular and physiological output processes, often in the context of environmental stimuli. Transcriptome studies with temporal and/or spatial resolution are increasingly being carried out and the resulting comprehensive datasets can be mined to predict new oscillator components. Most clock genes show stronger oscillatory expression patterns compared to other genes in the genome. By selecting from transcriptome data genes that are significantly and robustly rhythmic, putative clock genes can be identified and characterized.