Circadian-Controlled Pathways Facilitate Adaptation to a Changing Environment

The Science

Plants and other organisms synchronize their internal processes with the environment through circadian clocks to cope with natural cycles of light and temperature. These temporal rhythms coordinate physiological and metabolic processes with daily and seasonal changes by helping coordinate gene expression that enable organisms to adapt. Researchers at Oregon State University and collaborators used a combination of genomics and bioinformatics technologies to investigate daily rhythms in gene expression in the monocot plant rice and the dicot plant poplar. Using a combination of oligonucleotide microarrays and data mining pipelines, researcgers examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven) and circadian (free running) light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar.

They compared their findings to work previously performed in the model plant Arabidopsis. They found a high degree of conservation across the three species among the cycling patterns of many circadian clock genes. This new research indicates that a core regulatory network is conserved across higher plants, although some cases of species-specific diurnal/circadian-associated regulatory circuits were observed. The findings have implications for engineering plants with enhanced vigor, fitness, and adaptation to changing environments. The research was supported in part by the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy program.


Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants.

BER Program Manager

Kari Perez

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Filichkin, S. A., G. Breton, H. D. Priest, P. Dharmawardhana, P. Jaiswal, S. E. Fox, T. P. Michael, J. Chory, S. A. Kay, and T. C. Mockler. 2011. “Global Profiling of Rice and Poplar Transcriptomes Highlights Key Conserved Circadian-Controlled Pathways and Cis-Regulatory Modules,” PLoS ONE 6(6), e16907. DOI:10.1371/journal.pone.0016907.