Circadian control of global gene expression patterns

Abstract

An internal time-keeping mechanism has been observed in almost every organism studied from archaea to humans. This circadian clock provides a competitive advantage in fitness and survival ( 18, 30, 95, 129, 137 ). Researchers have uncovered the molecular composition of this internal clock by combining enzymology, molecular biology, genetics, and modeling approaches. However, understanding the mechanistic link between the clock and output responses has been elusive. In three model organisms, Arabidopsis thaliana, Drosophila melanogaster, and Mus musculus, whole-genome expression arrays have enabled researchers to investigate how maintaining a time-keeping mechanism connects to an adaptive advantage. Here, we review the impacts transcriptomics have had on our understanding of the clock and how this molecular clock connects with system-level circadian responses. We explore the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions.

Figure 1

A simplified schematic model diagram to highlight the similarities between the circadian-clock oscillators of Mus musculus, Drosophila melanogaster, and Arabidopsis thaliana. Abbreviations: BMAL1, brain and muscle ARNT-like 1; CBS, CCA1 binding site; CCA1, CIRCADIAN CLOCK ASSOCIATED 1; CHE, CCA1 hiking expedition; CLK, circadian locomotor output cycles protein kaput; CRY, cryptochrome; DBP, D-box binding protein; dCYC, Drosophila cycle; dCLK, Drosophila circadian locomotor output cycles protein kaput; E4BP4, E4 promoter-binding protein 4; EE, evening element; LHY, late elongated hypocotyl; PDP1, PAR-domain protein 1; PER, period; PRR7, pseudoresponse regulator 7; PRR9, pseudoresponse regulator 9; REV-ERB, reverse erb; RORa, RAR-related orphan receptor A; RORE, REV-ERB/ROR response element; TBS, TCP binding site; TIM, timeless; TOC1, timing of CAB expression 1; V/P-box, Vrille/PDP1 binding box; VRI, Vrille.

Figure 2

Integration of the circadian transcriptome with other high-throughput levels of data. Circadian expression information can be integrated with multiple layers. (a) Expression levels of RNA transcripts are collected at multiple time points throughout a circadian cycle. (b) This circadian transcriptome can be integrated with genomics, protein pathway networks, information on tissue specificity, and phenotypic information. (c) By combining these multiple layers of global data, timing of molecular events, such as cis-element regulation and metabolic coordination, can be developed. The ultimate goal of these network-analysis approaches is to understand the regulatory mechanisms by which an organism’s internal circadian clock is able to temporally regulate biological processes.

Figure 3

Predicted pathway regulation by the circadian clock. (a) The first arrays identified many pathways as circadian regulated that have since been confirmed. Combining multiple arrays together allows for the identification of multiple pathways with transcripts enriched for circadian regulation. (b) Cycling transcripts were selected from meta-analysis studies of each organism (51, 79, 136). A selected subset of gene ontology (GO) terms that are enriched (adjusted p-value <0.05) for the GO category of biological function at levels 3 and 4 and the GO category of molecular function at level 3 are listed here. (c) Some examples of pathways with a verified molecular connection to the circadian clock.