The interplay of cis-regulatory elements rules circadian rhythms in mouse liver

PLoS One. 2012;7(11):e46835. doi: 10.1371/journal.pone.0046835. Epub 2012 Nov 5.


The mammalian circadian clock is driven by cell-autonomous transcriptional feedback loops that involve E-boxes, D-boxes, and ROR-elements. In peripheral organs, circadian rhythms are additionally affected by systemic factors. We show that intrinsic combinatorial gene regulation governs the liver clock. With a temporal resolution of 2 h, we measured the expression of 21 clock genes in mouse liver under constant darkness and equinoctial light-dark cycles. Based on these data and known transcription factor binding sites, we develop a six-variable gene regulatory network. The transcriptional feedback loops are represented by equations with time-delayed variables, which substantially simplifies modelling of intermediate protein dynamics. Our model accurately reproduces measured phases, amplitudes, and waveforms of clock genes. Analysis of the network reveals properties of the clock: overcritical delays generate oscillations; synergy of inhibition and activation enhances amplitudes; and combinatorial modulation of transcription controls the phases. The agreement of measurements and simulations suggests that the intrinsic gene regulatory network primarily determines the circadian clock in liver, whereas systemic cues such as light-dark cycles serve to fine-tune the rhythms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ARNTL Transcription Factors / genetics
  • Animals
  • Circadian Clocks
  • Circadian Rhythm Signaling Peptides and Proteins / genetics*
  • Circadian Rhythm*
  • Cryptochromes / genetics
  • DNA-Binding Proteins / genetics
  • E-Box Elements
  • Gene Expression Regulation
  • Gene Regulatory Networks*
  • Liver / metabolism*
  • Mice
  • Mice, Inbred C57BL
  • Models, Genetic
  • Period Circadian Proteins / genetics
  • Photoperiod
  • Transcription Factors / genetics


  • ARNTL Transcription Factors
  • Arntl protein, mouse
  • Circadian Rhythm Signaling Peptides and Proteins
  • Cry1 protein, mouse
  • Cryptochromes
  • DNA-Binding Proteins
  • Dbp protein, mouse
  • Per2 protein, mouse
  • Period Circadian Proteins
  • Transcription Factors

Grant support

A.K. and R.K. thank the Slovene Research Agency for Young Researcher Fellowships. A.K. is also indebted to the Slovene Human Resources Development and Scholarship Fund, and to Federation of European Biochemical Societies (FEBS) for FEBS Collaborative Experimental Scholarship. This work was financially supported by the Slovene Research Agency (grants P1-170 to M.G. and P1-104 to D.R.) and the Deutsche Forschungsgemeinschaft (SFB 618, SPP InKomBio). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.