The Interplay of cis-Regulatory Elements Rules Circadian Rhythms in Mouse Liver

Abstract

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.

Identifying Novel Transcriptional Regulators with Circadian Expression

“…Several of these studies formulated mechanistic models of (parts of) the core clock and conceptually analyzed how different transcriptional regulatory modes among core clock TFs affect the dynamic behavior of clock-controlled genes (78,79,98,99). Others created a network description of the core clock genes based on large-scale promoter analyses (76) or based on a careful analysis of different TF knockout or mutant strain data sets as well as binding site predictions (77,100).…”

“…Having identified a number of novel circadian genes, we next investigated by using a mathematical modeling approach if they could regulate each other. Previous theoretical work on the circadian clock established qualitative networks of clock-controlled genes (76,77), or formulated mechanistic models of the core clock, mainly based on prior knowledge (55,(78)(79)(80)(81). In contrast, we focused on a network reconstruction approach, in which we asked in an unbiased way whether the cyclical genes identified from the RNA-seq data could, in principle, be regulated by one of the core clock factors or any other cyclically expressed transcription factor.…”

Inducible cAMP Early Repressor Regulates the Period 1 Gene of the Hepatic and Adrenal Clocks

“…Fitting Trigonometric Functions to Gene Expression DataExperimental data were fitted by trigonometric functions as described (18). Briefly, in addition to the 24-h period, 12-h harmonics were included to reproduce variable waveforms and peak width (Equation 1).…”

Inference of Circadian Regulatory Pathways Based on Delay Differential Equations

“…Mathematical models are being developed to describe the dynamics of the clock transcriptional network and its downstream regulation, for Arabidopsis, see [11], [12], and for the mouse liver and adrenal gland, see [8], [9]. The field is now sufficiently mature for us to consider validating, comparing and extending these models in the presence of experimental data.…”

“…This reduces the network to gene transcripts and is convenient for parameter estimation and model selection since this data is more readily available than protein data. Proteins are sometimes treated as missing data and modelled using latent variables; employing timedelayed variables is an alternative approach [8].…”