Daily variation of gene expression in diverse rat tissues

<div><p>Circadian information is maintained in mammalian tissues by a cell-autonomous network of transcriptional feedback loops that have evolved to optimally regulate tissue-specific functions. An analysis of daily gene expression in different tissues, as well as an evaluation of inter-tissue circadian variability, is crucial for a systems-level understanding of this transcriptional circuitry. Affymetrix gene chip measurements of liver, muscle, adipose, and lung tissues were obtained from a rich time series light/dark experiment, involving 54 normal rats sacrificed at 18 time points within the 24-hr cycle. Our analysis revealed a high degree of circadian regulation with a variable distribution of phases among the four tissues. Interestingly, only a small number of common genes maintain circadian activity in all tissues, with many of them consisting of “core-clock” components with synchronous rhythms. Our results suggest that inter-tissue circadian variability is a critical component of homeostatic body function and is mediated by diverse signaling pathways that ultimately lead to highly tissue-specific transcription regulation.</p></div

Common genes that maintain circadian rhythmicity in the four tissues.

<p>A: Venn diagram of the four tissues. B: Temporal profiles of core-clock genes that are oscillating in all four tissues. Dots represent the average expression values from 3 animals sacrificed at three consecutive days and error bars the standard deviation of these three replicates.</p

Temporal profiles of genes maintaining circadian rhythmicity in liver, muscle, adipose, and lung.

<p>Upper panel: Heatmaps showing mean expression data from 3 animals sacrificed at the same time point during three consecutive days. Rows represent the different genes, and columns the mean expression values at the different times of the day. From blue to yellow, the expression intensity is increasing. Ordering of genes in the different rows is based on their phase. Heatmap titles indicate the tissue, and the respective bar plots at the top of each subplot represent the 12 h light (white) 12 h dark (grey) periods. The n is for the number of genes found to retain circadian rhythmicity in each tissue Lower panel: Respective phase histograms for the tissues shown in the upper panel. Circular coordinates indicate the time of day and numbers on the nested circles the number of genes. Dark semicircles at the perimeter of the circles indicate the dark phase.</p

Parameter values used for the simulation of the different rat tissue core-clock gene array data (Eqs 1–5).

<p>Transcriptional delays (τ_i) and degradation rates (d_i) were varied using literature-based values in order to simulate the observed data. Other parameters were set constant to their original values [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197534#pone.0197534.ref014" target="_blank">14</a>]. The All-Tissues parameters were calculated when gene array data from all tissues (liver, muscle, adipose, lung) were used in parameter estimation.</p

Conserved genes in mouse and rat for liver, muscle, adipose and lung.

<p>Upper panel: Venn diagrams showing number of genes in each tissue for mouse and rat as well as the number of overlapping genes. Lower panel: Scatterplots of phases (ϕ) in rat and mouse for the different tissues compared with the identity line. Phases for 4 periods were concantenated for visualization purposes. r values at the title of the graphs indicate the circular correlation coefficient.</p

Local sensitivity analysis of the phases of core-clock genes upon changing transcriptional delays and degradation rates.

<p>Different subplots represent different sensitivity outputs that are the phases of the various core-clock genes (<i>Bmal1</i>, <i>Rev-Erba</i>, <i>Per2</i>, <i>Cry1</i>, <i>Dbp</i>). Bars indicate the sensitivity indices resulting by varying different parameters (transcriptional delays, degradation rates). The y-axis represents the absolute values of the normalized sensitivity coefficients (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197534#pone.0197534.e021" target="_blank">Eq 20</a>).</p

Schematic of the model.

<p>After heterodimerizing and translocating to the nucleus, CLOCK/BMAL1 induces the expression of target genes retaining an Ebox at their promoter (e.g. <i>Rev-Erba</i>, <i>Per2</i>, <i>Cry1</i>, <i>Dbp</i>). The PER/CRY heterocomplexes further inhibit this CLOCK/BMAL1 driven transcription. The REV-ERBa and DBP conclude the core-clock gene network by inhibiting or inducing genes that retain either an RRE or a DBP complex in their promoter regions. Clock-controlled genes (CCGs) are further regulated by core-clock transcription factors through binding to the respective Ebox, RRE, or Dbox elements at the promoter of the target gene.</p

Correlation of phases (ϕ) between circadian genes oscillating in combination of 2 tissues.

<p>A: Scatterplots of phases (ϕ) in combinations of two tissues compared with the identity line. Phases for 4 periods were concantenated for visualization purposes B: Caclulated circular correlation coefficients (r) for the phases of circadian genes in the respective combinations of tissues.</p

Model fittings (curves) of core-clock gene expression (mRNA—circles) in different rat’s tissues.

<p>Time of light/dark cycles are denoted by white/grey shading.</p

Phase histograms for the circadian genes in the individual tissues, relative to their three main biological functions.

<p>Circular coordinates indicate the time of day and numbers on the nested circles the numbers of genes. Different colors depict different functional groups.</p