Genome-wide Expression Analysis of Mouse Liver Reveals CLOCK-regulated Circadian Output Genes

Abstract

CLOCK is a positive component of a transcription/ translation-based negative feedback loop of the central circadian oscillator in the suprachiasmatic nucleus in mammals. To examine CLOCK-regulated circadian transcription in peripheral tissues, we performed microarray analyses using liver RNA isolated from Clock mutant mice. We also compared expression profiles with those of Cryptochromes (Cry1 and Cry2) double knockout mice. We identified more than 100 genes that fluctuated from day to night and of which expression levels were decreased in Clock mutant mice. In Cry-deficient mice, the expression levels of most CLOCK-regulated genes were elevated to the upper range of normal oscillation. Most of the screened genes had a CLOCK/BMAL1 binding site (E box) in the 5-flanking region. We found that CLOCK was absolutely concerned with the circadian transcription of one type of liver genes (such as DBP, TEF, and Usp2) and partially with another (such as mPer1, mPer2, mDec1, Nocturnin, P450 oxidoreductase, and FKBP51) because the latter were damped but remained rhythmic in the mutant mice. Our results showed that CLOCK and CRY proteins are involved in the transcriptional regulation of many circadian output genes in the mouse liver. In addition to being a core component of the negative feedback loop that drives the circadian oscillator, CLOCK also appears to be involved in various physiological functions such as cell cycle, lipid metabolism, immune functions, and proteolysis in peripheral tissues.

Characterization of Peripheral Circadian Clocks in Adipose Tissues

“…Although our detection of Ͼ5,300 genes exceeds previously reported values in the liver (23,41), we believe our analysis is a valid description of the temporal gene expression in these tissues. As described in RESEARCH DESIGN AND METHODS, we used a frequency conversion approach to ensure that we detect all periodically expressed genes, regardless of their amplitude and "noise" level.…”

Pharmacological modulators of the circadian clock as potential therapeutic drugs

“…Components of a molecular clock underlying rhythmic gene expression have been characterized in neurons of the suprachiasmatic nucleus (SCN) [23,24], in liver [23][24][25][26][27], heart [26], synchronized fibroblasts [28], adipose tissue [29], adrenal gland [30], skeletal muscle [31], pituitary [32] and pineal [33] glands, calvarial bone [34], as well as in epithelial cells of lung [35,36] and gastrointestinal tract [37][38][39]. In order to ensure proper temporal organization in metabolism and behavior at the level of an organism, the multiple tissue-specific transcriptional oscillations have to be synchronized with the natural 24-hr cycle.…”

Biological aging alters circadian mechanisms in murine adipose tissue depots

“…Moreover, transcription factors regulating adipocyte gene markers (PPARα, Rev-Erbα, SREBP) display a circadian expression profile (Lemberger et al 1996;Torra et al 2000;Patel et al 2001). Global transcriptomic approaches by ourselves and others have demonstrated the diurnal/circadian oscillation of up to 20% of expressed genes in adipose tissue as well as the suprachiasmatic nuclei, liver, and heart (Akhtar et al 2002;Duffield et al 2002;Panda et al 2002a, b;Ueda et al 2002;Hogenesch et al 2003;Oishi et al 2003;Sato et al 2003Sato et al , 2004. Oscillating genes in adipose tissue included those encoding proteins related to glycolysis, lipolysis, steroidogenesis, redox potential, and iron/ heme metabolism (Ptitysn et al 2006;Zvonic et al 2006).…”